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 < 0000176a9d5ebad7-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 <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 > ######################################################################## 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/
