Figure 5.

The Active Site

(A) The active site with overlaid 2F_o − F_c simulated annealing omit electron density map contoured at 1 σ. The direction of the attack on the phosphorus atom by the putative nucleophile is shown with an arrow. RNA is shown in red and DNA in blue. Calcium ions and their coordination are shown in green. Water molecules are shown as red spheres.

(B) Stereoview of the active site.

(C) Close-up view of the coupling of the active site with the junction-sensing module. Active site residues are shown as orange ball and stick and tyrosine 163 as yellow ball and stick. Calcium ions are shown as green spheres.

(D) Same view but with a fragment of ideal A-form RNA superimposed on the Tm-RNase H2 substrate to show the deformations induced at the (5′)RNA-DNA(3′) junction (indicated with arrows).

(E) Superposition of structures solved in the presence of different metal ions. Metal ions are shown as spheres and the coordination of metal ion A as dashed lines. The structures are colored in green for wild-type protein with Ca²⁺, purple for D107N mutant protein structure solved in the presence of Mg²⁺, and cyan for D107N mutant protein with Mn²⁺.