Mg2+ is (almost) aways octahedrally coordinated, usually by oxygen atoms, with distances of ~2A. Phil
On 20 Dec 2010, at 21:16, jlliu liu 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 > > > <test.png.odp>
