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 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/
