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 <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 <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/ > ######################################################################## 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/
