(A, C, E) Detailed interactions of DNA with three pairs of subunits within the LT hexamer: subunit pair i & iv (A), ii & v (C), and iii & vi (E). The β-hairpin residues K512/H513 and DRF loop residues D455/R456/F459 that bind to the DNA are labeled. (B, D, F) The detailed interactions of the oriDNA with the same three pairs of LT subunits shown in (A) [matching B], (C) [matching D], and (E) [matching F]. Dashed lines indicate hydrogen-bond interactions between LT residues and DNA (in the stick model). Some of LT residues are 5–7 Å away from DNA, and would be suitable for the water-mediated formation of hydrogen bonding. In addition, a number of LT residues are within Van der Waals distance of the bound DNA, forming hydrophobic packing interactions; these residues include K512 of subunit i (i-K512), i-F459, iv-F459, ii-F459, v-F459, vi-F459, and vi-H513. The dislocated bases in the disrupted bases-pairs (in the partially melted DNA region) are drawn in thick sticks, with the DNA sequences of this region shown to the left of panel B. The structure shows clearly that identical residues on different subunits make unique contacts with the phosphate backbones and the major or minor gr oves of the DNA; this is possible due to the near-planar arrangement of the six subunits.