Fig. 3: MD simulations reveal binding pockets for MAH in TodX and CymD.
From: Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion
a Cartoon model showing state II TodX residues mediating the largest number of interactions with benzene (blue) from equilibrium MD simulations as green stick models. These residues form the P-pocket. b Comparison of the location of residues in TodX and CymD that form the largest number of interactions with benzene and p-cymene respectively. Residues are coloured by the percentage of simulation time for which the interactions occur, with data included for both independent simulations of each protein. Interactions are defined as an inter-atomic distance of <4.0 Å.
