Uma,

It is possible you have either S-hydroxycysteine (CSO) or S-oxycysteine 
(CSX). The only difference, crystallographically, is that the CSO S-O 
bond is about 1.78A and the CSX S-O bond is about 1.50A. You may not be 
able to differentiate this difference in your electron density maps. A 
SH - HOH contact should be considerably longer than 1.8 A between heavy 
atoms, certainly more like 3.0A+/-.

You can easily substitute either CSO or CSX for CYS in Coot by deleting 
the CYS residue and then using File...Get Monomer and typing in either 
CSO or CSX. (Both CSO and CSX are in the Refmac monomer library.) Rotate 
things into place and do a real-space refinement to get things closer, 
and you should be all set for the next Refmac round of refinement. There 
may be a more elegant way of doing this in Coot, but this will work. If 
you want to crudely see if your refinement with CSO or CSX is 
reasonable, create an omit map by setting the occupancy of the oxygen 
atom to zero. You should see some nicely centered positive difference 
density on the oxygen atom.

I encountered a surprise CSO residue when solving the structure of 3UAO. 
The protein was stored by a collaborator in a non-reducing medium, 
resulting in the oxidation of the active site Cys residue. (The only Cys 
in the protein that oxidized, natch.) The electron density near Cys was 
too close to be a water molecule, but CSO modeled nicely. The 
electron-density-suggested bond distance was about 1.70 A, so CSO looked 
better than CSX, but I bet both would model OK.

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: [log in to unmask]

On 5/4/2012 11:00 AM, Uma Ratu wrote:
> Dear All:
> My protein has a key cysteine residue involved in catalytic activity.
> The template structure used for the modeling has the same key 
> cysteine. In the template structure, this key cysteine residue is 
> assigned as CSX based on the observation from its electronic density.
> I compared the electron density from the template as well as my model. 
> I can't tell if the cysteine in my model is oxidized or not. The ones 
> from the template also looks different from each other, although both 
> assigned as CSX.
> I have the snapshots of these cysteines attached. The ones from my 
> model named as "M-", and the ones from the template named as "T-".
> Plus, how to change the residue label from Cys to CSX if the cystein 
> is oxidized? In coot, I could not find such function.
> Thank you very much for your advice
> Uma