Re: [ccp4bb] metal coordination at low resolution - restraints
lto:robbie_joos...@hotmail.com>>; Garib N
Murshudov
mailto:ga...@mrc-lmb.cam.ac.uk>>
Cc: CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>; Robert Nicholls
http://lmb.cam.ac.uk/>>
Subject: Re: [ccp4bb] metal coordination at low
resolution - restraints
Robbie - could that be added to the distributed
dictionaries? Zn binding is
common and at low resolution distance restraints
are not enough..
Eleanor
On Tue, 8 Sep 2020 at 10:33, Robbie Joosten
mailto:robbie_joos...@hotmail.com>
<mailto:robbie_joos...@hotmail.com> > wrote:
Hi Anna,
Yes you can do this in Refmac by adding external
restraints. If you
have structural Zinc sites (Zn coordinated by 4
histidines or cysteines) you
can also use PDB-REDO to generate the restraints
automatically. The
restraints are written to the output so you can
continue using them in
Refmac.
HTH,
Robbie
> -Original Message-
> From: CCP4 bulletin board
mailto:CCP4BB@JISCMAIL.AC.UK>
<mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of anna
> anna
> Sent: Tuesday, September 8, 2020 11:28
> To: CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>
<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] metal coordination at low
resolution - restraints
>
> Dear all,
>
> quickly: is there a way to restrain metal
coordination geometry
(even angles)
> in refmac?
>
> I am refining a low resolution structure
(3.3A) with 2 zinc binding
sites.
> I am pretty sure about metal position (strong
anomalous signal)
and what
> are the residues involved in coordination
since I solved the apo-
structure at
> good resolution and Zn-binding does not induce
huge structural
variations.
> However, as you can imagine, electron density
is poorly defined
and Refmac
> gives a very distorted coordination geometry.
> I noticed that in phenix it is possible to
generate restraints with
readyset but
> I'd like to work with refmac.
>
> Many thanks for your suggestions.
>
> Cheers,
> Anna
>
>
>
>
> To unsubscribe from the CCP4BB list, click the
following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-
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--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic
Tel. +420 325 873 758
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Re: [ccp4bb] metal coordination at low resolution - restraints
gt;> >> But as I said - in all our structures restraining the coordination >> geometry is not necessary, they hold nice. >> >> Jan >> >> >> Jan >> >> >> On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov >> wrote: >> >>> What are these numbers? >>> >>> If I understand these numbers correctly: none of your Zn atoms is >>> structural (4 coordinated tetrahedral). If that is the case then you need >>> specific links or restraints. If my reading of your numbers is correct then >>> there could be some chemistry change of the surrounding residues. >>> >>> If it is not structural Zn then it is likely that coordination is 6. But >>> without seeing coordinates and maps it is difficult to say what is there. >>> >>> Regards >>> Garib >>> >>> >>> On 8 Sep 2020, at 11:11, Eleanor Dodson >>> wrote: >>> >>> Hmm - here is my problem - a list of ZN contacts for the two molecules.. >>> residue 602 is a phosphate, and there possibly should be a few more >>> waters .. >>> No idea how best to tackle it.. >>> E >>> >>> >>> Z 401 ZN A W 21 NA 2.057 X,Y,Z 1.00 >>> 8.73 >>> Z 401 ZN A W 21 OA 2.220 X,Y,Z 1.00 >>> 8.76 >>> Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z 1.00 >>> 8.39 >>> Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z 1.00 >>> 8.61 >>> Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z 0.60 >>> 10.74 >>> Z 401 ZN A O 821 OC 2.006 X,Y,Z 0.40 >>> 7.51 >>> >>> Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z 1.00 >>> 8.94 >>> Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z 1.00 >>> 8.70 >>> Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z 1.00 >>> 8.70 >>> Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z 0.60 >>> 11.05 >>> Z 402 ZN A O 821 OC 1.829 X,Y,Z 0.40 >>> 7.81 >>> >>> Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z 1.00 >>> 10.50 >>> Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z 1.00 >>> 10.19 >>> Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 >>> 12.66 >>> Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 >>> 11.54 >>> Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.20 >>> 9.09 >>> Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 >>> 13.79 >>> >>> Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.00 >>> 8.73 >>> >>> >>> Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.00 >>> 9.22 >>> Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.00 >>> 8.91 >>> Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.00 >>> 8.79 >>> Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.00 >>> 8.76 >>> Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.70 >>> 9.31 >>> >>> Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.00 >>> 9.49 >>> Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.00 >>> 9.22 >>> Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z 1.00 >>> 9.70 >>> Z 402 ZN B Z 601 O3 B 1.973 X,Y,Z 0.70 >>> 9.58 >>> >>> Z 403 ZN B H 145 NE2 B 2.027 X,Y,Z 1.00 >>> 10.80 >>> Z 403 ZN B H 168 NE2 B 2.029 X,Y,Z 1.00 >>> 10.65 >>> Z 403 ZN B D 172 OD2 B 2.089 X,Y,Z 1.00 >>> 13.12 >>> Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 >>> 14.10 >>> Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 >>> 10.61 >>> ~ >>> >>> >>> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov >>> wrote: >>> >>>> Hi Robbie and Eleanor >>>> >>>> There are links for Zn-His and Zn-Cys. They meant to be used >>>>
Re: [ccp4bb] metal coordination at low resolution - restraints
...@mrc-lmb.cam.ac.uk>> wrote: >>>> Hi Robbie and Eleanor >>>> >>>> There are links for Zn-His and Zn-Cys. They meant to be used >>>> automatically, obviously something is not entirely right. >>>> >>>> Link names are: >>>> ZN-CYS >>>> >>>> It has a bond between Zn and S as well as an angle: >>>> ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 >>>> >>>> This also removes H of Cys to make covalent bond between Zn and Cys. >>>> >>>> Similar links are available for Zn and His ND1 and Zn - HIS NE2 >>>> Link names are: >>>> >>>> ZN-HISND >>>> ZN-HISNE >>>> >>>> Again these links have angles between Zn and atoms of His. >>>> >>>> Angle centred at Zn is missing. But these distances and angles defined in >>>> the link it should work fine. >>>> >>>> Regards >>>> Garib >>>> >>>> >>>> >>>>> On 8 Sep 2020, at 10:40, Robbie Joosten >>>> <mailto:robbie_joos...@hotmail.com>> wrote: >>>>> >>>>> Hi Elanor, >>>>> >>>>> The distances are in the dictionaries but the angles involve three >>>>> different residues so these cannot be in the current dictionary. We could >>>>> add the program that generates these restraints to CCP4 though. >>>>> >>>>> Cheers, >>>>> Robbie >>>>> >>>>>> -Original Message- >>>>>> From: Eleanor Dodson >>>>> <mailto:eleanor.dod...@york.ac.uk>> >>>>>> Sent: Tuesday, September 8, 2020 11:38 >>>>>> To: Robbie Joosten >>>>> <mailto:robbie_joos...@hotmail.com>>; Garib N Murshudov >>>>>> mailto:ga...@mrc-lmb.cam.ac.uk>> >>>>>> Cc: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>; Robert >>>>>> Nicholls >>>>> lmb.cam.ac.uk <http://lmb.cam.ac.uk/>> >>>>>> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints >>>>>> >>>>>> Robbie - could that be added to the distributed dictionaries? Zn binding >>>>>> is >>>>>> common and at low resolution distance restraints are not enough.. >>>>>> Eleanor >>>>>> >>>>>> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten >>>>> <mailto:robbie_joos...@hotmail.com> >>>>>> <mailto:robbie_joos...@hotmail.com <mailto:robbie_joos...@hotmail.com>> >>>>>> > wrote: >>>>>> >>>>>> >>>>>> Hi Anna, >>>>>> >>>>>> Yes you can do this in Refmac by adding external restraints. If you >>>>>> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) >>>>>> you >>>>>> can also use PDB-REDO to generate the restraints automatically. The >>>>>> restraints are written to the output so you can continue using them in >>>>>> Refmac. >>>>>> >>>>>> HTH, >>>>>> Robbie >>>>>> >>>>>> > -Original Message- >>>>>> > From: CCP4 bulletin board >>>>> <mailto:CCP4BB@JISCMAIL.AC.UK> >>>>>> <mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> > On >>>>>> Behalf Of anna >>>>>> > anna >>>>>> > Sent: Tuesday, September 8, 2020 11:28 >>>>>> > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> >>>>>> <mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> >>>>>> > Subject: [ccp4bb] metal coordination at low resolution - restraints >>>>>> > >>>>>> > Dear all, >>>>>> > >>>>>> > quickly: is there a way to restrain metal coordination geometry >>>>>> (even angles) >>>>>> > in refmac? >>>>>> > >>>>>> > I am refining a low resolution structure (3.3A) with 2 zinc binding >>>>>> sites. >>>>>> > I am pretty sure about metal position (strong anomalous signal) >>>>>> and what >>>>>> > are the residues involved in coordination since I solved the apo- >>>>>> structure at >>>>>> > good resolution and Zn-binding does not induce huge structural >>>>>> variations. >>>>>> > However, as you can imagine, electron density is poorly defined >>>>>> and Refmac >>>>>> > gives a very distorted coordination geometry. >>>>>> > I noticed that in phenix it is possible to generate restraints with >>>>>> readyset but >>>>>> > I'd like to work with refmac. >>>>>> > >>>>>> > Many thanks for your suggestions. >>>>>> > >>>>>> > Cheers, >>>>>> > Anna >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > To unsubscribe from the CCP4BB list, click the following link: >>>>>> > https://www.jiscmail.ac.uk/cgi-bin/WA- >>>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-> >>>>>> JISC.exe?SUBED1=CCP4BB=1 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>>> https://www.jiscmail.ac.uk/cgi-bin/WA- >>>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-> >>>>>> JISC.exe?SUBED1=CCP4BB=1 >>>>>> >>>>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB >>>>>> <http://www.jiscmail.ac.uk/CCP4BB> >>>>>> <http://www.jiscmail.ac.uk/CCP4BB <http://www.jiscmail.ac.uk/CCP4BB>> , >>>>>> a mailing list hosted by >>>>>> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/> >>>>>> <http://www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/>> , terms & >>>>>> conditions are >>>>>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>>>>> <https://www.jiscmail.ac.uk/policyandsecurity/> >>>>>> >>>>> >>>> >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> >>> >>> -- >>> Jan Dohnalek, Ph.D >>> Institute of Biotechnology >>> Academy of Sciences of the Czech Republic >>> Biocev >>> Prumyslova 595 >>> 252 50 Vestec near Prague >>> Czech Republic >>> >>> Tel. +420 325 873 758 >> >> >> >> -- >> Jan Dohnalek, Ph.D >> Institute of Biotechnology >> Academy of Sciences of the Czech Republic >> Biocev >> Prumyslova 595 >> 252 50 Vestec near Prague >> Czech Republic >> >> Tel. +420 325 873 758 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] metal coordination at low resolution - restraints
,Z 1.00 >> 10.19 >> Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 >> 12.66 >> Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 >> 11.54 >> Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.20 >> 9.09 >> Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 >> 13.79 >> >> Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.00 >> 8.73 >> >> >> Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.00 >> 9.22 >> Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.00 >> 8.91 >> Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.00 >> 8.79 >> Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.00 >> 8.76 >> Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.70 >> 9.31 >> >> Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.00 >> 9.49 >> Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.00 >> 9.22 >> Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z 1.00 >> 9.70 >> Z 402 ZN B Z 601 O3 B 1.973 X,Y,Z 0.70 >> 9.58 >> >> Z 403 ZN B H 145 NE2 B 2.027 X,Y,Z 1.00 >> 10.80 >> Z 403 ZN B H 168 NE2 B 2.029 X,Y,Z 1.00 >> 10.65 >> Z 403 ZN B D 172 OD2 B 2.089 X,Y,Z 1.00 >> 13.12 >> Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 >> 14.10 >> Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 >> 10.61 >> ~ >> >> >> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov >> wrote: >> >>> Hi Robbie and Eleanor >>> >>> There are links for Zn-His and Zn-Cys. They meant to be used >>> automatically, obviously something is not entirely right. >>> >>> Link names are: >>> ZN-CYS >>> >>> It has a bond between Zn and S as well as an angle: >>> ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 >>> >>> This also removes H of Cys to make covalent bond between Zn and Cys. >>> >>> Similar links are available for Zn and His ND1 and Zn - HIS NE2 >>> Link names are: >>> >>> ZN-HISND >>> ZN-HISNE >>> >>> Again these links have angles between Zn and atoms of His. >>> >>> Angle centred at Zn is missing. But these distances and angles defined >>> in the link it should work fine. >>> >>> Regards >>> Garib >>> >>> >>> >>> On 8 Sep 2020, at 10:40, Robbie Joosten >>> wrote: >>> >>> Hi Elanor, >>> >>> The distances are in the dictionaries but the angles involve three >>> different residues so these cannot be in the current dictionary. We could >>> add the program that generates these restraints to CCP4 though. >>> >>> Cheers, >>> Robbie >>> >>> -Original Message- >>> From: Eleanor Dodson >>> Sent: Tuesday, September 8, 2020 11:38 >>> To: Robbie Joosten ; Garib N Murshudov >>> >>> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls >> lmb.cam.ac.uk> >>> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints >>> >>> Robbie - could that be added to the distributed dictionaries? Zn binding >>> is >>> common and at low resolution distance restraints are not enough.. >>> Eleanor >>> >>> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten >> <mailto:robbie_joos...@hotmail.com > > >>> wrote: >>> >>> >>> Hi Anna, >>> >>> Yes you can do this in Refmac by adding external restraints. If you >>> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) >>> you >>> can also use PDB-REDO to generate the restraints automatically. The >>> restraints are written to the output so you can continue using them in >>> Refmac. >>> >>> HTH, >>> Robbie >>> >>> > -Original Message- >>> > From: CCP4 bulletin board >> <mailto:CCP4BB@JISCMAIL.AC.UK > > On Behalf Of >>> anna >>> > anna >>> > Sent: Tuesday, September 8, 2020 11:28 >>> > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK >>> > &
Re: [ccp4bb] metal coordination at low resolution - restraints
>>> 8.73 >>> >>> >>> Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.00 >>> 9.22 >>> Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.00 >>> 8.91 >>> Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.00 >>> 8.79 >>> Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.00 >>> 8.76 >>> Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.70 >>> 9.31 >>> >>> Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.00 >>> 9.49 >>> Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.00 >>> 9.22 >>> Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z 1.00 >>> 9.70 >>> Z 402 ZN B Z 601 O3 B 1.973 X,Y,Z 0.70 >>> 9.58 >>> >>> Z 403 ZN B H 145 NE2 B 2.027 X,Y,Z 1.00 >>> 10.80 >>> Z 403 ZN B H 168 NE2 B 2.029 X,Y,Z 1.00 >>> 10.65 >>> Z 403 ZN B D 172 OD2 B 2.089 X,Y,Z 1.00 >>> 13.12 >>> Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 >>> 14.10 >>> Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 >>> 10.61 >>> ~ >>> >>> >>> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov >> <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: >>> Hi Robbie and Eleanor >>> >>> There are links for Zn-His and Zn-Cys. They meant to be used automatically, >>> obviously something is not entirely right. >>> >>> Link names are: >>> ZN-CYS >>> >>> It has a bond between Zn and S as well as an angle: >>> ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 >>> >>> This also removes H of Cys to make covalent bond between Zn and Cys. >>> >>> Similar links are available for Zn and His ND1 and Zn - HIS NE2 >>> Link names are: >>> >>> ZN-HISND >>> ZN-HISNE >>> >>> Again these links have angles between Zn and atoms of His. >>> >>> Angle centred at Zn is missing. But these distances and angles defined in >>> the link it should work fine. >>> >>> Regards >>> Garib >>> >>> >>> >>>> On 8 Sep 2020, at 10:40, Robbie Joosten >>> <mailto:robbie_joos...@hotmail.com>> wrote: >>>> >>>> Hi Elanor, >>>> >>>> The distances are in the dictionaries but the angles involve three >>>> different residues so these cannot be in the current dictionary. We could >>>> add the program that generates these restraints to CCP4 though. >>>> >>>> Cheers, >>>> Robbie >>>> >>>>> -Original Message- >>>>> From: Eleanor Dodson >>>> <mailto:eleanor.dod...@york.ac.uk>> >>>>> Sent: Tuesday, September 8, 2020 11:38 >>>>> To: Robbie Joosten >>>> <mailto:robbie_joos...@hotmail.com>>; Garib N Murshudov >>>>> mailto:ga...@mrc-lmb.cam.ac.uk>> >>>>> Cc: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>; Robert Nicholls >>>>> >>>> lmb.cam.ac.uk <http://lmb.cam.ac.uk/>> >>>>> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints >>>>> >>>>> Robbie - could that be added to the distributed dictionaries? Zn binding >>>>> is >>>>> common and at low resolution distance restraints are not enough.. >>>>> Eleanor >>>>> >>>>> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten >>>> <mailto:robbie_joos...@hotmail.com> >>>>> <mailto:robbie_joos...@hotmail.com <mailto:robbie_joos...@hotmail.com>> > >>>>> wrote: >>>>> >>>>> >>>>> Hi Anna, >>>>> >>>>> Yes you can do this in Refmac by adding external restraints. If you >>>>> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) >>>>> you >>>>> can also use PDB-REDO to generate the restraints automatically. The >>>>> restraints are writt
Re: [ccp4bb] metal coordination at low resolution - restraints
I am glad to see that my question generated a useful discussion! I'm definitely not the only one with these troubles... Having a program able to generate specific restraints would be great!! I think that my case is quite tricky because my protein, that seems to be involved in zinc trafficking acting as an exchanger or a kind of sensor, has a relatively low affinity for zinc (kd 1 uM). Binding sites are exposed, coordination is tetrahedral with always 2 His and a Asp/Glu while the fourth position varies, I modelled it as H2O or His in different sites and monomers. In this context, it is very difficult for me to obtain a reasonable conformation after refinement, especially for His in the fourth position. I guess the best thing I can do is trying to model it properly and run refmac with 0 cycles. Thank you, Anna Il giorno mar 8 set 2020 alle ore 12:59 Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> ha scritto: > I guess I have lived with Zn since I first learnt what a crystal was - ZN > is part of insulin secretion and whether it is or is not present is > fundamental to the biochemistry.. > > I agree things have to be handled case by case - For insulin the three HIS > are generated by symmetry and that causes horrible headaches for any > restraint dictionary.. > And for Jan's case the resolution is excellent and the main links very > clear. (In fact they were not restrained but all distances finish up near > to 2A as expected.) > However maybe something can be learnt from this structure which would help > the query which started us off! > Eleanor > > On Tue, 8 Sep 2020 at 11:49, Robbie Joosten > wrote: > >> Hi Jan, >> >> If you want targets for your metal site you could have a look at MetalPDB >> (http://metalweb.cerm.unifi.it/). That has good tools to find similar >> sites and get some statistics you can use to generate case-specific >> restraints. >> >> Cheers, >> Robbie >> >> > -Original Message- >> > From: CCP4 bulletin board On Behalf Of Garib >> > Murshudov >> > Sent: Tuesday, September 8, 2020 12:44 >> > To: CCP4BB@JISCMAIL.AC.UK >> > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints >> > >> > Hi Jan, >> > >> > >> > >> > >> > On 8 Sep 2020, at 11:39, Jan Dohnalek > > <mailto:dohnalek...@gmail.com> > wrote: >> > >> > These are structural. >> > >> > >> > Are they tetrahedral or octahedral? From the list of neighbours they do >> not >> > look like tetrahedral. Some of them do look like octahedral. >> > >> > >> > They form the active site of our enzyme. >> > >> > >> > So,are they involved in reaction? >> > >> > >> > Normally there is no need to restrain these, they "behave". >> > >> > But in general having such standard "restraint angles" available >> > would be of use, I agree. >> > >> > >> > >> > For tetrahedral Zn we do have “bonds” and “angles” between Zn and >> > coordinating residues. For general solution we need a bit different >> approach >> > (e.g. coordination analysis). >> > >> > >> > >> > Regards >> > Garib >> > >> > >> > >> > >> > Jan >> > >> > >> > On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov > > lmb.cam.ac.uk <mailto:ga...@mrc-lmb.cam.ac.uk> > wrote: >> > >> > >> > What are these numbers? >> > >> > If I understand these numbers correctly: none of your Zn >> > atoms is structural (4 coordinated tetrahedral). If that is the case >> then you >> > need specific links or restraints. If my reading of your numbers is >> correct >> > then there could be some chemistry change of the surrounding residues. >> > >> > If it is not structural Zn then it is likely that >> coordination is 6. >> > But without seeing coordinates and maps it is difficult to say what is >> there. >> > >> > Regards >> > Garib >> > >> > >> > >> > On 8 Sep 2020, at 11:11, Eleanor Dodson >> > mailto:eleanor.dod...@york.ac.uk> > wrote: >> > >> > Hmm - here is my problem - a list of ZN contacts >> for >> > the two molecules.. >> > residue 60
Re: [ccp4bb] metal coordination at low resolution - restraints
It is the active site which is very well defined, with high occupancy and tight binding. We also have high resolution structures of these .. However, restraints (for protein-metal contacs) were not necessary to refine these sites. Atoms site where they should be ... Jan On Tue, Sep 8, 2020 at 2:08 PM Oganesyan, Vaheh < vaheh.oganes...@astrazeneca.com> wrote: > Hi Jan, > > > > They hold nice because of high occupancy or because you have very high > resolution and no restraints are necessary at all (even for protein part)? > > > > Thank you > > > > Vaheh > > > > *From:* CCP4 bulletin board * On Behalf Of *Jan > Dohnalek > *Sent:* Tuesday, September 8, 2020 8:01 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] metal coordination at low resolution - restraints > > > > Hi Garib, > > > > > > > > On 8 Sep 2020, at 11:39, Jan Dohnalek wrote: > > > > These are structural. > > > > Are they tetrahedral or octahedral? From the list of neighbours they do > not look like tetrahedral. Some of them do look like octahedral. > > > > They are involved in reaction. > > Two are ~ octahedral (skewed though, two positions filled by catalysis > participant), one is ~tetrahedral, but actually can also accept a fifth > coordinating atom. > > > > But as I said - in all our structures restraining the coordination > geometry is not necessary, they hold nice. > > > > Jan > > > > > > Jan > > > > > > On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov > wrote: > > What are these numbers? > > > > If I understand these numbers correctly: none of your Zn atoms is > structural (4 coordinated tetrahedral). If that is the case then you need > specific links or restraints. If my reading of your numbers is correct then > there could be some chemistry change of the surrounding residues. > > > > If it is not structural Zn then it is likely that coordination is 6. But > without seeing coordinates and maps it is difficult to say what is there. > > > > Regards > > Garib > > > > > > On 8 Sep 2020, at 11:11, Eleanor Dodson wrote: > > > > Hmm - here is my problem - a list of ZN contacts for the two molecules.. > > residue 602 is a phosphate, and there possibly should be a few more waters > .. > > No idea how best to tackle it.. > > E > > > > > > Z 401 ZN A W 21 NA 2.057 X,Y,Z 1.00 > 8.73 > > Z 401 ZN A W 21 OA 2.220 X,Y,Z 1.00 > 8.76 > > Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z 1.00 > 8.39 > > Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z 1.00 > 8.61 > > Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z 0.60 > 10.74 > > Z 401 ZN A O 821 OC 2.006 X,Y,Z 0.40 > 7.51 > > > > Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z 1.00 > 8.94 > > Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z 1.00 > 8.70 > > Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z 1.00 > 8.70 > > Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z 0.60 > 11.05 > > Z 402 ZN A O 821 OC 1.829 X,Y,Z 0.40 > 7.81 > > > > Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z 1.00 > 10.50 > > Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z 1.00 > 10.19 > > Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 > 12.66 > > Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 > 11.54 > > Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.20 > 9.09 > > Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 > 13.79 > > > > Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.00 > 8.73 > > > > > > Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.00 > 9.22 > > Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.00 > 8.91 > > Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.00 > 8.79 > > Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.00 > 8.76 > > Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.70 > 9.31 > > > > Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.00 > 9.49 > > Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.00 > 9.22 > > Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z
Re: [ccp4bb] metal coordination at low resolution - restraints
Hi Jan, They hold nice because of high occupancy or because you have very high resolution and no restraints are necessary at all (even for protein part)? Thank you Vaheh From: CCP4 bulletin board On Behalf Of Jan Dohnalek Sent: Tuesday, September 8, 2020 8:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] metal coordination at low resolution - restraints Hi Garib, On 8 Sep 2020, at 11:39, Jan Dohnalek mailto:dohnalek...@gmail.com>> wrote: These are structural. Are they tetrahedral or octahedral? From the list of neighbours they do not look like tetrahedral. Some of them do look like octahedral. They are involved in reaction. Two are ~ octahedral (skewed though, two positions filled by catalysis participant), one is ~tetrahedral, but actually can also accept a fifth coordinating atom. But as I said - in all our structures restraining the coordination geometry is not necessary, they hold nice. Jan Jan On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: What are these numbers? If I understand these numbers correctly: none of your Zn atoms is structural (4 coordinated tetrahedral). If that is the case then you need specific links or restraints. If my reading of your numbers is correct then there could be some chemistry change of the surrounding residues. If it is not structural Zn then it is likely that coordination is 6. But without seeing coordinates and maps it is difficult to say what is there. Regards Garib On 8 Sep 2020, at 11:11, Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> wrote: Hmm - here is my problem - a list of ZN contacts for the two molecules.. residue 602 is a phosphate, and there possibly should be a few more waters .. No idea how best to tackle it.. E Z 401 ZN A W 21 NA 2.057 X,Y,Z 1.008.73 Z 401 ZN A W 21 OA 2.220 X,Y,Z 1.008.76 Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z 1.008.39 Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z 1.008.61 Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z 0.60 10.74 Z 401 ZN A O 821 OC 2.006 X,Y,Z 0.407.51 Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z 1.008.94 Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z 1.008.70 Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z 1.008.70 Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z 0.60 11.05 Z 402 ZN A O 821 OC 1.829 X,Y,Z 0.407.81 Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z 1.00 10.50 Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z 1.00 10.19 Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 12.66 Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 11.54 Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.209.09 Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 13.79 Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.008.73 Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.009.22 Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.008.91 Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.008.79 Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.008.76 Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.709.31 Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.009.49 Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.009.22 Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z 1.009.70 Z 402 ZN B Z 601 O3 B 1.973 X,Y,Z 0.709.58 Z 403 ZN B H 145 NE2 B 2.027 X,Y,Z 1.00 10.80 Z 403 ZN B H 168 NE2 B 2.029 X,Y,Z 1.00 10.65 Z 403 ZN B D 172 OD2 B 2.089 X,Y,Z 1.00 13.12 Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 14.10 Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 10.61 ~ On Tue, 8 Sep 2020 at 10:47, Garib Murshudov mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: Hi Robbie and Eleanor There are links for Zn-His and Zn-Cys. They meant to be used automatically, obviously something is not entirely right. Link names are: ZN-CYS It has a bond between Zn and S as well as an angle: ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 This also removes H of Cys to make covalent bond between Zn and Cys. Similar links are available for Zn and His ND1 and Zn - HIS NE2 Link names are: ZN-HISND ZN-HISNE Again these links have angles between Zn and atoms of His. Angle centred at Zn is missing. But these distances and ang
Re: [ccp4bb] metal coordination at low resolution - restraints
ween Zn and atoms of His. >> >> Angle centred at Zn is missing. But these distances and angles defined in >> the link it should work fine. >> >> Regards >> Garib >> >> >> >> On 8 Sep 2020, at 10:40, Robbie Joosten >> wrote: >> >> Hi Elanor, >> >> The distances are in the dictionaries but the angles involve three >> different residues so these cannot be in the current dictionary. We could >> add the program that generates these restraints to CCP4 though. >> >> Cheers, >> Robbie >> >> -Original Message- >> From: Eleanor Dodson >> Sent: Tuesday, September 8, 2020 11:38 >> To: Robbie Joosten ; Garib N Murshudov >> >> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls > lmb.cam.ac.uk> >> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints >> >> Robbie - could that be added to the distributed dictionaries? Zn binding >> is >> common and at low resolution distance restraints are not enough.. >> Eleanor >> >> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten > <mailto:robbie_joos...@hotmail.com > > wrote: >> >> >> Hi Anna, >> >> Yes you can do this in Refmac by adding external restraints. If you >> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) >> you >> can also use PDB-REDO to generate the restraints automatically. The >> restraints are written to the output so you can continue using them in >> Refmac. >> >> HTH, >> Robbie >> >> > -Original Message- >> > From: CCP4 bulletin board > <mailto:CCP4BB@JISCMAIL.AC.UK > > On Behalf Of >> anna >> > anna >> > Sent: Tuesday, September 8, 2020 11:28 >> > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK >> > >> > Subject: [ccp4bb] metal coordination at low resolution - restraints >> > >> > Dear all, >> > >> > quickly: is there a way to restrain metal coordination geometry >> (even angles) >> > in refmac? >> > >> > I am refining a low resolution structure (3.3A) with 2 zinc binding >> sites. >> > I am pretty sure about metal position (strong anomalous signal) >> and what >> > are the residues involved in coordination since I solved the apo- >> structure at >> > good resolution and Zn-binding does not induce huge structural >> variations. >> > However, as you can imagine, electron density is poorly defined >> and Refmac >> > gives a very distorted coordination geometry. >> > I noticed that in phenix it is possible to generate restraints with >> readyset but >> > I'd like to work with refmac. >> > >> > Many thanks for your suggestions. >> > >> > Cheers, >> > Anna >> > >> > >> > >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/WA- >> JISC.exe?SUBED1=CCP4BB=1 >> >> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA- >> JISC.exe?SUBED1=CCP4BB=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB >> <http://www.jiscmail.ac.uk/CCP4BB> , a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> >> >> >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] metal coordination at low resolution - restraints
Yes, and the Zn is tetrahedral with a vacancy which makes then angles a bit more open. It's a good thing insulin makes nice crystals Cheers, Robbie > -Original Message- > From: Eleanor Dodson > Sent: Tuesday, September 8, 2020 12:59 > To: Robbie Joosten > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints > > I guess I have lived with Zn since I first learnt what a crystal was - ZN is > part > of insulin secretion and whether it is or is not present is fundamental to the > biochemistry.. > > I agree things have to be handled case by case - For insulin the three HIS are > generated by symmetry and that causes horrible headaches for any restraint > dictionary.. > And for Jan's case the resolution is excellent and the main links very clear. > (In > fact they were not restrained but all distances finish up near to 2A as > expected.) However maybe something can be learnt from this structure > which would help the query which started us off! > Eleanor > > On Tue, 8 Sep 2020 at 11:49, Robbie Joosten <mailto:robbie_joos...@hotmail.com> > wrote: > > > Hi Jan, > > If you want targets for your metal site you could have a look at > MetalPDB (http://metalweb.cerm.unifi.it/). That has good tools to find > similar sites and get some statistics you can use to generate case-specific > restraints. > > Cheers, > Robbie > > > -Original Message- > > From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Garib > > Murshudov > > Sent: Tuesday, September 8, 2020 12:44 > > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > > Subject: Re: [ccp4bb] metal coordination at low resolution - > restraints > > > > Hi Jan, > > > > > > > > > > On 8 Sep 2020, at 11:39, Jan Dohnalek > mailto:dohnalek...@gmail.com> > > <mailto:dohnalek...@gmail.com > <mailto:dohnalek...@gmail.com> > > wrote: > > > > These are structural. > > > > > > Are they tetrahedral or octahedral? From the list of neighbours > they do not > > look like tetrahedral. Some of them do look like octahedral. > > > > > > They form the active site of our enzyme. > > > > > > So,are they involved in reaction? > > > > > > Normally there is no need to restrain these, they "behave". > > > > But in general having such standard "restraint angles" available > > would be of use, I agree. > > > > > > > > For tetrahedral Zn we do have “bonds” and “angles” between Zn > and > > coordinating residues. For general solution we need a bit different > approach > > (e.g. coordination analysis). > > > > > > > > Regards > > Garib > > > > > > > > > > Jan > > > > > > On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov> lmb.cam.ac.uk <http://lmb.cam.ac.uk> <mailto:garib@mrc- > lmb.cam.ac.uk <mailto:ga...@mrc-lmb.cam.ac.uk> > > wrote: > > > > > > What are these numbers? > > > > If I understand these numbers correctly: none of your Zn > > atoms is structural (4 coordinated tetrahedral). If that is the case > then you > > need specific links or restraints. If my reading of your numbers is > correct > > then there could be some chemistry change of the surrounding > residues. > > > > If it is not structural Zn then it is likely that > coordination is > 6. > > But without seeing coordinates and maps it is difficult to say what > is there. > > > > Regards > > Garib > > > > > > > > On 8 Sep 2020, at 11:11, Eleanor Dodson > > <mailto:eleanor.dod...@york.ac.uk> <mailto:eleanor.dod...@york.ac.uk > <mailto:eleanor.dod...@york.ac.uk> > > wrote: > > > > Hmm - here is my problem - a list of ZN > contacts for > > the two molecules.. > > residue 602 is a phosp
Re: [ccp4bb] metal coordination at low resolution - restraints
I guess I have lived with Zn since I first learnt what a crystal was - ZN is part of insulin secretion and whether it is or is not present is fundamental to the biochemistry.. I agree things have to be handled case by case - For insulin the three HIS are generated by symmetry and that causes horrible headaches for any restraint dictionary.. And for Jan's case the resolution is excellent and the main links very clear. (In fact they were not restrained but all distances finish up near to 2A as expected.) However maybe something can be learnt from this structure which would help the query which started us off! Eleanor On Tue, 8 Sep 2020 at 11:49, Robbie Joosten wrote: > Hi Jan, > > If you want targets for your metal site you could have a look at MetalPDB ( > http://metalweb.cerm.unifi.it/). That has good tools to find similar > sites and get some statistics you can use to generate case-specific > restraints. > > Cheers, > Robbie > > > -Original Message- > > From: CCP4 bulletin board On Behalf Of Garib > > Murshudov > > Sent: Tuesday, September 8, 2020 12:44 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints > > > > Hi Jan, > > > > > > > > > > On 8 Sep 2020, at 11:39, Jan Dohnalek > <mailto:dohnalek...@gmail.com> > wrote: > > > > These are structural. > > > > > > Are they tetrahedral or octahedral? From the list of neighbours they do > not > > look like tetrahedral. Some of them do look like octahedral. > > > > > > They form the active site of our enzyme. > > > > > > So,are they involved in reaction? > > > > > > Normally there is no need to restrain these, they "behave". > > > > But in general having such standard "restraint angles" available > > would be of use, I agree. > > > > > > > > For tetrahedral Zn we do have “bonds” and “angles” between Zn and > > coordinating residues. For general solution we need a bit different > approach > > (e.g. coordination analysis). > > > > > > > > Regards > > Garib > > > > > > > > > > Jan > > > > > > On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov > lmb.cam.ac.uk <mailto:ga...@mrc-lmb.cam.ac.uk> > wrote: > > > > > > What are these numbers? > > > > If I understand these numbers correctly: none of your Zn > > atoms is structural (4 coordinated tetrahedral). If that is the case > then you > > need specific links or restraints. If my reading of your numbers is > correct > > then there could be some chemistry change of the surrounding residues. > > > > If it is not structural Zn then it is likely that > coordination is 6. > > But without seeing coordinates and maps it is difficult to say what is > there. > > > > Regards > > Garib > > > > > > > > On 8 Sep 2020, at 11:11, Eleanor Dodson > > mailto:eleanor.dod...@york.ac.uk> > wrote: > > > > Hmm - here is my problem - a list of ZN contacts > for > > the two molecules.. > > residue 602 is a phosphate, and there possibly > should > > be a few more waters .. > > No idea how best to tackle it.. > > E > > > > > >Z 401 ZN A W 21 NA 2.057 X,Y,Z > > 1.008.73 > >Z 401 ZN A W 21 OA 2.220 X,Y,Z > > 1.008.76 > >Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z > > 1.008.39 > >Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z > > 1.008.61 > >Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z > > 0.60 10.74 > >Z 401 ZN A O 821 OC 2.006 X,Y,Z > > 0.407.51 > > > > > >Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z > > 1.008.94 > >Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z > > 1.008.70 > >Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z > > 1.008.70 > >Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z > > 0.60 11.05 > >Z 402 ZN A O 821 OC 1.829 X,Y,Z > > 0.407.81 > > > > > >
Re: [ccp4bb] metal coordination at low resolution - restraints
Hi Jan, If you want targets for your metal site you could have a look at MetalPDB (http://metalweb.cerm.unifi.it/). That has good tools to find similar sites and get some statistics you can use to generate case-specific restraints. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Garib > Murshudov > Sent: Tuesday, September 8, 2020 12:44 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints > > Hi Jan, > > > > > On 8 Sep 2020, at 11:39, Jan Dohnalek <mailto:dohnalek...@gmail.com> > wrote: > > These are structural. > > > Are they tetrahedral or octahedral? From the list of neighbours they do not > look like tetrahedral. Some of them do look like octahedral. > > > They form the active site of our enzyme. > > > So,are they involved in reaction? > > > Normally there is no need to restrain these, they "behave". > > But in general having such standard "restraint angles" available > would be of use, I agree. > > > > For tetrahedral Zn we do have “bonds” and “angles” between Zn and > coordinating residues. For general solution we need a bit different approach > (e.g. coordination analysis). > > > > Regards > Garib > > > > > Jan > > > On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov lmb.cam.ac.uk <mailto:ga...@mrc-lmb.cam.ac.uk> > wrote: > > > What are these numbers? > > If I understand these numbers correctly: none of your Zn > atoms is structural (4 coordinated tetrahedral). If that is the case then you > need specific links or restraints. If my reading of your numbers is correct > then there could be some chemistry change of the surrounding residues. > > If it is not structural Zn then it is likely that coordination > is 6. > But without seeing coordinates and maps it is difficult to say what is there. > > Regards > Garib > > > > On 8 Sep 2020, at 11:11, Eleanor Dodson > mailto:eleanor.dod...@york.ac.uk> > wrote: > > Hmm - here is my problem - a list of ZN contacts for > the two molecules.. > residue 602 is a phosphate, and there possibly should > be a few more waters .. > No idea how best to tackle it.. > E > > >Z 401 ZN A W 21 NA 2.057 X,Y,Z > 1.008.73 >Z 401 ZN A W 21 OA 2.220 X,Y,Z > 1.008.76 >Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z > 1.008.39 >Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z > 1.008.61 >Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z > 0.60 10.74 >Z 401 ZN A O 821 OC 2.006 X,Y,Z > 0.407.51 > > >Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z > 1.008.94 >Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z > 1.008.70 >Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z > 1.008.70 >Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z > 0.60 11.05 >Z 402 ZN A O 821 OC 1.829 X,Y,Z > 0.407.81 > > >Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z > 1.00 10.50 >Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z > 1.00 10.19 >Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z > 1.00 12.66 >Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z > 0.60 11.54 >Z 403 ZN A O 820 OC 2.207 X,Y,Z > 0.209.09 >Z 403 ZN A O 822 OC 2.059 X,Y,Z > 0.40 13.79 > > >Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z > 1.008.73 > > > > >Z 401 ZN B W 21 NB 2.099 X,Y,Z > 1.009.22 >Z 401 ZN B W 21 OB 2.184 X,Y,Z > 1.008.91 >Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z > 1.008.79 >Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z > 1.008.76 >Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z > 0.709.31 > > >Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z > 1.009.49 >
Re: [ccp4bb] metal coordination at low resolution - restraints
>> >> >> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov > <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: >> Hi Robbie and Eleanor >> >> There are links for Zn-His and Zn-Cys. They meant to be used automatically, >> obviously something is not entirely right. >> >> Link names are: >> ZN-CYS >> >> It has a bond between Zn and S as well as an angle: >> ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 >> >> This also removes H of Cys to make covalent bond between Zn and Cys. >> >> Similar links are available for Zn and His ND1 and Zn - HIS NE2 >> Link names are: >> >> ZN-HISND >> ZN-HISNE >> >> Again these links have angles between Zn and atoms of His. >> >> Angle centred at Zn is missing. But these distances and angles defined in >> the link it should work fine. >> >> Regards >> Garib >> >> >> >>> On 8 Sep 2020, at 10:40, Robbie Joosten >> <mailto:robbie_joos...@hotmail.com>> wrote: >>> >>> Hi Elanor, >>> >>> The distances are in the dictionaries but the angles involve three >>> different residues so these cannot be in the current dictionary. We could >>> add the program that generates these restraints to CCP4 though. >>> >>> Cheers, >>> Robbie >>> >>>> -Original Message- >>>> From: Eleanor Dodson >>> <mailto:eleanor.dod...@york.ac.uk>> >>>> Sent: Tuesday, September 8, 2020 11:38 >>>> To: Robbie Joosten >>> <mailto:robbie_joos...@hotmail.com>>; Garib N Murshudov >>>> mailto:ga...@mrc-lmb.cam.ac.uk>> >>>> Cc: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>; Robert Nicholls >>>> >>> lmb.cam.ac.uk <http://lmb.cam.ac.uk/>> >>>> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints >>>> >>>> Robbie - could that be added to the distributed dictionaries? Zn binding is >>>> common and at low resolution distance restraints are not enough.. >>>> Eleanor >>>> >>>> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten >>> <mailto:robbie_joos...@hotmail.com> >>>> <mailto:robbie_joos...@hotmail.com <mailto:robbie_joos...@hotmail.com>> > >>>> wrote: >>>> >>>> >>>>Hi Anna, >>>> >>>>Yes you can do this in Refmac by adding external restraints. If you >>>> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) >>>> you >>>> can also use PDB-REDO to generate the restraints automatically. The >>>> restraints are written to the output so you can continue using them in >>>> Refmac. >>>> >>>>HTH, >>>>Robbie >>>> >>>>> -Original Message- >>>>> From: CCP4 bulletin board >>> <mailto:CCP4BB@JISCMAIL.AC.UK> >>>> <mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> > On Behalf >>>> Of anna >>>>> anna >>>>> Sent: Tuesday, September 8, 2020 11:28 >>>>> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> >>>> <mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> >>>>> Subject: [ccp4bb] metal coordination at low resolution - restraints >>>>> >>>>> Dear all, >>>>> >>>>> quickly: is there a way to restrain metal coordination geometry >>>> (even angles) >>>>> in refmac? >>>>> >>>>> I am refining a low resolution structure (3.3A) with 2 zinc binding >>>> sites. >>>>> I am pretty sure about metal position (strong anomalous signal) >>>> and what >>>>> are the residues involved in coordination since I solved the apo- >>>> structure at >>>>> good resolution and Zn-binding does not induce huge structural >>>> variations. >>>>> However, as you can imagine, electron density is poorly defined >>>> and Refmac >>>>> gives a very distorted coordination geometry. >>>>> I noticed that in phenix it is possible to generate restraints with >>>> readyset but >>>>> I'd like to work with refmac. &g
Re: [ccp4bb] metal coordination at low resolution - restraints
These are structural. They form the active site of our enzyme. Normally there is no need to restrain these, they "behave". But in general having such standard "restraint angles" available would be of use, I agree. Jan On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov wrote: > What are these numbers? > > If I understand these numbers correctly: none of your Zn atoms is > structural (4 coordinated tetrahedral). If that is the case then you need > specific links or restraints. If my reading of your numbers is correct then > there could be some chemistry change of the surrounding residues. > > If it is not structural Zn then it is likely that coordination is 6. But > without seeing coordinates and maps it is difficult to say what is there. > > Regards > Garib > > > On 8 Sep 2020, at 11:11, Eleanor Dodson wrote: > > Hmm - here is my problem - a list of ZN contacts for the two molecules.. > residue 602 is a phosphate, and there possibly should be a few more waters > .. > No idea how best to tackle it.. > E > > > Z 401 ZN A W 21 NA 2.057 X,Y,Z 1.00 > 8.73 > Z 401 ZN A W 21 OA 2.220 X,Y,Z 1.00 > 8.76 > Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z 1.00 > 8.39 > Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z 1.00 > 8.61 > Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z 0.60 > 10.74 > Z 401 ZN A O 821 OC 2.006 X,Y,Z 0.40 > 7.51 > > Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z 1.00 > 8.94 > Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z 1.00 > 8.70 > Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z 1.00 > 8.70 > Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z 0.60 > 11.05 > Z 402 ZN A O 821 OC 1.829 X,Y,Z 0.40 > 7.81 > > Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z 1.00 > 10.50 > Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z 1.00 > 10.19 > Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 > 12.66 > Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 > 11.54 > Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.20 > 9.09 > Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 > 13.79 > > Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.00 > 8.73 > > > Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.00 > 9.22 > Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.00 > 8.91 > Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.00 > 8.79 > Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.00 > 8.76 > Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.70 > 9.31 > > Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.00 > 9.49 > Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.00 > 9.22 > Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z 1.00 > 9.70 > Z 402 ZN B Z 601 O3 B 1.973 X,Y,Z 0.70 > 9.58 > > Z 403 ZN B H 145 NE2 B 2.027 X,Y,Z 1.00 > 10.80 > Z 403 ZN B H 168 NE2 B 2.029 X,Y,Z 1.00 > 10.65 > Z 403 ZN B D 172 OD2 B 2.089 X,Y,Z 1.00 > 13.12 > Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 > 14.10 > Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 > 10.61 > ~ > > > On Tue, 8 Sep 2020 at 10:47, Garib Murshudov > wrote: > >> Hi Robbie and Eleanor >> >> There are links for Zn-His and Zn-Cys. They meant to be used >> automatically, obviously something is not entirely right. >> >> Link names are: >> ZN-CYS >> >> It has a bond between Zn and S as well as an angle: >> ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 >> >> This also removes H of Cys to make covalent bond between Zn and Cys. >> >> Similar links are available for Zn and His ND1 and Zn - HIS NE2 >> Link names are: >> >> ZN-HISND >> ZN-HISNE >> >> Again these links have angles between Zn and atoms of His. >> >> Angle centred at Zn is missing. But these distances and angles defined in >> the link it should work fine. >> >> Regards >> Garib >> >> >> >> On 8 Sep 2020, at 10:40, Robbie Joosten >> wrote: >> >> Hi Elanor, >> >> The dista
Re: [ccp4bb] metal coordination at low resolution - restraints
What are these numbers? If I understand these numbers correctly: none of your Zn atoms is structural (4 coordinated tetrahedral). If that is the case then you need specific links or restraints. If my reading of your numbers is correct then there could be some chemistry change of the surrounding residues. If it is not structural Zn then it is likely that coordination is 6. But without seeing coordinates and maps it is difficult to say what is there. Regards Garib > On 8 Sep 2020, at 11:11, Eleanor Dodson wrote: > > Hmm - here is my problem - a list of ZN contacts for the two molecules.. > residue 602 is a phosphate, and there possibly should be a few more waters .. > No idea how best to tackle it.. > E > > > Z 401 ZN A W 21 NA 2.057 X,Y,Z 1.008.73 > Z 401 ZN A W 21 OA 2.220 X,Y,Z 1.008.76 > Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z 1.008.39 > Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z 1.008.61 > Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z 0.60 10.74 > Z 401 ZN A O 821 OC 2.006 X,Y,Z 0.407.51 > > Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z 1.008.94 > Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z 1.008.70 > Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z 1.008.70 > Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z 0.60 11.05 > Z 402 ZN A O 821 OC 1.829 X,Y,Z 0.407.81 > > Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z 1.00 10.50 > Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z 1.00 10.19 > Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 12.66 > Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 11.54 > Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.209.09 > Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 13.79 > > Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.008.73 > > > Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.009.22 > Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.008.91 > Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.008.79 > Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.008.76 > Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.709.31 > > Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.009.49 > Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.009.22 > Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z 1.009.70 > Z 402 ZN B Z 601 O3 B 1.973 X,Y,Z 0.709.58 > > Z 403 ZN B H 145 NE2 B 2.027 X,Y,Z 1.00 10.80 > Z 403 ZN B H 168 NE2 B 2.029 X,Y,Z 1.00 10.65 > Z 403 ZN B D 172 OD2 B 2.089 X,Y,Z 1.00 13.12 > Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 14.10 > Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 10.61 > ~ > > > On Tue, 8 Sep 2020 at 10:47, Garib Murshudov <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: > Hi Robbie and Eleanor > > There are links for Zn-His and Zn-Cys. They meant to be used automatically, > obviously something is not entirely right. > > Link names are: > ZN-CYS > > It has a bond between Zn and S as well as an angle: > ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 > > This also removes H of Cys to make covalent bond between Zn and Cys. > > Similar links are available for Zn and His ND1 and Zn - HIS NE2 > Link names are: > > ZN-HISND > ZN-HISNE > > Again these links have angles between Zn and atoms of His. > > Angle centred at Zn is missing. But these distances and angles defined in the > link it should work fine. > > Regards > Garib > > > >> On 8 Sep 2020, at 10:40, Robbie Joosten > <mailto:robbie_joos...@hotmail.com>> wrote: >> >> Hi Elanor, >> >> The distances are in the dictionaries but the angles involve three different >> residues so these cannot be in the current dictionary. We could add the >> program that generates these restraints to CCP4 though. >> >> Cheers, >> Robbie >> >>> -Original Message- >>> From: Eleanor Dodson >> <mailto:elean
Re: [ccp4bb] metal coordination at low resolution - restraints
Hmm - here is my problem - a list of ZN contacts for the two molecules.. residue 602 is a phosphate, and there possibly should be a few more waters .. No idea how best to tackle it.. E Z 401 ZN A W 21 NA 2.057 X,Y,Z 1.00 8.73 Z 401 ZN A W 21 OA 2.220 X,Y,Z 1.00 8.76 Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z 1.00 8.39 Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z 1.00 8.61 Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z 0.60 10.74 Z 401 ZN A O 821 OC 2.006 X,Y,Z 0.40 7.51 Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z 1.00 8.94 Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z 1.00 8.70 Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z 1.00 8.70 Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z 0.60 11.05 Z 402 ZN A O 821 OC 1.829 X,Y,Z 0.40 7.81 Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z 1.00 10.50 Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z 1.00 10.19 Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 12.66 Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 11.54 Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.20 9.09 Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 13.79 Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.00 8.73 Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.00 9.22 Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.00 8.91 Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.00 8.79 Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.00 8.76 Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.70 9.31 Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.00 9.49 Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.00 9.22 Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z 1.00 9.70 Z 402 ZN B Z 601 O3 B 1.973 X,Y,Z 0.70 9.58 Z 403 ZN B H 145 NE2 B 2.027 X,Y,Z 1.00 10.80 Z 403 ZN B H 168 NE2 B 2.029 X,Y,Z 1.00 10.65 Z 403 ZN B D 172 OD2 B 2.089 X,Y,Z 1.00 13.12 Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 14.10 Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 10.61 ~ On Tue, 8 Sep 2020 at 10:47, Garib Murshudov wrote: > Hi Robbie and Eleanor > > There are links for Zn-His and Zn-Cys. They meant to be used > automatically, obviously something is not entirely right. > > Link names are: > ZN-CYS > > It has a bond between Zn and S as well as an angle: > ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 > > This also removes H of Cys to make covalent bond between Zn and Cys. > > Similar links are available for Zn and His ND1 and Zn - HIS NE2 > Link names are: > > ZN-HISND > ZN-HISNE > > Again these links have angles between Zn and atoms of His. > > Angle centred at Zn is missing. But these distances and angles defined in > the link it should work fine. > > Regards > Garib > > > > On 8 Sep 2020, at 10:40, Robbie Joosten > wrote: > > Hi Elanor, > > The distances are in the dictionaries but the angles involve three > different residues so these cannot be in the current dictionary. We could > add the program that generates these restraints to CCP4 though. > > Cheers, > Robbie > > -Original Message- > From: Eleanor Dodson > Sent: Tuesday, September 8, 2020 11:38 > To: Robbie Joosten ; Garib N Murshudov > > Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls lmb.cam.ac.uk> > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints > > Robbie - could that be added to the distributed dictionaries? Zn binding is > common and at low resolution distance restraints are not enough.. > Eleanor > > On Tue, 8 Sep 2020 at 10:33, Robbie Joosten <mailto:robbie_joos...@hotmail.com > > wrote: > > > Hi Anna, > > Yes you can do this in Refmac by adding external restraints. If you > have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) > you > can also use PDB-REDO to generate the restraints automatically. The > restraints are written to the output so you can continue using them in > Refmac. > > HTH, > Robbie > > > -Original Message- > > From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK > > On Behalf Of anna > > anna > > Sent: Tuesday, September 8, 2020 11:28 > &
Re: [ccp4bb] metal coordination at low resolution - restraints
Hi Robbie and Eleanor There are links for Zn-His and Zn-Cys. They meant to be used automatically, obviously something is not entirely right. Link names are: ZN-CYS It has a bond between Zn and S as well as an angle: ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 This also removes H of Cys to make covalent bond between Zn and Cys. Similar links are available for Zn and His ND1 and Zn - HIS NE2 Link names are: ZN-HISND ZN-HISNE Again these links have angles between Zn and atoms of His. Angle centred at Zn is missing. But these distances and angles defined in the link it should work fine. Regards Garib > On 8 Sep 2020, at 10:40, Robbie Joosten wrote: > > Hi Elanor, > > The distances are in the dictionaries but the angles involve three different > residues so these cannot be in the current dictionary. We could add the > program that generates these restraints to CCP4 though. > > Cheers, > Robbie > >> -Original Message- >> From: Eleanor Dodson >> Sent: Tuesday, September 8, 2020 11:38 >> To: Robbie Joosten ; Garib N Murshudov >> >> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls > lmb.cam.ac.uk> >> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints >> >> Robbie - could that be added to the distributed dictionaries? Zn binding is >> common and at low resolution distance restraints are not enough.. >> Eleanor >> >> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten > <mailto:robbie_joos...@hotmail.com> > wrote: >> >> >> Hi Anna, >> >> Yes you can do this in Refmac by adding external restraints. If you >> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) you >> can also use PDB-REDO to generate the restraints automatically. The >> restraints are written to the output so you can continue using them in >> Refmac. >> >> HTH, >> Robbie >> >> > -Original Message- >> > From: CCP4 bulletin board > <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of anna >> > anna >> > Sent: Tuesday, September 8, 2020 11:28 >> > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> >> > Subject: [ccp4bb] metal coordination at low resolution - restraints >> > >> > Dear all, >> > >> > quickly: is there a way to restrain metal coordination geometry >> (even angles) >> > in refmac? >> > >> > I am refining a low resolution structure (3.3A) with 2 zinc binding >> sites. >> > I am pretty sure about metal position (strong anomalous signal) >> and what >> > are the residues involved in coordination since I solved the apo- >> structure at >> > good resolution and Zn-binding does not induce huge structural >> variations. >> > However, as you can imagine, electron density is poorly defined >> and Refmac >> > gives a very distorted coordination geometry. >> > I noticed that in phenix it is possible to generate restraints with >> readyset but >> > I'd like to work with refmac. >> > >> > Many thanks for your suggestions. >> > >> > Cheers, >> > Anna >> > >> > >> > >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/WA- >> JISC.exe?SUBED1=CCP4BB=1 >> >> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA- >> JISC.exe?SUBED1=CCP4BB=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB >> <http://www.jiscmail.ac.uk/CCP4BB> , a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] metal coordination at low resolution - restraints
That seems an excellent idea - I have been struggling with a Zn complex in a ineffectual way and something like that would help, Eleanor On Tue, 8 Sep 2020 at 10:40, Robbie Joosten wrote: > Hi Elanor, > > The distances are in the dictionaries but the angles involve three > different residues so these cannot be in the current dictionary. We could > add the program that generates these restraints to CCP4 though. > > Cheers, > Robbie > > > -Original Message- > > From: Eleanor Dodson > > Sent: Tuesday, September 8, 2020 11:38 > > To: Robbie Joosten ; Garib N Murshudov > > > > Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls > lmb.cam.ac.uk> > > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints > > > > Robbie - could that be added to the distributed dictionaries? Zn binding > is > > common and at low resolution distance restraints are not enough.. > > Eleanor > > > > On Tue, 8 Sep 2020 at 10:33, Robbie Joosten > <mailto:robbie_joos...@hotmail.com> > wrote: > > > > > > Hi Anna, > > > > Yes you can do this in Refmac by adding external restraints. If you > > have structural Zinc sites (Zn coordinated by 4 histidines or > cysteines) you > > can also use PDB-REDO to generate the restraints automatically. The > > restraints are written to the output so you can continue using them in > > Refmac. > > > > HTH, > > Robbie > > > > > -Original Message- > > > From: CCP4 bulletin board > <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of anna > > > anna > > > Sent: Tuesday, September 8, 2020 11:28 > > > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > > > Subject: [ccp4bb] metal coordination at low resolution - > restraints > > > > > > Dear all, > > > > > > quickly: is there a way to restrain metal coordination geometry > > (even angles) > > > in refmac? > > > > > > I am refining a low resolution structure (3.3A) with 2 zinc > binding > > sites. > > > I am pretty sure about metal position (strong anomalous signal) > > and what > > > are the residues involved in coordination since I solved the apo- > > structure at > > > good resolution and Zn-binding does not induce huge structural > > variations. > > > However, as you can imagine, electron density is poorly defined > > and Refmac > > > gives a very distorted coordination geometry. > > > I noticed that in phenix it is possible to generate restraints > with > > readyset but > > > I'd like to work with refmac. > > > > > > Many thanks for your suggestions. > > > > > > Cheers, > > > Anna > > > > > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA- > > JISC.exe?SUBED1=CCP4BB=1 > > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA- > > JISC.exe?SUBED1=CCP4BB=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB > > <http://www.jiscmail.ac.uk/CCP4BB> , a mailing list hosted by > > www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are > > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] metal coordination at low resolution - restraints
Hi Elanor, The distances are in the dictionaries but the angles involve three different residues so these cannot be in the current dictionary. We could add the program that generates these restraints to CCP4 though. Cheers, Robbie > -Original Message- > From: Eleanor Dodson > Sent: Tuesday, September 8, 2020 11:38 > To: Robbie Joosten ; Garib N Murshudov > > Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls lmb.cam.ac.uk> > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints > > Robbie - could that be added to the distributed dictionaries? Zn binding is > common and at low resolution distance restraints are not enough.. > Eleanor > > On Tue, 8 Sep 2020 at 10:33, Robbie Joosten <mailto:robbie_joos...@hotmail.com> > wrote: > > > Hi Anna, > > Yes you can do this in Refmac by adding external restraints. If you > have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) you > can also use PDB-REDO to generate the restraints automatically. The > restraints are written to the output so you can continue using them in > Refmac. > > HTH, > Robbie > > > -Original Message- > > From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of anna > > anna > > Sent: Tuesday, September 8, 2020 11:28 > > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > > Subject: [ccp4bb] metal coordination at low resolution - restraints > > > > Dear all, > > > > quickly: is there a way to restrain metal coordination geometry > (even angles) > > in refmac? > > > > I am refining a low resolution structure (3.3A) with 2 zinc binding > sites. > > I am pretty sure about metal position (strong anomalous signal) > and what > > are the residues involved in coordination since I solved the apo- > structure at > > good resolution and Zn-binding does not induce huge structural > variations. > > However, as you can imagine, electron density is poorly defined > and Refmac > > gives a very distorted coordination geometry. > > I noticed that in phenix it is possible to generate restraints with > readyset but > > I'd like to work with refmac. > > > > Many thanks for your suggestions. > > > > Cheers, > > Anna > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA- > JISC.exe?SUBED1=CCP4BB=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA- > JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB > <http://www.jiscmail.ac.uk/CCP4BB> , a mailing list hosted by > www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] metal coordination at low resolution - restraints
Robbie - could that be added to the distributed dictionaries? Zn binding is common and at low resolution distance restraints are not enough.. Eleanor On Tue, 8 Sep 2020 at 10:33, Robbie Joosten wrote: > Hi Anna, > > Yes you can do this in Refmac by adding external restraints. If you have > structural Zinc sites (Zn coordinated by 4 histidines or cysteines) you > can also use PDB-REDO to generate the restraints automatically. The > restraints are written to the output so you can continue using them in > Refmac. > > HTH, > Robbie > > > -Original Message- > > From: CCP4 bulletin board On Behalf Of anna > > anna > > Sent: Tuesday, September 8, 2020 11:28 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] metal coordination at low resolution - restraints > > > > Dear all, > > > > quickly: is there a way to restrain metal coordination geometry (even > angles) > > in refmac? > > > > I am refining a low resolution structure (3.3A) with 2 zinc binding > sites. > > I am pretty sure about metal position (strong anomalous signal) and what > > are the residues involved in coordination since I solved the > apo-structure at > > good resolution and Zn-binding does not induce huge structural > variations. > > However, as you can imagine, electron density is poorly defined and > Refmac > > gives a very distorted coordination geometry. > > I noticed that in phenix it is possible to generate restraints with > readyset but > > I'd like to work with refmac. > > > > Many thanks for your suggestions. > > > > Cheers, > > Anna > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] metal coordination at low resolution - restraints
Hi Anna, Yes you can do this in Refmac by adding external restraints. If you have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) you can also use PDB-REDO to generate the restraints automatically. The restraints are written to the output so you can continue using them in Refmac. HTH, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of anna > anna > Sent: Tuesday, September 8, 2020 11:28 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] metal coordination at low resolution - restraints > > Dear all, > > quickly: is there a way to restrain metal coordination geometry (even angles) > in refmac? > > I am refining a low resolution structure (3.3A) with 2 zinc binding sites. > I am pretty sure about metal position (strong anomalous signal) and what > are the residues involved in coordination since I solved the apo-structure at > good resolution and Zn-binding does not induce huge structural variations. > However, as you can imagine, electron density is poorly defined and Refmac > gives a very distorted coordination geometry. > I noticed that in phenix it is possible to generate restraints with readyset > but > I'd like to work with refmac. > > Many thanks for your suggestions. > > Cheers, > Anna > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
