Figure 6.

Structural features underlying the tighter binding between AF113-18 PS2-modified RNA aptamer and α-thrombin. Superimposition of the crystal structures of the AF113-18:thrombin and native RNA:thrombin complexes. The color scheme is as follows: atoms in the AF113-18 RNA:thrombin complex are colored by atom, with RNA carbons in magenta and protein carbons in green, sulfur atoms are drawn as yellow spheres, 2′-fluorine atoms are light green and water molecules are cyan spheres of smaller radius; all RNA, protein and water oxygen atoms in the native complex are colored in gray. Selected residues and moieties are labeled, and selected contacts are marked with thin solid lines with distances in Å. Inset: The P18 environment in the structure of the native aptamer:thrombin complex. The drawing was generated with the program UCSF Chimera.