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 <eleanor.dod...@york.ac.uk> > Sent: Tuesday, September 8, 2020 12:59 > To: Robbie Joosten <robbie_joos...@hotmail.com> > 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 <robbie_joos...@hotmail.com > <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 <CCP4BB@JISCMAIL.AC.UK > <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 > <dohnalek...@gmail.com <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 <garib@mrc- > > 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 > > <eleanor.dod...@york.ac.uk > <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 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> > <mailto: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> > > <mailto: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> <mailto: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> > <mailto: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> > > <mailto:ga...@mrc-lmb.cam.ac.uk <mailto:garib@mrc- > lmb.cam.ac.uk> > > > > Cc: CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK> > > <mailto:CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK> > ; Robert Nicholls <nicholls@mrc- > > lmb.cam.ac.uk > <http://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 > <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 > > <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > <mailto:CCP4BB@JISCMAIL.AC.UK <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> > <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> > > > <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 > > <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 > <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 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/
