Extended Data Fig. 6: Computational analyses for the SoBcmB-catalysed epoxidation reaction. | Nature Catalysis

Extended Data Fig. 6: Computational analyses for the SoBcmB-catalysed epoxidation reaction.

From: Enzymatic catalysis favours eight-membered over five-membered ring closure in bicyclomycin biosynthesis

Extended Data Fig. 6

a, Representative MD snapshot of the reactant FeIV-oxo species of WT SoBcmB in complex with 2a. Key residues (carbon in purple blue) and intermediate 2a (carbon in cyan) are in stick modes. b, r.m.s.d. of backbone heavy atoms relative to the first snapshot during 10 ns classical MD simulation on enzyme-intermediate 2a complex. c, Distances (d1 to d2) between the oxygen of the FeIV-oxo species and C1 or C1’ of 2a. d, Free energy profiles (kcal mol-1) relative to complex reactants for epoxidation of the desaturated intermediate 2a based on a theozyme model. All data refer to Gibbs free energies obtained in the quintet state at the B3LYP-D3/6-311 + G(2d,p)[SDD(Fe)] level with ZPE corrections at the B3LYP-D3/6-31 G(d,p)[LanL2DZ(Fe)] level of theory. Solvation by chlorobenzene was considered by using the CPCM model for all the above calculations.

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