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 <[email protected]> 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 <[email protected]> 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 >>
