Looks to me like a metal binding site with those histidines, perhaps--any chance of that? That might also explain the weird geometry issues.
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.
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,