Almost certainly a metal ion, possibly Ni(2+) if a Ni-NTA column was used for purification. Ni-N bond lengths are typically around 2.0 A. Additional density is probably coordinated water molecules, which should have similar Ni-O bond distances around 1.9 A. It is fairly common to find adventitious metal ions (zinc, copper, nickel) bound to His residues.
_______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor, Emeritus Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 email: rrowl...@colgate.edu On Mon, Jul 20, 2020 at 12:17 PM samer halabi < 000030c2162795b2-dmarc-requ...@jiscmail.ac.uk> 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 > ######################################################################## 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/
