Dear All; Thank you very much for your comments and advices.
My protein is homo-tetramer. Based on difference density, only one cysteine (among the four catalytic cysteins) has observed two positive density along SG-group. This one could be modeled into OCS, while the rest will be modeled as non-oxidized. I very much appreciate for all your inputs regards Uma On Fri, May 4, 2012 at 6:09 PM, Savvas Savvides <savvas.savvi...@ugent.be>wrote: > 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> > >
