(color online) Intermediate position of Tyr639 and an intermediate semi-closed conformation of the fingers domain. (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 1 where PPi is removed and 3′-deoxyadenosine is converted to adenosine in the pre-translocation complex (PDB 1S77). The latter trace is offset by −0.2 nm on the y axis for clarity. (b) A snapshot of the structure produced from the trajectory shown in panel (a), where Tyr639 is in PRE position and the O helix and fingers domain are in the semi-closed conformation (yellow). For comparison, the structure of the enzyme in the pre-translocation complex with Tyr639 in the PRE position and the O helix and fingers domain in the closed conformation (red) and the structure of the enzyme in the post-translocation complex with Tyr639 in POST position and the O helix and fingers domain in the open conformation (green) are also shown. (c) The position distribution of Tyr639 for system 1 with 20 trajectories with a simulation period of 10 ns. The blue line represents the Gaussian fit. (d) The position distribution of Arg627 for system 1 with 20 trajectories for which the simulation period is 10 ns. The blue line represents the Gaussian fit. (e) The time series of the change in position of Tyr639 relative to the POST position (red line) and that of Arg627 relative to the position when the O helix and fingers domain are in the open conformation (blue line) for system 2 which is the post-translocation complex (PDB 1H38). The latter trace is offset by −0.2 nm on the y axis for clarity. (f) A snapshot of the structure obtained from the trajectory shown in panel (e), where Tyr639 is in the ITM position and the O helix and fingers domain are in the open conformation (yellow). The structures of the enzyme shown in red and green are the same as those in panel (b). (g) The position distribution of Tyr639 for system 2 with 20 trajectories for which the simulation period is 10 ns. Yellow and green lines represent Gaussian fits; the blue line represents the sum of two Gaussians. (h) The position distribution of Arg627 in system 2 with 20 trajectories with a simulation period of 10 ns. The blue line represents the Gaussian fit.