Fig. 8
Structural analysis of the bound TtPreQ1 aptamers. a Ligand-binding site of the ab13_14-2 co-crystal structure, superimposed on the |Fo|−|Fc| electron-density map calculated before addition of the ligand to the crystallographic model (blue mesh, 3.0 σ contour). Hydrogen bonds are indicated as dotted lines. b Ligand-binding site of the ab13_14_15-3 co-crystal structure. The |Fo|−|Fc| electron density map for the compound is colored blue and contoured at 3.0 σ. c Comparison of binding modes of 1 (magenta), 2 (cyan), and 3 (green). Ligand-binding site and continuous base stack of the aptamer domains of the d WT-PreQ1, e WT free, f ab13_14-PreQ1, and g ab13_14-1 forms. (Upper) Cartoon representations with ligands and key nucleotides labeled and colored cyan, magenta, yellow, and green in the WT-PreQ1, WT free, ab13_14-PreQ1, and ab13_14-1 forms, respectively. To compare the locations of A32 and G33 among these structures, dashed lines are indicated. (Lower) Detail of the ligand-binding site. PreQ1 and 1 are in yellow. Key nucleotides responsible for forming the base stack are colored cyan. U12 in the ab13_14-PreQ1 structure, which occupies a similar location to A14 in the WT-PreQ1 structure, is in green. Hydrogen bonds between PreQ1 and C15 are indicated as dotted lines
