English: Schematic diagrams of the three base-stacking conformational isomers of the Holliday junction. The unstacked conformer, top, is only stable in the absence of divalent cations such as Mg²⁺, while the two possible stacked conformers (bottom) exists in the presence of these ions. The stacked conformers differ in which sets of two arms are bound by coaxial stacking: at left, the stacks are red–blue and cyan–magenta, while at right the stacks are red–cyan and blue–magenta. The sequence of bases nearest to the junction point determines which of the two stacked isomers dominates, or whether an equilibrium exists between them. These diagrams correctly show secondary structure and the overall three-dimensional geometry of the junction, but omits the double-helical tertiary structure of the molecule. The diagrams are drawn so that the red arm at bottom is always in the same orientation.