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Re: [ccp4bb]: C-H...O type interaction
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BS"D
This type of H-bond certainly exists in the world; Thomas Steiner
has discussed this in quite a number of papers. See for example
Steiner, T. (1997) Chem. Commun.
Steiner, T. (2002), Biophys Chem. Mar 28;95(3) p195-201
(2001), Acta Cryst C, 57, p 775-6
Not all the above references are C-H...O bonds, but they give you an
idea of the various types of "non-classical" hydrogen bonds.
He has many other papers as well on this topic. In fact, he and
Gautam Desiraju wrote a book on the weak hydrogen bond put out by the
IUCr, published in 1999 (ISBN 0 19 850252).
> 2) How does the negative density of a Asp carboxyl group get affected
> by an aromatic residue?
The edges of the aromatic residue side chain are delta+, so it's like
bringing a weak positive charge close to a delocalized negative charge.
I imagine slightly more negative charge will build up on the OD that
forms the interaction.
> 3) Can the pKa of the carboxyl group be affected in the wild type or
> in the mutants?
Presumably, yes. Of course the answer to that question depends on
how exposed the Aspartate residue is, and whether it is relevant to
talk about pKa if it can't see solvent. But that is a different
argument.
> The resolution is 2.0 A and the distance is 3.2 A.
A bit far for such a weak interaction. See Steiner et al, Chem.
Commun. 1998, where they propose that weak C-H---O bonds could be
formed at longer distances (2.92A). Your example is even longer. Yet
the mutation effects are interesting......????
I hope these references are informative....
HMG
------------------------------------------------------------------------
-------------------------
Harry M. Greenblatt
Research Associate
Dept of Structural Biology harry.greenblatt@weizmann.ac.il
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel