Fig. 4.

Comparisons between the crystal structures (experimental) and the structures obtained by the QM/MM simulations (calculated). (A) Three structures of state R (reactant) are compared: the crystal structure R_xtal (AMPPNP-F) (gray), R_xtal-based-R (orange), which is the geometry optimized R_xtal, and P_xtal-based-R (blue), which is the QM/MM simulated based on P_xtal. (B) Three structures of state P (product) are compared: the crystal structure P_xtal (ADP-Pi-F) (gray), P_xtal-based-P (blue), which is the geometry-optimized P_xtal, and R_xtal-based-P (orange), which is the QM/MM simulated based on R_xtal. In A and B, small balls indicate the positions of oxygen atoms of selected water molecules, while large balls are Mg²⁺, color-coded in the same manner as for the peptides and nucleotides. The dashed lines centered at Mg²⁺ indicate the coordinate bonds between Mg²⁺ ion and oxygen atoms. (C) Keys for the structures compared in A and in B. Note that, in the natural actin, the hydrolysis reaction is irreversible (7); therefore, the backward reaction, from state P to state R, does not proceed.