Dear all,
Thanks for all of your replies. The crystallizatin pH is 5.5, above pKa of
aspartate, which is 3.8. In addition, the protein functions at neutral pH, and
this aspartate is part of the active site. So it doesn't appear that the
aspartate is protonated due to low crystallization pH or working pH.
Could it be protonated due to a low local pKa? I am not familiar with
calculation of local pKa, but the aspartate is located inside a loop, and also
interacts with two or three main chain nitrogens other than the main chain
carbonyl oxygen. The carbonyl oxygen in question is from a proline.
My new question here is: do these factors above justify a low local pKa and,
further, a hydrogen bond between the aspartate and the carbonyl oxygen?
Thanks a lot!
Frank
Hi,
In a new structure we observed a hydrogen bond between an aspartate side chain
and a main chain carbonyl group. Because both of them are electronegative, I am
puzzled.
My questions are: does this hydrogen bond make sense at all? any precedent for
such a hydrogen bond?
I would appreciate your help very much!
Frank
