Hard-to-believe changes in R-free

[Yoram Puius]

Many thanks to Drs. Badger, Merritt, and Hyvonnen, who helped me
decide on whether I had a Na+ ion in my structure.  I think I do --
it helped to have someone who worked on a protein which required Na+
look at it.  Basically, the contacts were just too short for water and
the orientation of the ligands did not favor any divalent cation.
The change in free-R when I changed the H2O to Na+ seemed consistent
over a wide variety of conditions, also.

Although I have not yet received the WASP program for screening
waters and deciding if they are cations, I used a formula in the
paper which suggested that an index called v(Na+) for the ion was
~0.9, where the average for water is 0.18 +/- 0.13,  and values
> 1.0 are "unambiguously" sodium.

For anyone who cares, the two references most helpful to me:

Jenny P. Glusker, "Structural Aspects of Metal Liganding to
Functional Groups in Proteins," Adv. Prot. Chem. 42, 1-76 (1991)

Nayal, M. & Di Cera, E.  "Valence Screening of Water in Protein Crystals
Reveals Potential Na+ Binding Sites," J. Mol. Biol. 256, 228-234 (1996).

Thanks all,
		Yoram


-- 
_______________________________________________________________________
Yoram A. Puius                Albert Einstein College of Medicine
6th year M.D.-Ph.D.           Department of Biochemistry
mailto:puius at aecom.yu.edu     1300 Morris Park Avenue, Bronx, NY  10461
        http://www.geocities.com/Athens/Forum/7504
_______________________________________________________________________
"Naturally I have other work here, crystal structure, but often I
wonder which is more useful, silly hobby or vital science."
				- Don DeLillo, "Ratner's Star"