Figure 3.
FIG. 3. [BP]dG-induced distortions to the BF polymerase
active site. A, the C:[BP]dG base pair surrounded by omit
electron density contoured at 3 with hydrogen bonds
represented in black (dashed lines) accompanied by lengths. B,
superposition of the BP-modified DNA duplex (red) and an
unmodified DNA duplex (gray). The BP moiety of the [BP]dG
protrudes into the DNA minor groove. C, comparison of BF protein
side chain conformations when BF is bound to C:[BP]dG (red) and
C:G (gray) at the post-insertion site (n-1 position). Hydrogen
bonds are represented as dashed lines. D, model of BF in a
ternary complex with [BP]dG (yellow) obstructing the insertion
site to an incoming dCTP. A cognate base pair is shown in gray,
and hydrogen bonds are represented by dashed lines.
The above figure is reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
3764-3770)
copyright 2005.
with hydrogen bonds
represented in black (dashed lines) accompanied by lengths. B,
superposition of the BP-modified DNA duplex (red) and an
unmodified DNA duplex (gray). The BP moiety of the [BP]dG
protrudes into the DNA minor groove. C, comparison of BF protein
side chain conformations when BF is bound to C:[BP]dG (red) and
C:G (gray) at the post-insertion site (n-1 position). Hydrogen
bonds are represented as dashed lines. D, model of BF in a
ternary complex with [BP]dG (yellow) obstructing the insertion
site to an incoming dCTP. A cognate base pair is shown in gray,
and hydrogen bonds are represented by dashed lines.