FIGURE 3.

Stacking and polar interactions between Bs-CspB and the ligands (A,C) rC7 and (B) rU₆. (A) A stereo representation of the Bs-CspB molecule with the longest observed nucleotide sequence of rC7 is shown. The backbone of the protein molecule is depicted as gray object; protein groups involved in stacking interactions and water-mediated or direct hydrogen bonding are colored according to the CPK scheme with the exception of carbon, which is in gray. The RNA is colored according to the CPK scheme with the exception of carbon, which is green. Direct hydrogen bonds between protein and RNA are shown as dotted lines. In a schematic depiction of ligand binding the RNA strands (B) rU₆ and (C) rC7 are depicted in black and groups of Bs-CspB in dark gray (bb, protein backbone). The longest observed nucleotide sequence of rC7 is presented. A group belonging to a symmetry-related Bs-CspB is displayed in light gray. Stacking interactions between aromatic sidechains and RNA bases are shown as solid gray lines. Hydrogen bonds are displayed as dotted lines. The numbers of the contact subsites for individual bases are given at the bottom, using the numbering scheme introduced earlier (Max et al. 2006).