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Figure 5.
Fig. 5. Conformation of the oligonucleotide containing a
B[c]Ph DE-adducted templating guanine in the single-nucleotide
gapped DNA substrate bound to Pol  . (A) F[o] –
F[c]-simulated annealing electron density omit map (gray)
contoured at 2.5  showing density
corresponding to the B[c]Ph DE–dG adduct (adduct shown in
yellow). The dideoxy-terminated primer terminus (3') form
Watson–Crick hydrogen bonds (orange) with its templating base.
(B) The gapped DNA substrate is bent 90° at the 5' phosphate
of the adducted deoxyguanosine monophosphate (G*, purple
nucleotide with the B[c]Ph DE in yellow). Pol is
omitted for clarity, and the 3' ends of the primer and template
strands are indicated. Note that the adducted G* base is rotated
out of the normal templating position (shown in green for the
analogous unadducted templating guanine; Protein Data Bank ID
code 1BPX). The duplex portions of the two structures are nearly
identical (rmsd = 0.60 Å; not shown). (C) A detailed view
of the conformation of the templating adducted (G*) and
unadducted (G) guanine bases. The B[c]Ph DE moiety (yellow)
bound at N^2 of G* is positioned where an unadducted guanine
base would be found in the DNA binary polymerase complex. It is
able to stack with the upstream duplex in this position. The
adducted deoxyguanosine is in a syn-conformation and displaced
outside of the coding template position.
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