Hydrogen bond alternatives for PEPCK polymorphic site Gly/Ser 335. Models are of the cytosol form in lid-open conformation. Color codes: polymorphic amino acid yellow, others’ carbon skeletons white with oxygens red and nitrogens blue. Hydrogen bonds between Asp 334 backbone nitrogen and Val 338 carbonyl, Asp 334 carboxyl and Asp 336 backbone nitrogen, and Asp 334 carbonyl and Gly 337 backbone nitrogen are invariant, while others change with alleles. a) allele GEV, Gly 335 with no hydrogen bonds; b) allele SEV, Ser 335 with no hydrogen bonds; c) allele SEI, Ser 335 hydrogen bonding between its backbone nitrogen and Asp 334’s carboxyl, and also hydrogen bonding between its sidechain hydroxyl and the carboxyls of either Asp 334 or Asp 336. These models do not prioritize among alternative potential hydrogen bonds in case of multiple such bonds per atom.
Watt et al. BMC Evolutionary Biology 2013 13:9 doi:10.1186/1471-2148-13-9