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Figure 1.
Fig. 1. (a) Ribbon diagram of HincII dimer (subunits shown in
light and dark green) showing bound DNA (pale beige, red, and
blue), site of Gln138 (cyan) intercalation, position of Ca^2+
(yellow) in the two active sites, and center step of the
recognition sequence (red, blue). (b) The numbering scheme used
throughout the paper for the HincII recognition sequence. Y
indicates either C or T, R indicates either G or A. (c)
Structure of the pyrimidine–purine step as found in the
structure of wild-type HincII bound to cognate DNA containing
GTCGAC (left) and in B-form DNA (right). The Y7 is unstacked
from R8 within the same strand in the HincII bound DNA, and the
center step purines (R8 and R8′) have increased stacking
across the DNA duplex, forming a cross-strand purine stack
(CSPS). (d) Overlay of portions of the structures of
wtHincII/CG/Ca^2+ (white) and Q138F/TA/Ca^2+ (cocrystal)
(color); nuc, putative water nucleophile of the DNA-cleavage
reaction; SP, phosphate at the scissile phosphodiester bond.
Arrows emphasize the largest structural differences: the side
chain of residue 138 sits differently between the adjacent
cytosine bases at the site of intercalation and the main chain
around Phe138 is shifted away from the DNA to accommodate this
different position (1). As a result, the side chain of Ala137 no
longer makes a van der Waals contact to the DNA (2), which may
be the reason for the altered pucker of the deoxyribose at Cyt10
from C1′exo to C2′endo (3). The different pucker at Cyt 0
causes a twisting of the sugar–phosphate backbone of the DNA
strand (4) propagating to the phosphate between the Pyr7 and
Pur8, potentially resulting in the O5′ of Ade9 jutting into
the space normally occupied by the side chain of Thr130 (5). To
avoid the steric conflict, the phosphate of Ade9 is rotated,
blocking the position of the putative nucleophilic water (6).
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