[phenixbb] Magnesium or calcium

Ed. Pozharski epozh001 at umaryland.edu
Sat Mar 2 10:08:05 PST 2013

Magnesium has fewer electrons.  So if you place it and it's actually calcium you should see extra density and the B-factor will be unreasonably lower than surrounding atoms.

Distances are less reliable at intermediate resolutions as they are largely controlled by restraints. Maybe.

Assuming that you have 100% occupancy.

-------- Original message --------
From: Daniel Slade <DSlade at scripps.edu> 
To: phenixbb at phenix-online.org 
Subject: [phenixbb] Magnesium or calcium 
I have several structures that has multiple known calcium binding sites, and I found a new site that seems to accept calcium or magnesium.  I say this because if a magnesium is put in the structure, the bond lengths are ~ 2.1.  But if you put a calcium in it, they go to ~2.6.  All of these  refinements were done without ReadySet, which I recently used with metal restraints and it seemed to change the bond length of calcium to ~2.4.  I'm a bit confused as to what to do here as either metal seems to be right.  Worth noting, this is a very strong metal binding site that can't be removed with 10 mM EDTA.

Any help here on how to figure this out which ion this is would be great.

Thanks in advance


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