I'm voting with Roger this time. If I were you I would model a nickel in there (unless you have a better candidate) if it is right, the distances to the His should be like seen in a SOD active site. Then you can model the bonds and waters. You may need partial occupancy on the metal.
Reminds me of the time I found a 6th water in MnSOD as I was making the token electron denisty figure of the active site. Found myself doing more refinement and a much better paper. On Thu, Feb 24, 2011 at 8:15 AM, Roger Rowlett <rrowl...@colgate.edu> wrote: > This looks suspiciously like a metal ion with 3 or more resolved water > ligands. It's hard to tell from the images provided, but it looks like the > metal could be close to octahedral, with 2 His and 3 water ligands > well-defined. The estimated metal-nitrogen bond distances might help narrow > down the metal ion. For example, tetrahedral Zn(II) has a Zn-N bond distance > of around 2.0 A. I suppose this could be a Mg(II) ion, since that is in your > crystallization mix, but I think that Mg(II) typically prefers harder > protein ligands, e.g., carboxylates. Zn(II) is a very common contaminant in > solution, however, and should not necessarily be discounted; indeed Zn(II) > and other first row transition metal ions would be expected to have a > reasonable affinity for medium hard/soft ligands such as vicinial His > residues. > > Cheers. > > On 2/23/2011 7:34 PM, Alex Singer wrote: > > > cocrystallized in 2.5mM Glycero-3Phosphocholine and cryoprotected by > dipping in > > -- > ------------------------------ > Roger S. Rowlett > Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: rrowl...@colgate.edu >
