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Figure 2.
Fig 2. Three-bond and four-bond modes of Mn2+ binding in
the DNA major groove. (A and C) The three-bond mode is shown for
sites 1-GG and 5-GC, respectively. (B and D) The four-bond mode
is shown for sites 4-GG and 6-GC, respectively. The guanine N7
and O6 atoms defining the metal binding mode and the
contributing bases are labeled (G' indicates the complementary
base to C in the GC step). A nonzero shift parameter for a base
pair step is visualized as a deviation of the double helix axis
(green). Coordination bonds (magenta) between metal ion
(magenta) and water molecules (red), and hydrogen bonds (yellow)
between bases and first and second shell, coordinated water
molecules are shown. (E) The site 1-GG (A) is shown with its
full hydrogen bonding network. A hydrogen bond occurs between
the N7 atom of the adenine base (5' A) adjacent to the GG base
step and a metal-coordinated water molecule, contributing to the
orientation of the metal ion-hydrate. (F) Site 3-GG binds Mn2+
in the same three-bond mode as site 1-GG, but lacks the
additional coordination shell bond from the adjacent thymine
base (5' T).
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