Re: [ccp4bb]: Waters.......??

["Aleks Roszak" <aleks@chem.gla.ac.uk>]

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Raji,

The strongest and shortest hydrogen bonds observed in small molecules are as
short as 2.4A but I would expect typical H-bonds in proteins to be rather
longer than that. Look at some very high resolution protein structures and you
will see H-bonds usually in the range of 2.6-3.1A. And they typically do not
show connecting density between the interacting atoms, if that what you meant
to say. Therefore, I don't think your densities at the distance of 2A represent
water molecules. I suspect you may rather have muliple conformations of some
sidechains. I find those at such resolution for Arg, Glu and Asp residues
frequently and they can be refined easily in Refmac5. I hope that will be of
help to you.

Cheers,

Aleks

On Oct 29, raji wrote:
> Subject: [ccp4bb]: Waters.......??
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>
> Hello Everyone,
> I am learning to add waters to my structure. My structure is at 2A
resolution.
> I can see Fo-Fc peaks upto 3.5 sigma (also see 2Fo-Fc) in my density in
> regions very close to the sidechains of amino acid like lys, arg, glu, asp.
> There is often a water molecule within H-bonding distance to the observed
> peak.
> I suspect that these peaks are waters. However, the distance between the peak
> and the N-/O-atom is about 2A, lesser than what I expected. What is the min.
> distance for it to be a water ? The density provides a continuous H-bonding
> chemistry and so I think it may be a water.
> How does one deal with these peaks ???
> Pl. share your suggestions/comments.
> Thank you very much.
> Raji
>
> Rajeswari Edayathumangalam
> Dept. of Biochemistry & Molecular Biology
> Colorado State University
> Fort Collins, CO 80523 USA
>
>-- End of excerpt from raji



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