It's probably much less likely than metal coordination and it's hard to judge from only one angle, but phospho-histidine might be something else to consider.
http://www.jbc.org/content/276/5/3247.full Shane On Mon, Jun 22, 2015 at 2:15 PM, Roger Rowlett <rrowl...@colgate.edu> wrote: > 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 >>> >>>
