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Figure 2.
Fig 2. (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 C  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.
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