On 1/12/12 9:42 AM, Ed Pozharski wrote:
On Thu, 2012-01-12 at 09:52 +0000, Patel, Joe wrote:
Do you have ultra-high resolution? Something I did not…. Are there
many examples in the pdb of proteins with Li+ refined?
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI
39 in total. Some are fairly low resolution (2.8A), and only five are
higher than 1.2A. I'd think that placing lithium ion should be based on
some extra-crystallographic evidence, plus maybe some structural
considerations such as correctly placed coordinating ligands.
Since I'm responsible for eight of those structures, I'll just say that
I thought fairly hard before building a lithium into that peak, knowing
that I couldn't really distinguish it from water or sodium. I was
working with a 1.7 A map, and I put the lithium there based on three
criteria:
- the crystals grew in something like 2 M lithium sulfate, whereas the
only source of sodium would have been from the buffer or the protein
solution
- there were two negatively charged residues coordinating the peak in
question, suggesting it was a cation
- the bond distances were consistent with lithium coordination, for what
that's worth at this resolution
That was the first structure (1TW7), and all of the others were treated
the same since it was the same crystals soaked with different compounds
in the same conditions.
- Matt
--
Matthew Franklin, Ph. D.
Senior Research Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(646) 275-7165
