Bicarbonate ion is a weak base and is normally protonated near neutral pH. (Nitrate is a pathetically weak base and is not protonated at any reasonable biological pH.) Therefore, bicarbonate will have one hydrogen bond donor group (the -OH group) and two hydrogen bond acceptor groups, whereas nitrate will have only acceptor groups. This distinguishing feature is clearly seen, for example, in the allosteric site of beta-carbonic anhydrase (2A8D) where the bicarbonate binding site has one critically placed hydrogen bond acceptor group (carbonyl oxygen of Val47) among a sea of donor groups. Bicarbonate ions will populate this site in crystals after a few minutes soak at 100 mM concentration. The same crystals soaked in as much as 1M (!) nitrate overnight do not bind nitrate ion in this site.
Roger Rowlett On Nov 10, 2016 3:42 PM, "Keller, Jacob" <kell...@janelia.hhmi.org> wrote: > Dear Crystallographers, > > > > I don’t think there is any feasible way crystallographically to > distinguish between nitrate and carbonate or bicarbonate—correct? But that > is not my main question. > > > > My main question is: given that nitrate and carbonate are both very > important and also very different physiologically, and therefore they must > be distinguished/recognized by cells, how is this done, since the ions are > so similar in structure? Is there some aspect of these ions that differs > dramatically of which I am not aware? What kind of “handles” could a > protein grab onto to distinguish between nitrate and carbonate/bicarbonate? > > > > JPK > > > > > > ******************************************* > > Jacob Pearson Keller, PhD > > Research Scientist > > HHMI Janelia Research Campus / Looger lab > > Phone: (571)209-4000 x3159 > > Email: kell...@janelia.hhmi.org > > ******************************************* > > >
