(color online) The movement of Tyr639 and the rotation of the O helix are weakly coupled to each other. (a) The time series of the change in position of Tyr639 relative to the PRE position (red line) and that of Arg627 relative to the position when the O helix and fingers domain are in the closed conformation (blue line) for system 3 where the αβ methylene ATP and the template nucleotide i + 1 are removed in the insertion complex (PDB 1S76). The latter trace is offset by −0.2 nm on the y axis for clarity. (b) A snapshot of the structure obtained from the trajectory shown in panel (a), where Tyr639 is in POST position and the O helix and fingers domain are in the semi-closed conformation (yellow). The structures of the enzyme shown in red and green are the same as those in Fig. 2(b). (c) The position distribution of Tyr639 for system 3 with 20 trajectories with a simulation period of 10 ns. Yellow and green lines represent the Gaussian fits; the blue line represents the sum of two Gaussians. (d) The position distribution of Arg627 for system 3 with 20 trajectories with a simulation period of 10 ns. The blue line represents the Gaussian fit. (e) The time series of the change in position of Tyr639 relative to the PRE position (red line) for system 4 where residue Arg627 was restrained in system 3. (f) A snapshot of the structure obtained from the trajectory shown in panel (e), where Tyr639 is in the POST position and the O helix and fingers domain are in the closed conformation (yellow). The structures of the enzyme shown in red and green are the same as those in Fig. 2(b). (g) The position distribution of Tyr639 for system 4 with 20 trajectories with a simulation period of 10 ns. Yellow and green lines represent Gaussian fits; the blue line represents the sum of two Gaussians.