|
Figure 2.
Fig. 2. dG-AAF adopts the syn conformation with the
fluorene ring intercalated into the polymerase fingers domain.
(a) dG-AAF lies outside the polymerase active site, and the
fingers domain of the polymerase is in an open conformation. The
T7 gene 5 protein (gray) and the thioredoxin (green)
processivity factor are shown as ribbons, with the O-helix
within the fingers highlighted in red. The primer strand of the
DNA is in light red, the template is in yellow, and dG-AAF is in
cyan and green. The region around the dG-AAF binding site is
circled. (b) Enlarged view of the circled region in a. The
fluorene ring (green) of dG-AAF (cyan and green) is inserted
into the fingers domain between helices L, O, O1, O2, and P. (c)
The simulated annealing omit electron density around the region
of the syn dG-AAF of the dG-AAF-containing complex is shown in
stereo, contoured at 2.5  above the mean value.
(d) Interaction between dG-AAF and the protein. Hydrophobic side
chains (gold) of the fingers form a pocket around the fluorene
ring. Two charged residues (pink), Arg-566 and Asp-534, form
hydrogen bonding interactions with the G base.
|
