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metal binding site for a nuclease

Luca Jovine ljovine at nki.nl
Wed Jun 2 02:07:51 EST 1999

> 	I'm looking for a software to predict the potential metal binding 
> sites (especially, Mg++) for a nuclease. (Although I doubt that when DNA 
> substrate binds protein, location of Mg++ will be somewhat different). 
> Any suggestion is welcome and appreciated.

Hello, you might want to have a look at this paper:

Structure 1998 Oct 15;6(10):1303-14

Exploration of metal ion binding sites in RNA folds by Brownian-dynamics

Hermann T, Westhof E

Institut de Biologie Moleculaire et Cellulaire du CNRS UPR 9002, 15 rue
Rene Descartes, F-67084, Strasbourg, France.

BACKGROUND: Metal ions participate in the three-dimensional folding of RNA
and provide active centers in catalytic RNA molecules. The positions of
metal ions are known for a few RNA structures determined by X-ray
crystallography. In addition to the crystallographically identified sites,
solution studies point to many more metal ion binding sites around
structured RNAs. Metal ions are also present in RNA structures determined
by nuclear magnetic resonance (NMR) spectroscopy, but the positions of the
ions are usually not revealed. RESULTS: A novel method for predicting
metal ion binding sites in RNA folds has been successfully applied to a
number of different RNA structures. The method is based on
Brownian-dynamics simulations of cations diffusing under the influence of
random Brownian motion within the electrostatic field generated by the
static three-dimensional fold of an RNA molecule. In test runs, the
crystallographic positions of Mg2+ ions were reproduced with deviations
between 0.3 and 2.7 A for several RNA molecules for which X-ray structures
are available. In addition to the crystallographically identified metal
ions, more binding sites for cations were revealed: for example, tRNAs
were shown to bind more than ten Mg2+ ions in solution. Predictions for
metal ion binding sites in four NMR structures of RNA molecules are
discussed. CONCLUSIONS: The successful reproduction of experimentally
observed metal ion binding sites demonstrates the efficiency of the
prediction method. A promising application of the method is the prediction
of cation-binding sites in RNA solution structures, determined by NMR.

As you can see, this was tried on RNA, but I don't see any good reason why
it should also not work for a protein...
Good luck!


Luca Jovine

Protein Crystallography Group       Voice: +31.(0)20.512-1959/1964/1969
The Netherlands Cancer Institute    FAX: +31.(0)20.512-1954
Molecular Carcinogenesis Division   E-mail: ljovine at nki.nl OR luca at nki.nl
Plesmanlaan 121                     
1066 CX Amsterdam, The Netherlands


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