Figure 4.

Structure of the Holliday junction center. (A) Fo-Fc annealed omit electron density map (>2.5 σ) showing a DNA moiety within the junction center. The two bases closest to the junction center, indicated by a white stick model, were omitted from the map calculation. (B) Environments around unpaired bases in the tetrameric RuvA center. Arg-54, Glu-55, and Asp-56 of each RuvA subunit, which form the acidic pin, are shown by a ball-and-stick representation. (C) Schematic drawing of the Holliday junction structure. The synthetic Holliday junction was designed to form two pairs of opposite arms with different lengths: the north and south arms of a 12-bp DNA duplex and the east and west arms of a 13-bp DNA duplex with a single base overhang at the 5′ end. Two AT base pairs disrupted at the crossover are colored by magenta. The topological features of the unpaired bases may reflect a scene during branch migration, in which the base pair rearrangements are in progress and the new base pairs will be subsequently formed.