After having seen many Na+ ions very likely correctly built and refined and many potential Na+ sites with a very clear indication that the bond valence sum is already on the border of being water and being an ion I would say that Na+ binding in proteins happens quite often and probably escapes "unobserved" by which I mean that we do not notice because it simply is not so clear in so many cases.
If one assumes the very likely alternative of Na+/water alternative occupancy it muddles the distances sufficiently for us not to be able to say a clear YES or NO. I sometimes wish we had a "sodium detector" for such structures .. Jan On Tue, Feb 16, 2010 at 12:00 PM, George M. Sheldrick < gshe...@shelx.uni-ac.gwdg.de> wrote: > A few years ago we thought that the bond valence method might provide > an answer to this problem and wrote a paper on the subject (Acta Cryst. > 2003 D59 32-37). Subsequent experience has convinced me that although > this method works well for identifying ions such as Mg2+ and Ca2+ with > good resolution data, it is not reliable in other cases such as Na+, > and for this reason I never distributed the version of SHELXPRO that > includes the bond valence test (I would not like my programs to get a > bad name). > > In fact we currently have a protein crystallized from a high NaCl > concentration that is giving us a lot of problems distinguishing > between Na+ and water molecules. Since we were able to find some > chlorides in the anomalous map we know that cations must also be > present, but the anomalous data are too weak to help much with Na+ > because of its lower f". > > There are however some tentative indicators for Na+. The bond valence > sum (the sum of the 'bond orders' to the surrounding atoms estimated > from the distances) tends to be higher than for Cl- or H2O. > Tetrahedral coordination is more likely to be water or Cl-, Na+ > prefers 5 or 6 neighbors. And of course two cations (or two anions) > that are close to each other should not have an occupancy sum greater > than unity. > > George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > On Tue, 16 Feb 2010, Eleanor Dodson wrote: > > > Yes - we are puzzling over the same phenomena. > > > > Look at this web site set up by Marjorie Harding > > > > http://tanna.bch.ed.ac.uk/ > > > > It lists the likely coordination patterns. > > > > We certainly have ideal Na bonding in our structure - but unfortunately > we > > wanted to find Ca which has a very similar pattern!! > > > > Grrr > > > > Eleanor > > > > > > > > > > > > > > Jacob Keller wrote: > > > Dear Crystallographers, > > > > > > I am looking at a 1.0 Angstrom structure which contains many waters, > but I > > > am wondering whether some of them might really be sodium ions. Is there > any > > > straightforward way to distinguish between these two, and if so, what > is the > > > software which implements this? Although the electron density > difference > > > between sodium and water should be very small, perhaps the binding > geometry > > > would provide a clearer distinction? Has anybody encountered this > question > > > before? > > > > > > Regards, > > > > > > Jacob Keller > > > > > > ******************************************* > > > Jacob Pearson Keller > > > Northwestern University > > > Medical Scientist Training Program > > > Dallos Laboratory > > > F. Searle 1-240 > > > 2240 Campus Drive > > > Evanston IL 60208 > > > lab: 847.491.2438 > > > cel: 773.608.9185 > > > email: j-kell...@northwestern.edu > > > ******************************************* > > > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
