Dear Uma Your modeling of a Cysteine sulfenic group (SOH) is reasonable given the observed difference density but do keep in mind that sulfenic groups are very susceptible to further oxidation to sulfinic and sulfonic acids. Stabilization of sulfenic and sulfinic groups in enzyme active sites is possible as shown crystallographically by Becker et al Nat Struct Biol 5:267-271 (1998). Also make sure that you flip the Histidine in the active site that faces the SOH group to account for a possible hydrogen bond.
Best regards Savvas On 04 May 2012, at 20:24, Uma Ratu <rosiso2...@gmail.com> wrote: > Dear All: > > Thank you very much for your advices and comments. > > Following your instructions, I am able to change the CYS to CSX. > > Both "Get Monomer" and "Replace Residue" work well. > > I have the refined conformation CSX (by "real space refinment" ) attached > (named as M-CSX-1). > > The Fo-Fc map is shown with sigma @2.0. > > Is this conformation reasonable? Why there are two bond conformation there? > > Thank you for comments. > > Uma > > On Fri, May 4, 2012 at 12:10 PM, Hugo Correia <h.corr...@campus.fct.unl.pt> > wrote: > Dear Uma, > > You can do this using coot. Go to Extensions > Modelling > Replace Residue... > and enter the three letter code. > > Cheers > > Hugo Correia > > > 2012/5/4 Uma Ratu <rosiso2...@gmail.com> > 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 > > > <M-CSX-1.tif>
