Stepwise model for phosphoryl transfer and product release. (J. Gan, G. Shaw, J.E. Tropea, D.S. Waugh, D.L. Court and X. Ji, Mol. Microbiol. 2008; 67:143-154. Abstract). (A) Model of the protein-substrate complex. (B) Model of the protein-reaction intermediate complex (transition state). (C) The catalytic site arrangement immediately after dsRNA cleavage is represented by the minor conformation of the Aa-RNase III•MgRNA 9 structure. (D) Step 1 toward product release is represented by the major conformation of the Aa-RNase III•MgRNA 9 structure. (E) Step 2 toward product release is represented by the Aa-RNase III•MgRNA 8 structure. The aa and nt residues are shown as stick models and Mg²⁺ ions and water oxygens as spheres (C, gray; N, blue; O, red; P, orange; and Mg, black). Metal coordination bonds are illustrated as solid lines and hydrogen bonds as dashed lines. The nt residue in the middle is numbered “R 0” and the rest are numbered according to the polarity of the RNA strand.