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Figure 5.
Figure 5. Model for the Recognition of A-Tract DNA by
L1-EN(A) Surface representation of L1-EN (colors as in Figure 2)
with a docked NMR model of substrate DNA (Stefl et al., 2004)
represented as ribbons. The upstream (5') and downstream (3')
duplexes are lime-green and magenta, respectively. Sulfate ions
on the surface of L1-EN used to position backbone phosphates of
the DNA are yellow, and the scissile phosphate in the active
site is cyan. Loop Bb6-Bb5 with H198 (asterisk) on its tip
inserts into the wide minor groove at the TpA step. This likely
bends or unwinds downstream (3') DNA, promoting the adenine to
flip. Left: view as in Figure 4; Right: view as in Figure 2.(B)
Model including only upstream (5') DNA and the flipped adenine
downstream of the scissile bond (views and colors as in [A]).(C)
APE1 bound to substrate DNA (style, views, and colors as in
[A]). Surface patches corresponding to residues that have no
equivalent in L1-EN and that occlude the active site cleft are
in orange.
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