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

Phan, Jason jason.phan at vanderbilt.edu
Fri Sep 26 08:42:59 PDT 2014

Thanks, Tim & Nate. I'm using the riding model as implemented. I grabbed this catalytic triad pic from Wikimedia which is very similar to what I have. What I was trying to say is in my phenix refinement, the Ser-O-H----NE2-His angle is greater than 90 degrees. The serine O-H bond is projected perpendicularly to the O----N imaginary straight line, instead of pointing along that line or say 0-60 degrees off of it, which is a stronger hydrogen bonding angle than say 90 or greater. Nate made a good point but like I said, if the acceptor is an oxygen be it from the back bone, side chain or water, the hydroxyl hydrogen would "point" at it at an angle close to 180, a straight line, as seen in this picture. But when you have a histidine NE2 and not an oxygen, the hydroxyl O-H bond would rotate more than 90 degrees relative to that straight line. That made me think that Phenix does model hydrogen bonding interactions, just maybe not as consistently. I'll send Pavel the Phenix refined and the Primex refined models as requested.


On Sep 26, 2014, at 4:59 AM, Nathaniel Echols wrote:

On Fri, Sep 26, 2014 at 1:16 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de<mailto:tg at shelx.uni-ac.gwdg.de>> wrote:
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.


Jason, I think you may be misunderstanding how hydrogens are handled internally.  The geometry restraints used in Phenix (and Refmac, etc.) are based on the assumption that the data guide the atoms reasonably well, and do not include any attractive forces or explicit hydrogen-bonding.  Reduce will take hydrogen bonding into account when it adds hydrogens to the model, but that's it - and I'm not sure how well this will handle hydroxyl hydrogens.


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