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Figure 3.
Figure 3. Details of ALSHG/LoxM7 ComplexCre/LoxP (green
sticks) was superimposed on ALSHG/LoxM7 (atom-colored balls and
sticks) as described in Figure 2. The dashed lines represent
potential hydrogen bonds in ALSHG/LoxM7 (black) and Cre/LoxP
(yellow).(A) Specific contacts to bases C7 and T8. Residues
258–266 of helix J are rolled 7° and shifted 0.6 Å
toward the DNA as a consequence of steric interactions between
Leu258 and Ala175. This repositioning facilitates hydrogen
bonding between Ser259 O^γ and C7 O^4 atoms. In addition, a
network involving water molecules Sol67, Sol179, and Sol503 (B
factors of 45, 52, and 50 Å^2, respectively) and the
Ser257 O^γ atom, the Leu258 N atom, and the Ser259 N and O^γ
atoms couples recognition of bases C7 and T8 and replaces the
water bridge between Thr258 O^γ1 atom and the N^4 atom of base
C8 in Cre/LoxP.(B) Coupled recognition of nucleotide T26, base
A27, and the phosphate backbone via a tripartite hydrogen bond
bridge. Base A27 is contacted by a hydrogen bond bridge mediated
by Sol501 and Sol502 with the Ser259 carbonyl. His262 is rotated
from the position of Glu262 in Cre/LoxP, which avoids a steric
clash and forms a tight Van der Waals contact with the 5-methyl
group of base T26. In addition, His262 forms a hydrogen bond
bridge between Sol501 and the phosphate of nucleotide 26,
connecting the T26 and A27 contacts.(C) Atomic level details of
ALSHG/LoxM7 interactions. Symbols and distances are as described
in Figure 1D.
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