Structural characterization of the apta-FRET complexes and chimeras. (A) Binding pocket of Mango-III (cartoon) bound to YO3-Biotin (orange, ball-stick). |Fo| − |Fc| electron density map prior to ligand placement contoured at 2.0 σ is shown in gray mesh. (B) Structural superposition of Mango-III/YO3-Biotin and Mango-III/TO1-Biotin (PDB: 6E8S) binding pockets. Binding pocket of the Mango-III/YO3-Biotin complex (cartoon) with YO3-Biotin (orange, ball-stick) and TO1-Biotin (gray, ball-stick). (C) Binding pocket of iSpinach (cartoon) bound to DFHBI-1T (cyan, ball-stick). |Fo| − |Fc| electron density map prior to ligand placement contoured at 2.5 σ (gray mesh). (D) 90° rotation of (C) highlighting trifluoromethane packing against residue A50. (E) Structural superposition of non-hydrogen, RNA atoms of iSpinach/DFHBI-1T and iSpinach/DFHBI (PDB: 5OB3) binding pockets. iSpinach/DFHBI-1T complex (cartoon) with DFHBI-1T (cyan, ball-stick) and DFHBI (gray, ball-stick). (F) Structural model of Broc-6bp-M3 with side (left) and top (right) views demonstrating parallel dipole alignment. (G) Structural model of Broc-9bp-M3 with side (left) and top (right) views demonstrating perpendicular dipole alignment. P1 helices (see Fig. 1D) in panels F and G are deleted for clarity.
