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. Author manuscript; available in PMC: 2010 Jun 10.
Published in final edited form as: Structure. 2009 Jun 10;17(6):857–868. doi: 10.1016/j.str.2009.04.009

Figure 3. 6-position derivatives binding to a guanine binding RNA (GR).

Figure 3

(A) Binding pocket of the 6ClG:GR structure. The electron density map of the ligand and surrounding nucleotides (orange mesh, contoured at 1σ) is a simulated annealing omit map in which the shown nucleotides have been omitted from the model used to calculate the map. Hydrogen bonding interactions between the ligand and the specificity pyrimidine (C/U74) are depicted as grey dashed lines. Similar maps are shown throughout Figures 3, 5, and 6. (B) Ligand and binding pocket of the 6OMeG:GR structure. (C) Superposition of structures of wild type hypoxanthine:GR (red), 6ClG:GR (blue), and 6OMeG:GR (green). While U22, U47, and U51 in each structure are in nearly identical positions, the ligand and C74 in the 6OMeG:GR have shifted. The largest positional shift is C74, which is moved towards the minor groove, allowing for an altered hydrogen bonding pattern with the ligand. (D) Ligand and binding pocket of the 2AP:GR structure.