Hi Jan,
> 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 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 <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 <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 <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 <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 ######################################################################## 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/
