FIG. 8.
Molecular modeling of the 3Dpol NTP binding pocket. (A) van der Waal's representation of the amino acids present in the NTP binding pocket of 3Dpol. Amino acid side chains are labeled. The incoming nucleotide (ATP) is also labeled. (B) The same view as in panel A; however, the N297 side chain has been removed (i.e., N297A- or N297G-containing derivatives), resulting in an expansion of the NTP binding pocket. (C) 286L/297A derivative. (D) 239G/297A derivative. (E) 239G/297A derivative, rotated by 90° counterclockwise about the vertical axis of the page. In this view the gap produced by the A239G substitution is observable. The N297A substitution is occluded by the D238 side chain. In addition, replacement of the alanine at position 239 by glycine might result in additional rotational freedom for the adjacent side chain (D238).