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[ccp4bb]: summary: monovalent cations

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Thanks for very many helpful comments to get me started.  I have not yet
had time to digest and compare the suggestions, but in the interest of
posting information quickly after the question, I try to summarize the
replies below.  It goes without saying that resolution of data is
critical in differentiating possibilites (my data are to 1.5 A).

1. Different number of electrons for different metals will obviously
give different local electron densities (possibly can also make use of
differences in anomalous signals for metal sites).

2. Look at USF program XPAND ( http://xray.bmc.uu.se/usf/)-- "water
scrutinizer" option -- which checks for possibilities other than HOH --
I think using the approach of M Nayal & E Di Cera, JMB 256, 228-234
(1996) -- this paper describes the calculation of valence for
metal-to-ligand interactions [the valence calculation quantitates
distances for all metal-to-ligand interactions for a putative metal
site, and relates these to expected distances and coordination numbers
for potential ions; e.g., (K+) should have longer metal-to-ligand bonds,
on average, than (Na+)-to-ligand].  The Di Cera valence analysis has
been developed by the author into the WASP program (WAter Screening
Program) -- contact enrico@caesar.wustl.edu

3. Valence bond calculation methods are being implemented by George
Sheldrick (I'm not sure if part of ShelX) -- suggested to contact Dr.
Sheldrick directly to inquire.

4. Some general references were also suggested:

SJ Cooper .. WN Hunter (1996) Structure 4: 1303-1315 The crystal
structure of a class II fructose-1,6-bisphosphate aldolase shows a novel
binuclear metal-binding site embedded in a familiar fold [includes table
comparing Metal-N, Metal-O distances [Metal = K(+), Zn(++)] from CCDC]

CA Bonagura .. TL Poulos (1999) Biochemistry 38: 5538-5545 The effects
of an engineered cation site on the structure, activity, and
EPR properties of cytochrome c peroxidase

S Rhee .. DR Davies (1996) Biochemistry 35: 4211-4221. Exchange of K+ or
Cs+ for Na+ induces long-range changes in the thre-dimensional structure
of the tryptophan synthase a2b2 complex [tabulates Na(+)-O, K(+)-O and
Cs(+)-O distances in tryp synthase]

5. Bond-valence calculations can be done using a different equation than
that used in the above Di Cera paper [see instead -- (1) Brese, N. E. &
O'Keeffe, M. 1991. Acta Cryst. B47: 192-197. Bond-Valence Parameters for
Solids. and (2) Carugo, O., Djinovic, K. & Rizzi, M. 1993. Comparison of
the Co-oridnative Behaviour of Calcium (II) and Magnesium (II) from
Crystallographic Data. J. Chem. Soc. Dalton Trans. 2127-2135.]  An
example using this alternate equation was kindly provided:



vij-bond valence for bond between i and j
dij-bond length between i and j
Rij-bond-valence parameter
[K+ 2.13 for O, 1.99 for F, 2.52 for Cl
Na+ 1.80 for O, 1.677 for F, 2.15 for Cl]
b-"universal" constant b=0.37


V-valence of the metal centre

dij (O-Me)      vij (Na+)
2.78            0.07
2.47            0.16
2.30            0.26
2.58            0.12
2.30            0.26
2.25            0.30

V=1.17 (in my case I was sure that it cannot
be Ca2+ - I checked anomalous signal)

**Thanks again for helpful replies!


David R. Buckler

679 Hoes Lane
Piscataway, NJ  08854
phone: (732) 235-5164
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e-mail: buckler@cabm.rutgers.edu