Putative position of branching nucleotide. Possible locations of branching adenosine were modeled by manually docking the residue into the intron active site. Panel A shows a series of sterically allowed conformations (adenosine is represented by sticks, carbon atoms of the base are in various colors, the ribose moiety and the surface of the intron active site are in green). Among these conformations, only a subset of structures orients the nucleophilic 2′-OH group (red spheres in panel A) in line with the scissile P-O bond, in the same position as the water molecule that acts as the nucleophile for hydrolytic splicing (see Figure 3). The latter subset of structures is shown in panel B (oriented and color coded as in Figure 3).