Figure 2
From: Structure and Dynamics of Cas9 HNH Domain Catalytic State
Catalytic state coordination at the interface of HNH ββα fold and tDNA (a,b) and comparison with the one-metal-ion catalysis by T4 Endo VII (c). (a,b) The representative coordination configurations derived from post targeted MD (tMD) simulations (a) and conventional ensemble MD (cMDens) simulations (b) through cluster analysis (see Supplementary Text). (c) Close-up view of the active center of T4 Endo VII (N62D) resolving a DNA Holliday junction (PDB code: 2QNC). (d) Schematic representation of the one-metal-ion dependent catalysis in ββα-metal nucleases. The pro-Sp and pro-Rp oxygens of the scissile phosphate are indicated with Sp and Rp, respectively. The putative active residues in Cas9 HNH domain and the corresponding residues in T4 Endo VII are labeled in boldface. In panels a to c, the nucleobases are omitted for clarity, and the potential nucleophilic water are depicted in a ball and stick model and colored by atom types (O, red; H, white). Mg2+ is shown as a cyan sphere and the nucleophile is denoted by a curved arrow. The dashed lines indicate the coordination bonds involving Mg2+ and hydrogen-bonds.
