[ccp4bb]: Buried protonated acids

[Stephen Graham <stepheng@mail.usyd.edu.au>]

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Hey CCP4ers,

Apologies for the not-directly-CCP4-related question.  I am working on a
structure at 2.4 A resolution where I see what I believe to be a
protonated acid buried in the core of the protein.  Specifically, I have
an Asp residue whose OD2 is 2.93 A from an amide nitrogen (forming a
nice H-bond) and whose OD1 is 2.56 A from a carbonyl oxygen.  All
residues mentioned are very well ordered (low Bs) and are well defined
in electron density.  The pH of the crystallisation conditions is 8.5.

>From my understanding such protonated acids are not especially unusual.
I have, however, been unable to find any literature references for such
buried protonated acids.  MEDLINE and the Acta Cryst. archives have not
proved allies in my search.  Can anyone point me towards examples of
such buried protonated acids in the literature?

Thanks in advance

Stephen

-- 
Stephen Graham
PhD candidate and nasty sysadmin
Crystallography Group
School of Molecular and Microbial Biosciences
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University of Sydney
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Australia
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