A coordination distance table (metals, Cl) is in Marjorie Harding's papers
1. Harding M (2006) Small revisions to predicted distances around metal
sites in proteins. Acta Crystallogr. D62(6), 678-682.
2. Harding M (2004) The architecture of metal coordination groups in
proteins. Acta Crystallogr. D60(5), 849-859.
and my (book)appendix.
For anions see various Weiss, Dauter, & Cie soaking papers
A figure of a typical Cl which often mask/pass as 'heavy' waters (improbably
low B) around 3.2 A coord dist here:
http://www.ruppweb.org/garland/gallery/Ch12/pages/Biomolecular_Crystallograp
hy_Fig_12-42.htm
BR
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Jacob
Keller
Sent: Tuesday, June 14, 2011 4:27 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] non-waters among structured solvent atoms
How about halides? Anyone know of criteria for their binding sites?
JPK
ps Funny how my recent post was about almost exactly the same
thing--serendipity, I guess?
On Tue, Jun 14, 2011 at 5:07 PM, Nat Echols <[log in to unmask]>
wrote:
> On Tue, Jun 14, 2011 at 2:51 PM, wtempel <[log in to unmask]> wrote:
>>
>> Dear colleagues,
>> following a discussion in our lab, I have volunteered to dig out
>> articles from the literature about erroneous assignments of non-water
>> entities such as metal ions, halides in protein models. For example I
>> have the faint recollection that data mining of the PDB for suspect
>> "water" assemblies matching the geometry of coordinated cations has
>> previously been described. But none of my google searches has turned
>> up the references I was looking for. Could someone point me in the
>> right direction, please?
>
> Do you mean metals incorrectly annotated as waters, or vice-versa? The
> latter case is discussed here:
> http://www.ncbi.nlm.nih.gov/pubmed/18614239
> -Nat
--
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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: [log in to unmask]
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