Hi Andrew, Based on the atoms and distances you are mentioning, these don't sound like steric clashes, but like a chalcogen bond between the S and O atoms, and CH...O hydrogen bonds between the O and CH3. These are common and well-accepted interactions, but unfortunately aren't usually treated as such by refinement programs. Let me know if you want references for these interaction types.
Scott On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall < andrew.c.marsh...@adelaide.edu.au> wrote: > Hi all, > > Thank you for your suggestions. I tried the pdb file edit (making the > offending atoms of both the ligand and the protein 'B' altconf), but it > didn't seem to make any difference to their positions after a single round > of refinement..? > The atoms in the active site concern two acetyl groups - one from the > substrate, acetyl-CoA, and the other from an acetylated cysteine in the > protein - that I believe are poised ready for a condensation reaction. The > closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3 > (3.1A), but going off the density, I think these should be closer (more > like 2.8 or 2.7A). It may be that I've trapped another reaction > intermediate (which would be cool), but I don't think that fits the density > quite as well. Any thoughts/ideas? > > Thanks, > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > > On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz <horow...@umich.edu> > wrote: > >> Hi Andrew, >> >> I'm curious- what are the atoms that are clashing? I worked on this sort >> of thing back in my Ph.D., and so I might have some useful tidbits if, for >> example, the S is clashing with a carbon of some sort. >> >> Thanks, >> Scott >> >> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall < >> andrew.c.marsh...@adelaide.edu.au> wrote: >> >>> Hi all, >>> >>> I have a structure of a condensing enzyme with substrate bound. The >>> active site is very tight, requiring some of the substrate atoms to clash >>> with a catalytic cysteine. This means that although the substrate fits the >>> density nicely upon manual real-space refinement, phenix recognises the >>> clash, resulting in the displacement of substrate atoms so that they are >>> outside the density. I can mostly fix this by using distance restraints, >>> but I'd rather allow it to refine in a less biased manner, but ignore the >>> clash. Is this a acceptable way forward? If so, is there a parameter I can >>> edit to tell phenix to ignore clashes between these specific atoms? >>> >>> Thanks, >>> >>> Andrew Marshall >>> PhD Candidate >>> Laboratory of Protein Crystallography >>> Dept. of Molecular and Cellular Biology >>> School of Biological Sciences >>> The University of Adelaide >>> >>> >> >> >> -- >> Scott Horowitz, Ph.D. >> Postdoctoral Fellow >> >> University of Michigan >> Department of Molecular, Cellular, and Developmental Biology >> Bardwell lab >> 830 N. University Ave, Room 4007 >> Ann Arbor, MI 48109 >> phone: 734-647-6683 >> fax: 734-615-4226 >> > > -- Scott Horowitz, Ph.D. Postdoctoral Fellow University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
