Well, I was looking at two periplasmic binding proteins, one for NO3 and one for CO3/HCO3, and was wondering whether the obligate cooperative Ca ion adjacent to the ligand only in the CO3 binder was necessary, and how in any case it would help distinguish the two if at all. Roger’s comments about CA are interesting in light of this, since there is no Ca ion involved (from what he said), and still CA binds so specifically to HCO3 and not NO3. I wonder whether the Ca ion protein I am looking at is specific for CO3 alone? I have seen this Ca ion phenomenon also in a lactate binding protein. Or maybe the Ca ion just makes the affinity much stronger than in CA’s?
Jacob Pearson Keller From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Clement Angkawidjaja Sent: Friday, November 11, 2016 12:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Nitrate versus Carbonate Dear JPK What I know is we do not have much nitrate in the blood unlike carbonate/bicarbonate. Nitrite, a nitrate byproduct can cause problems but it has a different structure and probably does not interfere with bicarbonate binding to relevant proteins. Cheers, Clement From: Keller, Jacob<mailto:kell...@janelia.hhmi.org> Sent: Friday, November 11, 2016 5:41 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Nitrate versus Carbonate 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<mailto:kell...@janelia.hhmi.org> *******************************************
