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I'm not sure about Cd++ coordination, but Mg++ is smaller than Ca++ and
so prefers octahedral geometry; I would look for shorter coordination
distances for Mg++ than for Cd++. Cd++ has been used to rescue ribozyme
activity (eg, hammerhead and RNase P) from phosphorothioate
substitutions so, indeed, ligand hardness is a consideration. In any
event, I think it would be difficult to use these criteria to assign two
metal ions to a single site, unless you have, say, a cysteine ligand in
dual conformations.
best wishes
kevin
[EMAIL PROTECTED] wrote:
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.
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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:
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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
