[phenixbb] Histidine as a hydrogen bond acceptor in Phenix refine

Tim Gruene tg at shelx.uni-ac.gwdg.de
Fri Sep 26 01:16:23 PDT 2014

Hi Jason,

out of curiosity: By 'explicit hydrogen atoms' do you mean that you
refine the hydrogen parameters rather than using the riding hydrogen
model? This is very bold for even at and beyond Acta C resolution limits
(0.8A) one usually only uses the riding atom model for hydrogens.


On 09/25/2014 07:41 PM, Phan, Jason wrote:
> Hi All,
> I've been refining a 1.1 Å structure with explicit hydrogen atoms and noticed that the serine HG atom (hydrogen atom attached to oxygen gamma) is rotated more than 90 degrees from the OG - NE2 (histidine) line (5 cases observed). In this position, the HG is staggered with the two carbon beta hydrogens and should be the preferred configuration. However, there is a histidine nearby with atom NE2 at 2.7 Å from the serine OG and in good geometry for Hbond formation. The other nitrogen, ND1, is protonated and interacting with an aspartic acid (similar to the catalytic triad configuration). In this protomer, the NE2 atom has a lone pair and should act as an acceptor. Thus, the OG - H - NE2 angle should be as close to 180 as possible for an ideal hydrogen bond angle. The OG - H - NE2 angle of more than 90 degrees looks a little off to me. I checked the other program, e.g. Schrodinger Prime to see how it treats this situation and found that all the OG - H - NE2 angles are within 10-60 degre
es from the ideal value of 180, certainly not 90 as observed in Phenix refine. My question is is NE2 or ND1 atom of the HID or HIE protomer treated as a potential hydrogen bond acceptor in Phenix? For other acceptors like the backbone carbonyl oxygen, carboxylic acid oxygen, and water oxygen, the hydrogen bond angle OG -H -O looks good. Not when it involves histidine atom NE2 or ND1 though. The pH of the crystallization is 7 by the way. Also, there's no water nearby that would draw the HG away from the histidine.
> Jason
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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