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Optimized base extrusion path for 5caC in TDG. (A) The path is indicated by colored dots tracking the position of the carbon atom of the 5caC carboxylate group along the path. Color denotes the replica index from initial (red) to final (blue). Four snapshots along the path are shown. (B) Early intermediate with Arg275 intercalating into the DNA; (C) 5caC at the Pro198 loop; (D) 5caC positioned next to the gating helix; and (E) 5caC extruded into the TDG active site.
