Hi,
This may be of interest in this discussion (the abstract is enlightening in
itself):
"Water polygons in high‐resolution protein crystal structures"
Jonas Lee, Sung‐Hou Kim
https://pubmed.ncbi.nlm.nih.gov/19551896/
Download software here (you can analyze input pdb file to look at water
polygon structures): https://sourceforge.net/projects/pdbwaterpolygon/
Thanks,
Debanu
On Sun, Apr 4, 2021 at 10:27 AM Debanu wrote:
> Hi,
>
> This may be of interest in this discussion (the abstract is enlightening
> in itself):
>
> "Water polygons in high‐resolution protein crystal structures"
> Jonas Lee, Sung‐Hou Kim
> https://pubmed.ncbi.nlm.nih.gov/19551896/
>
> Download software here (you can analyze input pdb file to look at water
> polygon structures): https://sourceforge.net/projects/pdbwaterpolygon/
>
> Thanks,
> Debanu
>
> On Tue, Mar 23, 2021 at 2:15 AM Barone, Matthias
> wrote:
>
>> can confirm jon´s comment. I find these in virtually every high-res
>> structure. some of them wobble a bit given the AA close by, such as Arg.
>>
>>
>> Dr. Matthias Barone
>>
>> AG Kuehne, Rational Drug Design
>>
>> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
>> Robert-Rössle-Strasse 10
>> 13125 Berlin
>>
>> Germany
>> Phone: +49 (0)30 94793-284
>> --
>> *From:* CCP4 bulletin board on behalf of Jon
>> Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
>> *Sent:* Monday, March 22, 2021 5:38:40 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] unknown density
>>
>> Definitely water pentamer, no doubt at all ;-0
>> Cheers, Jon.C.
>>
>> Sent from ProtonMail mobile
>>
>>
>>
>> Original Message
>> On 22 Mar 2021, 14:16, Mark J. van Raaij < mjvanra...@cnb.csic.es>
>> wrote:
>>
>>
>> The ring looks too big to be imidazole or a nucleotide or a carbohydrate,
>> so it’s probably mainly water molecules.
>> Perhaps partially replaced by PEG to explain the density between them
>> (i.e. water molecules in most copies of the protein and PEG in some other
>> copies). I’ve seen horse-shoe shaped PEG in a high-res structure before,
>> PEGs in several confirmations might explain a circle.
>> Practically speaking, I’d first model five waters and see if they refine
>> well.
>>
>> Mark
>>
>> On 22 Mar 2021, at 14:58, Sam Tang wrote:
>>
>> Hello fellow colleagues
>>
>> Hope you are all well while the pandemics persists. I just wonder if
>> anyone may have an idea what this density (looking like a pentagon) might
>> be. The data was collected to 1.8 A and crystal was grown in Bis-tris +
>> PEG3350. Imidazole residual? Nucleotide (the protein itself is
>> nucleotide-binding, but shouldn't be at this particular site)?
>>
>>
>> https://drive.google.com/file/d/1L9UBFmW72P214itM2HJR_DVy3FaA6FEZ/view?usp=sharing
>>
>> Thanks!
>>
>> BRS
>>
>> Sam
>>
>> --
>>
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