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Figure 7.
Comparison of the Npg-1 and Npg-2 structures. A,
superimposition of the refined Npg-1 (cyan) and Npg-2 (purple)
structures reveals similar overall topology (r.m.s.d. 0.52). B,
the DNA substrates from Npg-1 and Npg-2 were superimposed with
the DNA from the ternary complex of Dpo4 inserting dCTP opposite
8-oxoG (orange, pdb ID code 2c2e). A more pronounced bending of
the helical axis was observed in the N^2-NaphG-modified DNA.
Other perturbations in the N^2-NaphG DNA, e.g. buckling of the
bases and widening of the major groove near the
primer·template junction, are also evident. C, the active
site of the Npg-1 crystal structure is shown in schematic form.
The 3F[o] – 2F[c] electron density map (cyan mesh) is
contoured at the 1σ level around the N^2-NaphG residue. The
incoming dGTP (red) is shown along with the magnesium ions
(green spheres). D, base pairing and stacking interactions
observed in the Npg-1 structure. E, the active site of the Npg-1
crystal structure is shown in schematic form. The 3F[o] –
2F[c] electron density map (purple mesh) is contoured at the 1σ
level around the N^2-NaphG residue. The incoming dGTP (red) is
shown along with the magnesium ions (green spheres). F, base
pairing and stacking interactions observed in the Npg-2
structure.
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