Fig. 4: Water molecule networks of active site pockets in HvExoI computational models of wild-type (WT) and E220A covalent complexes. | Communications Biology

Fig. 4: Water molecule networks of active site pockets in HvExoI computational models of wild-type (WT) and E220A covalent complexes.

From: The structure and dynamics of water molecule networks underlie catalytic efficiency in a glycoside exo-hydrolase

Fig. 4

a Radial pair distribution function profiles (quantified by density variation as a function of distance from a reference particle) of water molecules centred on Cα atoms of D285 (average of three replicates). b Frequencies of water molecules located within 6.5 Å and 8 Å spheres of E220/E220A and E491. c Dispositions of active site residues and D285-Glc adduct (cpk sticks and lines) in WT and E220A covalent complexes are shown for three selected frames (represented by D285-Glc adduct) along cMD simulations. Water molecules at separations of ≤4.7, 6.5 and 9.5 Å from E220/E220A, E491, N219 and D285-Glc adduct are specified in red, green and blue spheres (displayed in-depth cue mode), respectively. Subsites −1, +1 and +2 are marked. Selected Glc moieties of L5 are displayed. Separation between E220 and E491, and water molecules of ≤3.6 Å are shown in dashed lines. Properties of surface morphologies coloured by electrostatic potentials are described in Fig. 1.

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