Figure 3.
Fig. 3. Theoretical model of the Int
catalytic core bound to a B-form half-att site. A full att site
contains a pair of inverted^ core-type Int binding sites. An Int
protomer at each site is responsible^ for cleaving one DNA
strand via formation of a covalent 3 phospho-tyrosine^
linkage and a free 5 -hydroxyl.
The two nicks are staggered by seven base pairs with a 5 overhang.
For clarity, only one subunit of the Int c170 dimer that was
modeled on DNA is shown. The catalytic^ Arg-His-Arg triad (cyan)
of Int is docked over one of the scissile^ phosphates (shown as
breaks in the DNA ribbon). The C trace of^
Int c170 (blue) is displayed with the active site loop
containing the Tyr342 nucleophile shown in two alternative
conformations. The orientation corresponding to cis cleavage
(orange tyrosine) is a theoretical model, whereas that
corresponding to trans cleavage (red tyrosine) is present in one
of two Int protomers in the crystal structure. The segment of
the loop that is disordered in both protomers (Lys334 to Gln341)
is modeled in pink.
The above figure is reprinted
by permission from the AAAs:
Science
(1997,
276,
126-131)
copyright 1997.
Int
catalytic core bound to a B-form half-att site. A full att site
contains a pair of inverted^ core-type Int binding sites. An Int
protomer at each site is responsible^ for cleaving one DNA
strand via formation of a covalent 3 
phospho-tyrosine^
linkage and a free 5 
trace of^
Int c170 (blue) is displayed with the active site loop
containing the Tyr342 nucleophile shown in two alternative
conformations. The orientation corresponding to cis cleavage
(orange tyrosine) is a theoretical model, whereas that
corresponding to trans cleavage (red tyrosine) is present in one
of two Int protomers in the crystal structure. The segment of
the loop that is disordered in both protomers (Lys334 to Gln341)
is modeled in pink.