Hi Andrew, Here are those references:
for CH...O hydrogen bonds I'd recommend our review: "Carbon-Oxygen Hydrogen Bonding in Biological Structure and Function" (2012) http://www.jbc.org/content/287/50/41576.full for chalcogen bonds, I don't know of a great recent review, but this recent article (2016) has a whole bunch of references (listed under 19 and 20) on it: https://www.ncbi.nlm.nih.gov/pubmed/27992115 Scott On Tue, Dec 20, 2016 at 8:45 PM, Andrew Marshall < andrew.c.marsh...@adelaide.edu.au> wrote: > Hi Scott, > > That would be great if you have some references handy? > Thanks very much, > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > > On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz <horow...@umich.edu> > wrote: > >> 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 >> > > -- 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
