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SENT ON BEHALF OF DR MARJORIE HARDING I would not rule out Mg++ ever coordinating with a primary amine, but it is much rarer than the reports in Mespeus suggest. Mg++ with arginine: Mespeus 10 finds 36 examples, but quick inspection of the list shows that almost all have coordination number 4 or less, and Mg-N distances in the region of 2.6-2.8A. These are surely water molecules (isoelectronic with Mg++). The few with coordination number 5,6,7 should be inspected more carefully; Mg-O, Mg-N distances should be ~ 2.1-2.2A, shape close to octahedral (perhaps with one position missing, not identified), and B values of Mg and N similar and reasonable. Coordination number 7 sometimes appears when there is a Mg-O-Mg bridge and the second Mg is listed (wrongly) as a donor group. Mg++ with lysine: Mespeus_10 finds 33 examples. The story is similar to arginine, above. The examples in 1iv4 and 3l8f just might be genuine. If they pass all the above tests, does the refinement look good ? what were the crystallisation conditions (pH etc) ? None of these is done at a resolution better than 1.5A and most are 2-2.5A. Mg++ with asn or gln: same considerations, but also the interpretation may have selected the wrong rotamer, substituing N where it should be O. There is a lot of 'rubbish' like this in the PDB. I have long wondered about devising a validating procedure but not found anyone else interested yet. Marjorie Harding Quoting Ed Pozharski <[log in to unmask]> on Fri, 30 Nov 2012 09:40:26 -0500: > On Tue, 2012-11-27 at 21:46 -0800, William G. Scott wrote: >> Are Mg++ ions ever observed to chelate primary amines? > > MESPEUS reports, for example, 13 structure where magnesium is > coordinated by a lysine. 7 with arginines and a bunch of asn/gln side > chains as well. It does not prove, of course, that primary amines > coordinate magnesium ions, only that in a limited number of cases > crystallographers have interpreted their data this way. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > > -- Malcolm Walkinshaw Chair of Structural Biochemistry Institute of Structural and Molecular Biology School of Biological Sciences University of Edinburgh Mayfield Rd Edinburgh EH9 3JR Phone 0044 131 650 7056 http://ctcb.bio.ed.ac.uk/member_Malcolm.php -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.