Fig. 3.
MD simulations of Rev1 binary, ternary, and product complexes. (A) Distance profiles for the M685N–N7 (Left) and the G686N–O6 (Right) in the Rev1 binary (black line), ternary (red line), and product (green line) MD simulations. This behavior was reproduced by a second independent trajectory in which the interactions break after about 200 ns. (B) Distance profiles for the R324NE and dCTPO2 (Left) and the R324Nn2 and dCTPn3 (Right) in the Rev1 ternary (black line) and product (red line) MD simulations. The average distance between these atoms is indicated for the entire trajectory. (C) Twenty conformations from MD simulations for the product complex (each 50-ns apart) showing the conformation of dCTP and R324. (D) Twenty conformations from MD simulations for the ternary complex (each 50-ns apart) showing the conformation of dCTP and R324.