Figure 6.

Loop 1–loop 2 complexes in natural hammerhead ribozymes. (A) and (B) are from the crystallographic structures of the Schistosoma (12) and sTRSV (+) hammerheads, respectively, and (C) is from a mutagenesis-supported model of the CChMVd (+) hammerhead (Materials and methods section). The views are from the minor groove of domain II and the major groove of domain I. The carbon atoms of loop 1 nucleotides are in blue, those of loop 2 in orange, and stem nucleotides in gray. The highlighted (green- and yellow-colored carbon atoms) contacts between IL1.U1, IL1.C8 and L2.A6 (A), L1.U1, L1.U6 and L2.A4 (B) and L1.U1, L1.U6, and L2.A6 (C) form the proposed tertiary interaction motif likely conserved in most natural hammerheads. Hydrogen atoms have been omitted for clarity.