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:[log in to unmask]] On Behalf Of
> Florian Sauer
> Sent: Thursday, December 01, 2011 19:40
> To: [log in to unmask]
> 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
|