Hi Kaherine, It seems its a modified lysine in to kcx (Carbamylated lysine) but its only the case if you used during entire purification or crystallization BME in your buffer
Best Regards AFSHAN On Wednesday, July 2, 2014 5:38 PM, Katherine Sippel <katherine.sip...@gmail.com> wrote: At various peoples' urgings (thanks for the contributions all) I went ahead and put in Mg based on the bond valence. If refines very nicely in the context of the density maps (see attached MgCl2_pH6point5_3.png). I ran it through the check my metal server and it clears the coordination geometry and bond distance parameters but is displeased with the coordinating ligands. I am also concerned about the rotamer (big ol' outlier) and the CE-NZ-Mg bond angle. Obviously the density looks good, but it feels weird from a basic chemical standpoint. The crystallization condition for the ion-coordinated lysine was 100 mM Bis Tris pH 6.5, 200 mM MgCl2, 19% PEG 3350. One of the other space groups has 100 mM Tris pH 8.5, 200 mM MgNO3, 27% PEG 1500 and there is no errant density (see attached MgNO3_pH8point5.png). The sodium I mentioned comes from NaCl in the protein storage buffer. Thank you for all of your help thus far. Katherine On Tue, Jul 1, 2014 at 9:35 PM, Nat Echols <nathaniel.ech...@gmail.com> wrote: 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 > -- "Nil illegitimo carborundum"- Didactylos
