I agree...one possibility is a M-His(2)-Lys-(OH2) site. Possible metal
ions would include Zn(II), although Lys is a relatively rare ligand in
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
13 Oak Drive
Hamilton, NY 13346
email: [log in to unmask]
On 6/22/2015 11:20 AM, Keller, Jacob wrote:
> Looks to me like a metal binding site with those histidines, perhaps--any chance of that? That might also explain the weird geometry issues.
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Dale Tronrud
> Sent: Monday, June 22, 2015 11:17 AM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] distorted phosphate molecule geometry after refinement
> It is possible that your PO4 has its atoms labeled with the wrong chirality. Yes, I know that PO4 is not chiral when you ignore hydrogen atoms and single/double bonds but adding labels creates an unnatural chriality. Try your refinement again after switching the labels on two oxygen atoms.
> Dale Tronrud
> On 6/22/2015 7:48 AM, ansuman biswas wrote:
>> Dear CCP4 users,
>> I am working on a protein from a hyperthermophilic archaeon.
>> I have collected mutliple X-Ray datasets, both from home source and
>> synchrotron and always found a clear density for tetrahedral geometry,
>> co-ordinated by two histidines and one lysine.
>> I tried fitting phosphate there, but its geometry always gets
>> distorted after each refinement cycle (Refmac 5.8.0073). Also I found
>> some short contacts between the coordinated residues and phosphate
>> which were very difficult to remove.
>> I am attaching a figure with the density and phosphate.
>> Kindly suggest -
>> 1. if this may be a possible modification of any of the associated
>> residues, and the code of the modified residue to be used.
>> 2. If the ligand requires separate restraints during refinement, I am
>> using the "restrained refinement" option available at the top of the
>> GUI for refmac.
>> Thanking you,
>> yours sincerely,
>> Ansuman Biswas,
>> PhD student,
>> Dept. of Physics,