Hard-to-believe changes in R-free
puius at aecom.yu.edu
Wed Jul 29 08:47:00 EST 1998
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).
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
"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"
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