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Figure 3.
Fig. 3. Mechanism of DNA binding. (a) Expanded view of the
major groove interface. Beta-sheet strands B1 (Leu16–Ile18),
B2 (Tyr24–Arg27), and B3 (Glu34–Gly38) insert into the major
groove. The side chains of Arg19 and Glu34 contact the
Cyt6–Gua19 base pair and simultaneously form a salt bridge.
The carboxyl group of Glu34 interacts with the N4 atom of Cyt6
and the guanidine group of Arg19 donates a hydrogen bond to the
O6 atom of Gua19. The side chains of Asn20 and Lys33 contact
phosphate groups of Glu19 and Ade7, respectively. The side chain
of Asn21 is juxtaposed with the Gua4–Cyt21 base step in the
major groove, stabilizing the binding interface. (b) Expanded
view of the minor groove interface and role of the amino
terminus in DNA binding. The side chain of Met1, the backbone
residues Met1–Gly2, and the side chain of Arg3 are deeply
inserted into the minor groove. Gly2 contacts the Ade9–Ade10
base step and the side chain of Arg3 contacts the Thy17–Thy18
base step. Arginine residues 3, 4, 5, 9, and 10 and the
amino-terminal amino group are favorably positioned for
electrostatic interactions with the phosphodiester backbone
adjacent to the minor groove interface and the 3[10] helix. (c)
Schematic summarizing the protein–DNA contacts in the
structure of the Int^N–DNA complex. Phosphodiester linkages
are shown as circles; those that are contacting by Int^N are
highlighted in blue. Bases shaded blue and green are contacted
by the protein from the major and minor groove, respectively. A
hydrogen bond is considered to be present when potential donor
and acceptor atoms are separated by less than 3 Å.
Salt-bridge interactions occur when appropriately charged groups
are separated by less than 4.5 Å. Interactions shown in
the figure occur in > 40% of the structures within the ensemble.
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