Search for Metal Cordination sites in Proteins.
It takes you to a site set up by Marjorie Harding which gives a table of
known metal coordination extracted from the PDB including Na.
Of course there may be errors in the PDB entries but it is very helpful I
find
Eleanorr
On Tue, 2 Aug 2011 13:31:09 -0500, Jacob Keller
<[log in to unmask]> wrote:
> I asked the CCP4 experts this question a while back--maybe try
> searching the archive? There were some very helpful comments.
>
> Jacob
>
> On Tue, Aug 2, 2011 at 1:24 PM, Young-Jin Cho <[log in to unmask]>
wrote:
>> Dear CCP4 experts,
>>
>> I would like to ask if there is a clear way to distinguish Na+ and HOH
>> molecules in the electron density map. The table I have suggests Na
>> to O distance lies between 2.35 and 2.45 that is very hard to discern
>> the difference of these two candidates. Na+ may have several
>> coordination though (5, 6).
>>
>> This started from if where the divalent metal locates can be
>> substituted by water or sodium. I would appreciate any valuable
>> suggestions.
>>
>> Best,
>> Young-Jin
>>
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