Figure 1.

(a) Scatter plot of the coordinates of backbone phosphorus atoms, z_p(h) versus z_p, used to divide the arrangements of basepair steps in high-resolution protein-DNA complexes into conformational families: B DNA (z_p < 0.5 Å, z_p(h) < 4.0 Å); AB DNA (0.5 ≤ z_p < 1.5 Å, z_p(h) < 4.0); TA DNA (z_p ≤ 1.5 Å, z_p(h) > 4.0 Å); A DNA (z_p ≥ 1.5 Å). Whereas z_p gives the out-of-plane displacement of the phosphorus atoms with respect to the local dimeric coordinate frame, z_p(h) measures the displacement of the cross-strand P···P vector along the helical axis of the basepair step (46); see images in (b). Occurrences of individual dimers are color-coded by sequence type: purine-purine RR, open cyan circles; purine-pyrimidine RY, solid blue squares; pyrimidine-purine YR, solid red circles. Highly deformed basepair steps from complexes with TATA-box binding proteins, which are omitted by the culling of step parameters but included in some calculations, are denoted by open magenta circles. (b) Illustrative examples of the relative positions of phosphorus atoms (black balls) in different DNA conformational states, i.e., z_p value with respect to the middle dimeric frame and z_p(h) value with respect to the middle helical plane of basepair steps: B-DNA state of CG·CG from the Cre recombinase-DNA structure (NDB_ID pd0003) (61); AB-DNA state of AC·GT from the ternary complex of DNA with the large fragment of Thermus aquaticus DNA polymerase I (NDB_ID pd0032) (62); A-DNA state of AC·GT from the complex of DNA with the D34G mutant of PvuII endonuclease (NDB_ID pd0006) (60); TA-DNA state of CA·TG from the ternary complex of DNA bound to the homeodomain repressor protein MATα2 and the MADS-box transcription factor MCM1 (NDB_ID pdr036) (63). Left: middle frames (dotted lines) of dimer steps determined by the coordinate axes on consecutive basepairs. Right: planes (dashed lines) normal to the local helical axes of the same basepair steps. Arrows denote positive directions of the z-axes in the two frames.