Fig. 6

Comparison of the catalytic site architectures between 8–17 DNAzyme and RNA-cleaving ribozymes. The catalytic site architectures observed in the a leadzyme (PDB_ID:1NUV), b HDV (PDB_ID:1JS3), c hairpin (PDB_ID: 1M5O), and d hammerhead (PDB_ID: 3ZP8) ribozymes. e Superposition of the catalytic site residues in the hammerhead ribozyme and 8–17 DNAzyme structures. 8–17 DNAzyme structure is colored in green in e. In a–e, the C-atoms are colored in yellow and light blue for ribozymes and substrates, respectively, whereas other atoms are colored with the same scheme (N, blue; O, red; P, orange) for both ribozymes and substrates. Sr²⁺ ion, water molecules, and Mg²⁺ ion captured in the leadzyme and HDV ribozyme structures are shown as spheres in black, red, and black, respectively