Figure 5.
Figure 5 (A) Ribbon representation of superposed polymerase
active sites (same basis of superposition as used for Figure 4)
of complex N and HIV-1 RT/DNA/dNTP ternary complex
[RT(ter)−ddNMP−dTTP complex] (Huang et al., 1998); PDB code
1RTD. Color scheme: side chains of complex N (cyan), primer
strand of complex N (magenta), incoming dNTP of the ternary
complex (yellow), metals A and B in the ternary complex
(yellow). In complex N, the corresponding metals (A' and B') are
either not seen in the structure and may have been released
together with PPi (A'), or are observed (Figure 3) at a position
shifted by 4.7
Å (metal B'). (B) Superposition of polymerase active sites
of the non-terminated [RT(P)−dNMP, green] (Ding et al., 1998;
PDB code 2HMI) and AZTMP-terminated P complex [RT(P)−AZTMP,
white]. The main structural difference is in the inclination of
the terminal nucleotide. (C) Superposition of the polymerase
active sites (aligned using p66 residues 107−112 and
155−215) of complex P (in white) on the RT(ter)−ddNMP/dTTP
ternary complex (in cyan) (Huang et al., 1998); PDB code 1RTD.
The ternary complex YMDD loop is displaced 1.0
Å from its position in the P complex. Steric conflicts (in
red) are mostly between the C5' of the incoming dNTP and the
side chain of Asp185.
The above figure is reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
6614-6624)
copyright 2002.
4.7
Å (metal B'). (B) Superposition of polymerase active sites
of the non-terminated [RT(P)−dNMP, green] (Ding et al., 1998;
PDB code 2HMI) and AZTMP-terminated P complex [RT(P)−AZTMP,
white]. The main structural difference is in the inclination of
the terminal nucleotide. (C) Superposition of the polymerase
active sites (aligned using p66 residues 107−112 and
155−215) of complex P (in white) on the RT(ter)−ddNMP/dTTP
ternary complex (in cyan) (Huang et al., 1998); PDB code 1RTD.
The ternary complex YMDD loop is displaced