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/
