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
zinc-metalloenzyme sites.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
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.
JPK
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale
Tronrud
Sent: Monday, June 22, 2015 11:17 AM
To: CCP4BB@JISCMAIL.AC.UK
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,
IISc
