Darren,
Identifying a cation using "only" the electron density even
at relatively high resolution is not a sure thing. However,
you can try the following:
1. Place each of the different choices at the site and refine,
positions and an isotropic B-factor for the cation. See
which falls in a reasonable range for the B-factor
when compared with the coordinating groups.
2. Look at the coordination geometry and charge distrbibution of
the coordinating residues. Calcium ions are often 7 coordinate
with three carboxyl ligands. Sodium ions are more often six
coordinate as are manganese and magnesium.
3. Look what cations you used in the protein purification and
crystallisation steps to see if what you find makes some sense.
4. Don't make certain claims and hope you get an understanding
referee.
5. Try chemical methods of identification such as AAS or Mass Spec
if you have enough material.
Cheers,
Mitchell Guss
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Dr Mitchell Guss
Department of Biochemistry - G08
University of Sydney
NSW 2006
Australia
Telephone: +61 2 9351 4302
Facsimile: +61 2 9351 4726
E-mail: M.Guss at biochem.usyd.edu.au
Internet: http://www.biochem.usyd.edu.au/
