Hello, what immediately comes into mind is phosphohistidine, especially since the density looks rather large, but the geometry seems a bit off for that but I cannot judge only from one angle. You could of course try to fit it in and see how it looks.
Cheers, Arne On Mon, Jul 20, 2020 at 6:17 PM samer halabi < [email protected]> wrote: > Hello all, > I have few blobs in an MHC II structure I am working on, especially > opposite to Histidine as in the accompanying screenshot, that I am confused > about. > > In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and > Glycerol. > Whatever ligand I am fitting in I am getting a clash (overlap -1.029), > which makes me think whether there is a covalent bond forming between > Histidine and other molecule. Perhaps by oxidation. > > I would greatly appreciate if you can advice me about it, whether there is > some kind of ligand I can try to fit and if this is something that occurs > in some structures. > Thank you. > Best regards, > Samer > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- -- Arne Raasakka PhD Biochemistry Department of Biomedicine, University of Bergen Norway ######################################################################## 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/
