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 <CCP4BB@JISCMAIL.AC.UK> * 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 <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 <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 <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 N A 2.057 X,Y,Z 1.00 > 8.73 > > Z 401 ZN A W 21 O A 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 O C 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 O C 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 O C 2.207 X,Y,Z 0.20 > 9.09 > > Z 403 ZN A O 822 O C 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 N B 2.099 X,Y,Z 1.00 > 9.22 > > Z 401 ZN B W 21 O B 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 O C 2.322 X,Y,Z 0.20 > 10.61 > > ~ > > > > > On Tue, 8 Sep 2020 at 10:47, Garib Murshudov <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 109.000 3.000 > > > > 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 <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 <eleanor.dod...@york.ac.uk> > Sent: Tuesday, September 8, 2020 11:38 > To: Robbie Joosten <robbie_joos...@hotmail.com>; Garib N Murshudov > <ga...@mrc-lmb.cam.ac.uk> > Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls <nicholls@mrc- > 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 <robbie_joos...@hotmail.com > <mailto:robbie_joos...@hotmail.com <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 <CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK <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 > <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&A=1 > > > ######################################################## > ################ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA- > JISC.exe?SUBED1=CCP4BB&A=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&A=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&A=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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
