Figure 4.
Figure 4. a, Superposition of the structures of EcoRV bound to
the wild-type site in the presence of Ca^2+ (green), and bound
to CI (red). The subunit II active site is shown, and the
superposition is carried out over all backbone atoms in the core
portion of this subunit^15. The position of the calcium ion (Ca)
and its bound water molecules in the active site of the cognate
structure are shown. b, 'Omit' (2F[o] - F[c]) electron density
map in the active site of subunit I of the EcoRV−CI complex,
contoured at 1.0 .
Side chains of Asp 90, Asp 74, Glu 45 and Lys 92, the center CI
step of the DNA, and all solvent molecules in the subunit I
active site were removed before positional refinement in X-PLOR.
Positions of side chains and water molecules (blue spheres) in
the final model are shown. B-factors for the water molecules
shown range from 30 to 35 Å^2. This and other maps through
the course of refinement show the lack of a well-defined Ca^2+
ion in the active site. c, Simulated annealing 'omit' electron
density map in the active site of subunit I of the
EcoRV−MI−Ca^2+ complex. Side chains of Asp 90, Asp 74, Glu
45 and Lys 92, the center MI step of the DNA, and all solvent
molecules in the subunit I active site were removed, and the
resulting model subjected to a simulated annealing refinement
protocol in X-PLOR. Electron density maps calculated with
coefficients (2F[o] - F[c]) (blue) and (F[o] - F[c]) (red) are
shown superimposed on the final model. Phases for this map were
derived from the model with these atoms deleted. The map is
computed in the resolution range from 2.0 Å to 20 Å.
The density is contoured at 1.0 for
the (2F[o] - F[c]) map and 6.0 for
the (F[o] - F[c]) map. The purple sphere represents a Ca^2+ ion
and blue spheres represent water molecules. Both map figures
were produced using SETOR^46.
.
Side chains of Asp 90, Asp 74, Glu 45 and Lys 92, the center CI
step of the DNA, and all solvent molecules in the subunit I
active site were removed before positional refinement in X-PLOR.
Positions of side chains and water molecules (blue spheres) in
the final model are shown. B-factors for the water molecules
shown range from 30 to 35 Å^2. This and other maps through
the course of refinement show the lack of a well-defined Ca^2+
ion in the active site. c, Simulated annealing 'omit' electron
density map in the active site of subunit I of the
EcoRV−MI−Ca^2+ complex. Side chains of Asp 90, Asp 74, Glu
45 and Lys 92, the center MI step of the DNA, and all solvent
molecules in the subunit I active site were removed, and the
resulting model subjected to a simulated annealing refinement
protocol in X-PLOR. Electron density maps calculated with
coefficients (2F[o] - F[c]) (blue) and (F[o] - F[c]) (red) are
shown superimposed on the final model. Phases for this map were
derived from the model with these atoms deleted. The map is
computed in the resolution range from 2.0 Å to 20 Å.
The density is contoured at 1.0