The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
Fig 5
Overview of the exit paths identified with COP and COD (A), RMSF and atom contacts (B for COP and C for COD) 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 cap path is coloured in orange, the FAD path in blue and the subunit interface path in magenta. B: Plot of simulations with COP, 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. C: Plot of simulations with COD, 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 the COP and COD (in green and black) to FAD.