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A secondary structure schematic of the ai5γ group II intron. Catalytically important regions of domain 3 (the internal loop (D3IL) and the pentaloop are highlighted in green and red, respectively. The interaction between the D3IL and ε-ε′ is denoted by solid green lines; the possible interaction between the D3IL and the bulge of D5 is denoted by a dotted purple line.
