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


El 12/01/2012, a las 18:16, Matthew Franklin escribió:

> 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
>
>
> On 1/12/12 11:22 AM, Ed Pozharski wrote:
>> 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.
>>
>> On Thu, 2012-01-12 at 10:23 -0500, Matthew Franklin wrote:
>>> On 1/12/12 9:42 AM, Ed Pozharski wrote:
>>>> On Thu, 2012-01-12 at 09:52 +0000, Patel, Joe wrote:
>>>>> Do you have ultra-high resolution? Something I did not…. Are there
>>>>> many examples in the pdb of proteins with Li+ refined?
>>>> 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.
>>>>
>>> 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
>>>
>>>
>
>
> --
> Matthew Franklin, Ph. D.
> Senior Research Scientist
> New York Structural Biology Center
> 89 Convent Avenue, New York, NY 10027
> (646) 275-7165