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Dear Sara, If I recall correctly, Cd perfers six ligands for coordination in an bipyramidal geometry with metal-ligand distances between 2.15 and 2.3 A, and likes nitrogen among its ligands. Magnesium prefers more ligands (I thought 7, like Ca), larger distances and only oxygen. These are parameters you can check independent from the electron density for the metal ion, to then decide on metal ion occupancy. It is interesting that Mg can substitute from Cd. Reviews from Jenny Glusker: Structural aspects of metal liganding to functional groups in proteins. Adv Protein Chem. 1991;42:1-76. and Marjory Harding in The architecture of metal coordination groups in proteins, Acta Crystallogr D Biol Crystallogr. 2004 May;60(Pt 5):849-59. could help you out further. Julie. >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > >At most wavelengths, you should see a peak for Cd in an anomalous >difference map, while Mg has very little signal. This test would >demonstrate the presence of Cd; I think that in the absense of other >evidence I would model the site simply as partially occupied Cd++. > >kmj > >Sara Elizabeth Cnudde wrote: >> *** For details on how to be removed from this list visit the *** >> *** CCP4 home page http://www.ccp4.ac.uk *** >> >> >> >> Hi, >> I have a structure that I'm refining that I believe has a metal site in >> which 50% of the time it's occupied by cadmium and the other 50% of the >> time this same site is occupied by magnesium. How can I really tell if >> this is true? If I put Mg in with 100% occupancy I see a lot of >> density in my fo-fc map contoured at 3 sigma indicating that this is >> incorrect. However, if I put in Cd with 50% occupancy I no longer see >> this density but if the Cd has 100% occupancy I see density in the fo-fc >> map contoured at -3 sigma. >> Thanks, >> Sara >> > >
