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 <CCP4BB@JISCMAIL.AC.UK> 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 <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 <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 > <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 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 <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 109.000 > 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 > <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 > <eleanor.dod...@york.ac.uk <mailto:eleanor.dod...@york.ac.uk> > > Sent: Tuesday, September 8, 2020 > 11:38 > To: Robbie Joosten > <robbie_joos...@hotmail.com <mailto:robbie_joos...@hotmail.com> >; > Garib N Murshudov > <ga...@mrc-lmb.cam.ac.uk > <mailto:ga...@mrc-lmb.cam.ac.uk> > > Cc: CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK> ; Robert Nicholls <nicholls@mrc- > 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 <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 > <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> > > 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> > <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/ > > > > > > > > ________________________________ > > 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 ######################################################################## 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/
