I agree. It is very unlikely to be Magnesium ion; may be an ordered water! I'd recommend to have a look at the following paper which discusses the different properties of Mg2+, Mn2+, and Zn2+.
Charles W. Bock, Amy Kaufman Katz, George D. Markham, and Jenny P. Glusker. Manganese as a replacement for Magnesium and Zinc: Functional comparison of the divalent ions. (J. Am. Chem. Soc. 1999, 121, 7360-7372) Ibrahim On 12/20/10 6:14 PM, "Dima Klenchin" <klenc...@facstaff.wisc.edu> wrote: >> Sorry, the attachment is in here. > > Doesn't look like Mg2+ at all. Distances are too long, Mg is never > coordinated by amides and if it were Mg you would have seen waters around it. > > Looks like tightly bound water to me. > > - Dima > > > >> On Mon, Dec 20, 2010 at 4:16 PM, jlliu liu >> <<mailto:jlliu20022...@gmail.com>jlliu20022...@gmail.com> wrote: >> Hi All, >> >> I am refining a structure and encountered a problem of modeling a >> difference density as water or Mg2+, and would like to hear opinions from >> the community. It has the following coordinations (attached): the >> water/Mg2+ forms salt bridge/H-bonding interaction with a carboxylate >> group from the ligand, it also forms salt bridge/H-bonding interaction >> with a Glu residue from the protein, it is also within hydrogen bonding >> distance to the main chain N of another protein residue. In provious >> publication, it was modelled as a Mg2+ and the author reasoned the dual >> salt-bridge stabilizes the liganding binding, also the Mg2+ is present in >> the protein solution for crystallization. For my case, I have no Mg2+ >> present in the protein buffer, also modelling it with water refines >> perfectly with no indication of positive difference density even at 2.0 >> sigma cut off. Should I modelled this density as water or as Mg2+. Your >> opinions are appreciated. >> >> JL >> >> >> >> Content-type: image/png; name=367-mgtest.png >> Content-disposition: attachment; filename=367-mgtest.png >> X-Attachment-Id: f_ghy0k5e31 >> >
