Figure 6.

(A) Ribbon scheme of the crystal structure of holo-EcNikR in complex with DNA. DBD are in orange and blue, while MBD are in light orange and light orange. Nickel ions are reported as dark red spheres and DNA is in green. The inset reports the details of the Ni(II) binding site. Nickel binding residues are reported as sticks colored according to atom type; (B) Schematic representation of the conformations of NikR found in the available crystal structures; (C) Ribbon diagram and solvent-excluded surface of the model structure of the HpNikR-DNA complex. HpNikR ribbons are colored in dark and light grey in the DBD and MBD, respectively. Active and passive residues used to guide the docking are in red and orange, respectively. Ni(II) ions are reported as dark brown spheres. The DNA ribbons are in dark red for the HpNikR operator and in light and dark blue for the terminal regions. The inset shows the details of HpNikR residues in the DBD in direct contact with the DNA major groove.