Figure 3 - full size

 

Figure 3.
Figure 3. The active site of NgoMIV. a, Stereo view of the coordination geometry of Mg2+ ions at the active site of NgoMIV in the enzyme -product complex. Two Mg2+ ions are shown as green spheres. Both Mg2+ exhibit octahedral coordination. The O2P of the 5' phosphate, the carboxylate of Asp 140 and the acetate molecule contribute to the coordination of both Mg2+ ions. The remaining three ligands of Mg 2+ ion A are the backbone oxygen of Cys 186 and water molecules 1 and 2 (shown as blue spheres). Water molecules 3 -5 complete the octahedral coordination of Mg2+ ion B. All Mg coordinated waters are fixed by either protein and/or DNA residues. The final 2F[o] - F[ c] electron density for the DNA is shown contoured at 1.5 . b, Stereo view of the superimposed active sites of NgoMIV and Cfr10I. The Cfr10I residues are shown in blue, the NgoMIV residues in green, with the two Mg2+ ions shown as green spheres. c, Stereo view of the superimposed active sites of BamHI and NgoMIV. The BamHI residues are shown in magenta, the NgoMIV residues in green with the two metal ions as magenta (Mn2+ in BamHI) and green (Mg2+ in NgoMIV) spheres. Note that four acidic residues (Glu 77, Asp 94, Glu 111 and Glu 113) are located in the vicinity of the Mn2+ ions at the active site of BamHI, while only three (Glu 70, Asp 140, Glu 201) are present at the active site of NgoMIV. Lys 187 of NgoMIV is structurally equivalent to Glu 113 of BamHI.

The above figure is reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 792-799) copyright 2000.