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Figure 1.
Figure 1. a, Ribbon representation of the EcoRV dimer showing
the dimerization domain at bottom (orange), the
DNA-binding/catalytic domains in yellow and the four flexible
linkers I−IV in each subunit^13. The major-groove binding
R-loops (red, residues 182−188 of each subunit) present all of
the primary determinants for direct readout of base-pair
functional groups in the GATATC target. The scissile phosphorus
atoms are shown by the pink spheres. The Gln-rich Q-loops that
bind in the minor groove are shown in blue. b, View of the bent
DNA conformation as seen in the complex of EcoRV with specific
DNA^13. The center TA step and the R-loops are drawn in purple
and blue, respectively. Van der Waals contacts of the Thr 186
side-chain methyl groups (red) with functional groups in the
major groove are shown. c, Hydrogen-bonding (dotted lines) and
van der Waals/electrostatic contacts (hatched lines) at the
center TA step in the wild-type EcoRV−DNA complex. Distances
in Å between nonhydrogen atoms are from the ternary
complex structure with Ca^2+ (ref. 15). The contacts between Thr
186 and the thymine O4/adenine N6 groups may contribute binding
energy but are considered to be nonspecific. The Watson−Crick
hydrogen bonds are designated WC. The distance between the Thr
186 and Thr 186' methyl groups from the two separate subunits is
4.2 Å.
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