Hi Jan, They hold nice because of high occupancy or because you have very high resolution and no restraints are necessary at all (even for protein part)?
Thank you Vaheh From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Jan Dohnalek Sent: Tuesday, September 8, 2020 8:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] metal coordination at low resolution - restraints Hi Garib, 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 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<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-<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-<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/>> , terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/<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<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<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/
