Figure 2. Structure of T7 RNAP EC with Bound AMPcPPThe
protein structure is shown by ribbon diagram. The refolded
N-terminal domain and the rest of the protein are cyan and
white, respectively. RNA, DNA template, and nontemplate
nucleotides are shown in yellow, red, and blue, respectively.
AMPcPP (green sticks) and protein side chains (white sticks)
involved in a substrate binding are shown by ball-and-stick
models. Mg^2+ ions are shown as magenta spheres.(A) Simulated
annealing |Fobs − Fcalc| omit electron density maps produced
after refinement for substrate (green, 3σ level) and Mg^2+ ions
(blue, 5σ level).(B) Overall view of the T7 RNAP EC with AMPcPP
bound in the substrate entry channel along the open O helix.(C)
Substrate binding site. Hydrogen bonds and Mg^2+ coordination
bonds are shown as white dashed sticks.
The above figure is reprinted
by permission from Cell Press: