Dear jlliu liu,
Also note that Mg2+ is significantly smaller than water. It fits in places
where water cannot go. This doesn't look like a magnesium site on first glance.
If you can (privately) give the PDBid of the previous publication, I can have a
look in 3D.
Cheers,
Robbie
> Date: Mon, 20 Dec 2010 21:31:58 +0000
> From: p...@mrc-lmb.cam.ac.uk
> Subject: Re: [ccp4bb] Mg2+ or water
> To: CCP4BB@JISCMAIL.AC.UK
>
> 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>