Figure 8

Trans-axial disposition of the interaction-network orchestrated by the sets 2 and 3. In A and B, the nature of the trans-axially positioned 140 and 188 residues are shown, respectively, for canonical and divergent DBDs. In A, the distance from the D140 acid oxygen atoms to the nearest backbone phosphate (repulsive to that residue) is assigned (5.4 Å). In C and D, the residues from, respectively, sets 2 and 3 (black spheres for the C _α atoms) regulate interactions with the major groove along distinct diagonals (double arrows) passing through the principal axes from the complex. The DNA major axis (red) was calculated as described in Methods and the blue perpendicular axis was traced in order to pass through the H-A geometric center. Dotted spheres represent the Zn²⁺ ions. Canonical B-form fragments of DNA were used for all the respective models (see text for details).