How to distinguish between Na+ and Mg2+?

From: Florian Sauer


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

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From: Robbie Joosten

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