Hi Florian, There are quite a few tools that do this check for you. To name a few: WASP (old but good, build the ion as water), WHAT_CHECK (http://swift.cmbi.ru.nl/servers/html/index.html), Check My Metal and probably quite a few others. All of them use the bond valence sum, but they all have a different implementation so the results may differ. That said, it is usually reasonably easy to tell Na+ and Mg2+ apart. At the risk of stating the obvious: think of what you added in the crystallization, buffer counter ions are easily overlooked.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Florian Sauer > Sent: Thursday, December 01, 2011 19:40 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] How to distinguish between Na+ and Mg2+? > > Dear CCP4BBers, > > I'm refining the structure of a Ca-binding protein with several EF-hands > against 2.2A data. > There is clear density for an ion in several EF-hands coordinated by Asp/Glu, > Ser, one backbone O and one water (coordination number 5 and 6). Ca2+ can > be excluded as there are no anomalous difference peaks at these sites when > I calculate a map from data collected at 2A wavelength. > I suppose that either Na+ or Mg2+ are bound. > I'd like to ask whether there is a clear way to distinguish between both ions in > a model from data at this resolution. > > Thank you in advance for your suggestions, > > Florian > > P.S. The distances between ion and protein are: > > Asp/Glu carboxyl O: 2.04-2.75A > Ser OH: 1.98-2.6A > Backbone O: 2.4-2.65A
