|
Figure 4.
Figure 4. Structure of the Substituted Region of the
LNSGG/LoxM7 ComplexFor comparison, Cre/LoxP (green sticks) or
ALSHG/LoxM7 (purple sticks) are superimposed on LNSGG/LoxM7
(atom-colored balls and sticks), as described in Figure 2.
Potential hydrogen bonds are denoted by dashed lines.(A)
LNSGG/LoxM7 has contacts between the DNA backbone and base C7
but not bases A27 and T26. Helix J maintains a position similar
to that in Cre/LoxP-G5. Ser259 forms a hydrogen bond with C7,
and Asn258 is positioned to form hydrogen bond with the
phosphate backbone at residue 24 (orange dashes). In addition,
Sol49 and new solvents Sol501 and Sol505 (B factors of 61, 52,
and 51 Å^2, respectively), form a hydrogen bond network
that interconnects the Ser259 carbonyl with the phosphates of
nucleotides 25 and 26. Sol49 and Sol84 occupy similar positions
in Cre/LoxP-G5. Although Sol502 is still bound by A27, the
increased length of the bridging contact with Sol501 (3.6
Å) indicates a weaker protein-DNA interaction.(B) Since
helix J is not rotated as in ALSHG/LoxM7 (purple) and Sol501 is
shifted toward Gly262, water molecules Sol501 and Sol502 are 1.2
Å farther apart (gray dashed lines) than in ALSHG/LoxM7
(cyan dashed lines), perhaps diminishing the strength of the
contact. Note the correspondences of Sol49 and Sol505 in LNSGG
and His262 in ALSHG. Sol84 is conserved in the Cre/LoxP-G5 and
1CRX structures.(C) Atomic level details of LNSGG/LoxM7
interactions. Symbols and distances are as described in Figure
1D. The gray stippled line indicates a weakened hydrogen bond
with a contact distance that is greater than 3.5 Å.
|
