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This may be true for many structures but in general I am not a friend of massive changes made to already deposited structures - it more likely produces more errors than better structures. 2.4 Angstrom hydorgen bonds for water are probably not entirely impossible and on the other hand some close distances can result just from bad structure refinement or relatively low resolution of the data (there are even examples of non-refined structures in the PDB) and in those cases making this kind of changes would be a complete disaster... Jan On Wed, Feb 17, 2010 at 6:32 PM, Jacob Keller <[log in to unmask] > wrote: > Dear Crystallographers, > > Having looked into the structure I mentioned using the "atomic contacts" > feature of the whatif server, it seems that both the 1.0 Ang structure I > previously mentioned, as well as another, lower-resolution related > structure, have a significant number of "waters" which are < 2.6 Ang from > polar atoms, with many in the 2.4 Ang regime (suggesting Na+). Both > structures were solved in the presence of Na+. It seems impossible for water > to bind at this distance, so would it not be best for the PDB to add some > distance cutoff to its validation process? Should the PDB retrospectively > review all structures for "waters" binding at these distances, > cross-checking, of course, for sodium in the protein stock and/or > crystallization condition? I am not sure about the profundity of the > consequences of such a natrification, but truth is truth, however mundane, > no? > > Regards, > > Jacob Keller > > ps I am curious about how many structures would be affected by this. > > > > ******************************************* > 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: [log in to unmask] > ******************************************* > > ----- Original Message ----- From: "George M. Sheldrick" < > [log in to unmask]> > > To: <[log in to unmask]> > Sent: Tuesday, February 16, 2010 5:00 AM > Subject: Re: [ccp4bb] Distinguishing Between Na+ and H2O > > > > 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: [log in to unmask] >>> > ******************************************* >>> >>> >> -- 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