Dear Tina, my guess would be minor oxidation of the cysteine. The green positive difference density suggests a bound atom in three different positions; this could however just be the first atom of something bigger like beta-mercaptoethanol, with the rest of that molecule too disordered to see. By eye-balling, the blue electron density does not look much bigger than expected for sulfur, so whatever it is, I would think it's very minor and probably not even worth modelling.
I am also guessing this map is after refinement is almost complete and the overall difference map quite flat, so three sigmas of difference density (if that is what is contoured) may correspond to quite few electrons, i.e. low occupancy of the adduct. Another explanation might be "anomalous behaviour" of the sulfur, similar to residual difference densities often observed near metal ions. A physicist will likely have a better idea about this than me. Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 21 Jun 2024, at 11:02, hsyu11gmail <hsy...@gmail.com> wrote: > > Dear all, > > We recently solved a structure to 2.1 A, and found an additional Fo-Fc > density on the side chain of a cysteine residue. The structure has been > reported previously, and no modification found at this site. The distances > between the cysteine and other residues also does not appear to be long > enough for any modifications. > > Does anyone has an idea about this map? > > Thanks. > > Kind regards, > Tina > <Catch(06-21-17-02-00).jpg> > <Catch0C4D(06-21-17-02-00).jpg> > > > hsyu11gmail > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
