On Tue, Jul 1, 2014 at 3:10 PM, Katherine Sippel <katherine.sip...@gmail.com > wrote:
> My google-fu has failed me once again so I am turning to the collective > knowledge of the bb. I'm working on a blobology challenge at the moment and > have hit a wall. Is anyone aware of an ion that coordinates to lysine and > prefers octahedral geometry. The mystery ion seems to have perfect > octahedral geometry with bond distances of ~2.1 angstrom, but the only > direct side chain interaction is to a lysine NZ, the rest are waters. > Lysine can coordinate a cation if the chemical environment is favorable - usually this means a high-pH buffer (what was the pH of your crystals?). The same is true for N-termini; I may be able to dig up a published example of this. (I think it is effectively impossible for Arg, however.) These interactions are certainly exceedingly rare (and I doubt they are ever present in vivo), but if the nitrogen loses a proton the lone pair will be able to coordinate a compatible ions. Since magnesium can be coordinated by the nitrogen histidine it seems like the most likely candidate - but I would still be very, very careful before assigning it, especially if the only other coordinating atoms are waters. -Nat
