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Water molecules os Sodium Ions?

Graheme Williams williams at delftny.com
Wed Feb 1 18:14:25 EST 1995

With reference to the original post asking about methods to distinguish water
molecules from Sodium and Potassium ions in electron density maps and the and 
the follow-up posting which suggested that sinf Na+ and K+ do not form  
hydrogen bonds then one can make the necessary distinction based upon the 
nature of the side chains near the subject peak.  With  temerity I suggest 
that this is by no means the complete story.  Both Sodium ions and H20 
molecules have 10 electrons and both will occupy locations about 3 angstroms 
from ionised carboxylate groups (these are the only kind which exist on the 
periphery of proteins) - hence they are indistinguishable.  On the other hand 
a water molecule will happily reside 3angstroms away from a neutral aromatic
NH group,or a protonated alkyl primary secondary or tertiary amine (>NH+, 
>NH2+, or -NH3+ groups) but a sodium ion will be found elswhere because of 
charge repulsion.  Hence the simple rule, - and the only one that is valid in 
this simple context, "if it's near an amine function it's most likely not a 
sodium ion".  Rules for K+ ions are the same as for Na+ but here there are an 
additional 8 electrons and so peak height will distinguish - if the site is 
fully occupied.
Sorry for the lecture in basic chemistry - I had a few moments to spare and 
needed the typing practice.

Best wishes   =Graheme=

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