Fig. 1. Secondary structural elements from group II intron ai5γ. (A) Schematic secondary structure of the ai5γ group II intron. The 5′ and 3′ splice sites are indicated as open and closed circles, respectively. The exon/intron pairing interactions (EBS1 and EBS2 pairing with IBS1 and IBS2) are shown as bold shaded boxes. Branching occurs during the first step of splicing, when the 2′-hydroxyl of A880 in D6 (bold) attacks the 5′-splice site (curved arrow). (B) The secondary structure of D56 is shown, with the branch site indicated by an arrow and the linker region by a bracket. Catalytically important residues in D5 are shaded.