Lithium versus Sodium

From: Scott Pegan
Date: 12 January 2012 06:09


Hey all,

Does anyone know of a good article that deals with differentiating between a lithium ion and sodium ion for density in a X-ray structures?

Scott

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From: Patel, Joe

Hi Scott

 

I may be completely wrong but I worked on a lithium and sodium  inhibited enzyme during my PhD.  At the time, it was considered that your chances of actually seeing density for a Li+ ion were slim to nil.  Only 2 electrons makes them as tough as hydrogens.  My efforts went into trying to prove I had a sodium ion bound over magnesium which is the catalytically active ion

 

Do you have ultra-high resolution? Something I did not….  Are there many examples in the pdb of proteins with Li+ refined?

 

Sorry no real help to you, but curious since it brings up old memories…

 

Joe P

 

 

Dr Joe Patel

 

 

 

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From: Ed Pozharski


http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html&param1=_LI

39 in total. Some are fairly low resolution (2.8A), and only five are
higher than 1.2A.  I'd think that placing lithium ion should be based on
some extra-crystallographic evidence, plus maybe some structural
considerations such as correctly placed coordinating ligands.

--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

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From: Matthew Franklin


Since I'm responsible for eight of those structures, I'll just say that I thought fairly hard before building a lithium into that peak, knowing that I couldn't really distinguish it from water or sodium.  I was working with a 1.7 A map, and I put the lithium there based on three criteria:

- the crystals grew in something like 2 M lithium sulfate, whereas the only source of sodium would have been from the buffer or the protein solution

- there were two negatively charged residues coordinating the peak in question, suggesting it was a cation

- the bond distances were consistent with lithium coordination, for what that's worth at this resolution

That was the first structure (1TW7), and all of the others were treated the same since it was the same crystals soaked with different compounds in the same conditions.

- Matt


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From: Ed Pozharski


Matt,

thank you, this is an excellent summary.  One question remains - the
lithium peak should be, afaiu, much lower than the water/sodium.  Was
there a peak in difference map or was placement based on identifying
something that looked like a coordination site?

Cheers,

Ed.

Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                               Julian, King of Lemurs

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From: Matthew Franklin


Hi Ed -

There was a peak in the difference maps, as I recall.  I believe it initially got built as a water, but that proved to be too many electrons, giving a negative peak.  I removed the water, but it was clear that something needed to be there, at which point I started casting about for alternative atoms, and settled on lithium.  I'm pretty sure I never tried to put sodium in there and see if it refined.

Caveat: this work was all done eight years ago, and I don't have access to any of the files anymore.  So I can't verify any of these statements!  However, I did deposit Fobs for these structures, if you care to make your own maps...

I just checked the structure in EDS, and the peak for the lithium is pretty low, around 0.6 sigma.  I would say that it looked better in the maps I was using.

Hope that helps,
Matt

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From: Armando Albert


Dear Matt,
We were working with Hal2p a lithium inhibited Ins-mono-PPase like protein 10 years ago.
 We had good biochemistry showing that lithium replaced mg at the active site. We grow crystals in presence of Li and we worked with 1.6 A diffraction data.  Unfortunatelly we did not see any electron density peak, however, the "Li" site displayed nice tetrahedral
coordination having four oxygen atoms as ligands.
Armando