Distinguish NH4 from Na?

From: Jacob Keller
Date: 16 November 2011 18:20


Dear Crystallographers,

I have crystals containing 666mM NH4 and 540mM Na, and there appears
to be a "water" which is only about 2.2 Ang from some polar atoms. It
is currently reasonably happy as a Na, but is there any reasonable way
to decide which cation is there?

JPK



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From: Steiner, Roberto


Bond valence sum

Muller et al. Acta Cryst. (2003). D59, 32-37 if the resolution is good (better than 1.8 A)


R

Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London


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From: Dr. STEPHEN SIN-YIN, CHUI


Dear JPK,

I think the coordination geometry of Na is a key, normally it adopts octahedral
geometry with Na---O distances of 2.1-2.2 ang, whereas water molecule is
h-bonded with H-acceptor or H-donor with the distances between 2.6-3.3 ang.
I am not sure it is correct, as i used to be small-molecule X-ray worker.


stephen

--
Dr. Stephen Sin-Yin Chui (徐先賢)


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From: Benini Stefano (P)


Dear Jacob,

You may find useful this web site by Marjorie Harding about metal coordination sites in proteins
http://tanna.bch.ed.ac.uk/

best regards


Stefano Benini, Ph.D.
Assistant Professor

http://pro.unibz.it/staff2/sbenini/

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From: Dirk Kostrewa

Dear Jacob,

for NH4+, you would expect a (partial) tetrahedral coordination with typical H-bond distances of ~2.9 A. For Na+, you would expect a (partial) octahedral coordination with Metal-to-ligand distances of ~2.4 A (see Harding, Acta Cryst., D62, 678-682 (2006); Harding, Acta Cryst., D58, 872-874 (2002); Glusker, Advances in Protein Chemistry, 42, 1-76 (1991)).
But depending on your data resolution and quality, and on the completeness of the coordination sphere, it might be difficult to distinguish between them.

Best regards,

Dirk.
WWW:    www.genzentrum.lmu.de
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