I know how difficult it is to get the chemistry right, and that really has to be up to the researcher.. a database of high resolution structures with metals would be useful as a sanity check. Robbie mentioned MetalPDB (http://metalweb.cerm.unifi.it/).
E On Wed, 9 Sep 2020 at 11:18, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk> wrote: > Hi Eleanor, > > Obviously I agree that people should use restraints for metals. It will > make metal refinement easy and coordination consistent with chemistry > > For distance and angle restraints there is an external distance restraint > mechanism. PDB-REDO can generate for some of the metals. Unfortunately it > is not easy in general. But can be done manually. > > If you know metal and coordinating atoms and coordination then putting > restraints manually in ccp4i2 refmac keyword part should be > straightforward. For example (I think it is correct) > > External distance first chain A residue 239 atom ZN second chain A residue > 500 atom O value 1.95 sigma 0.032 type 0 > External distance first chain A residue 239 atom ZN second chain A residue > 145 atom ND1 value 2.03 sigma 0.05 type 0 > External angle first chain A residue 500 atom O next chain A residue 239 > atom ZN next chain residue 145 atom ND1 value 109 sigma 5 type 0 > > > Unfortunately these restraints do not account for the fact that when Zn is > bound to O or N atoms then it may change the nature of bonds (i.e. ZN bonds > are often covalent like, as Robbie says: these are d-block atoms for you) > The values above assume that ZN coordination is 4 and it is tetrahedral. > For others similar restraints could be added. > > In future we would like to semi-automate metal refinement. At the moment > it is pretty much users’ responsibility to design correct restraints (it is > not ideal, not because we do not trust users but because the knowledge is > not easily transferable from one refinement to another). > > > Regards > Garib > > > > > On 8 Sep 2020, at 20:51, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > > Yes Garib - all true but I dont think people should try to impose > restraints initially in refinement of metals. > > I never (knowingly) keep the metals in my MR model. Searching for them > with phases from a putative MR solution is one of the best verifications > that it is right... > > You can use anomalous fouriers to fix the metals as accurately as > possible. That could help with issue 3. And peak heights give you a bit of > information re occupancy. > > Surely issue 2) shouldnt happen! Do you mean BUCCANEER builds the > sequence wrongly? > > Na etc.. Impossible - hate them.. > > 4) & 5) are more or less the same .. occupancy is tricky - again anom > peaks ? Occupancy refinement? all difficult at low resolution.. > > On Tue, 8 Sep 2020 at 20:29, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk> > wrote: > >> Hi Jan, >> >> >> It is my experience also that if atoms are in more or less correct >> positions then non-bonding interaction together keep metals in correct >> positions, perhaps with a little bit different metal-coordinating atom >> distances. >> Problems arise when 1) one or several of the corrdinating atoms are >> missing which is the case at low resolution. Light atoms are almost >> invisible around heavy atoms (series termination and B value effects); 2) >> there are conflicting restraints which often happens with SS-bond (wrong >> SS-bond) and Zn-Cys bonds; 3) Starting atomic coordinates are far from >> right positions (which happens after molecular replacement when >> conformations are not exactly same around metals; 4) Metals are not fully >> occupied (which happens when metals involve reaction and they arrive during >> or as a part of reaction); 5) non-specific metal binding sites (which >> happens when metals are not part of the molecule but are used as a part of >> sample preparation - crystallisation or otherwise). 6) light metals (Na and >> similar) when metals are difficult to distinguish from water molecules; 7) >> highly mobile metals. >> >> >> Regards >> Garib >> >> >> On 8 Sep 2020, at 13:01, Jan Dohnalek <dohnalek...@gmail.com> wrote: >> >> 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 >> > > ######################################################################## 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/
