Fig. 7: Larger substrate accessible volume is correlated with selectivity differences.
From: Degradation of complex arabinoxylans by human colonic Bacteroidetes
a Binding pocket volumes of Bi1033-CE1 (red), Bi1039-CE1 (green), and the FAE domain of BeGH43/FAE (cyan) trajectories are represented as histogram. Pocket volumes were calculated for the frames with 1 ns interval of each trajectory. Mean binding pocket volumes are represented as vertical lines. b, c, d Cartoon and surface representation of esterase domains of Bi1033-CE1, Bi1039-CE1, and BeGH43/FAE, respectively, are presented. Catalytic triad residues are shown as sticks. Representative mean pocket volumes are displayed as transparent blue surface. e Binding distance of FA(C9) & SER(OG) are represented as Markov state model (MSM) weighted 1-D histogram. f, g Cartoon representation of stable binding poses of FA substrate close to active site in Bi1039-CE1 and in the FAE domain of BeGH43/FAE, respectively.
