Comparison of the structure around residues 181 and 188 of the p55 subunit in HIV-2 RT with that of p51 subunit in HIV-1 RT. The main chains are shown as ribbons and coils, and side chains as ball-and-stick representations, with HIV-1 RT colored orange and red, and HIV-2 RT blue and green.

(A) 2|F_o| − |F_c| electron density map contoured at 1 σ showing residues from 400 to 406 in p68 of HIV-2 RT. (B) Ribbon diagram showing the overall fold of HIV-2 RT overlapped with unliganded HIV-1 RT (1hmv); the HIV-1 RT is shown in gray, and the domains of HIV-2 RT are colored as follows: fingers, blue; palm, green; thumb, orange; connection, red; and RNase H, purple. (C) Ribbon diagram showing the overall fold of HIV-2 RT overlapped with the HIV-1 RT/nevirapine complex (1rtv); the color scheme is as in B.

(A) Stereo diagram comparing the NNRTI site of an unliganded HIV-1 RT and the corresponding region of HIV-2 RT. The HIV-1 RT is colored in gray, and the main chain and side chains of HIV-2 RT are shown in green and orange, respectively. (B) Stereo diagram showing part of the HIV-2 RT p55 subunit containing the Ile-181 and Leu-188 side chains (blue and green) overlapped with the corresponding region of the p66 subunit in the nevirapine-bound HIV-1 RT (orange and red). Nevirapine is drawn as ball-and-sticks and colored by atoms. (C) Stereo diagram showing a cavity located at the junction of the p68 palm, p68 connection, and p55 fingers domains (ribbon and coils colored in green, red, and blue, respectively). Side chains of the residues lining the cavity, a bound glycerol and a sulfate are shown in ball-and-stick representation, and are colored by atoms, with carbon atoms in cyan for the side chains and black for the glycerol. Water molecules in the cavity are shown as small red spheres. Larger red spheres label the Cα position of the three catalytic Asp residues at the polymerase active site. Nevirapine colored in gray is shown to mark the NNRTI site in HIV-1 RT. The dashed yellow sticks indicate the four H-bonds from the glycerol to the carbonyl oxygen of Gly-99, the main-chain nitrogen of Ala-101, and a water molecule.