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Could this be a covalent interaction?

 

Difficult to judge without seeing anything

 

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Andrew Marshall
Sent: Tuesday, 20 December 2016 2:48 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Atom clashes in active site?

 

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 <[log in to unmask]> 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 <[log in to unmask]> 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
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