The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
Fig 7
Overview of the re path identified with dioxygen (OXO) and hydrogen peroxide (PER) (A), RMSF and atom contacts (B for dioxygen and C for hydrogen peroxide) and binding energies (D). A: The VAO dimer is shown as cartoon in grey and its FAD cofactor is shown as sticks in yellow. The paths identified in this work are shown through sphere representation of ligand positions in the trajectories. The re path is coloured in cyan. B: Plot of simulations with dioxygen, highest RMSF values (black boxplot boxes) and atom contact counts with the ligand (grey boxplot boxes) of residues in VAO. Cyan filling of the boxplots indicates that the residue belongs to the re path. C: Plot of simulations with hydrogen peroxide, highest RMSF values (black boxplot boxes) and atom contact counts with the ligand (grey boxplot boxes) of residues in VAO. Coloured filling of the boxplots indicates that the residue belongs to the path of that colour. D: Scatterplot of binding energies as a function of the distance between dioxygen (cyan) or hydrogen peroxide (black) to FAD.