Figure 6.

Metal ion binding. (A) Superposition of Form 2 structures with Ca²⁺ (yellow, Ca²⁺ shown as yellow sphere) and Mn²⁺ (green, red, orange, blue, Mn²⁺shown as purple spheres) using the alpha carbon atoms of residues 103, 149, 188 and 242. SP, phosphate of the scissile phosphodiester bond, 3′P, phosphate 3′ of SP, nuc, water molecule positioned for in-line attack on the SP, M1 and M2, metal ion binding sites, pink arrow, direction of nucleophilic attack, red line, scissile bond. (B) Schematic of the interactions around the two Ca²⁺ of the Form 2 Ca²⁺ bound structure of SgrAI, shown in Figure 6A. Dashed lines indicate ligation to the Ca²⁺ ions. Some water molecules ligated to the Ca²⁺ are shown as light blue circles. (C) Stereo diagram of the electron density around an M1 Mn²⁺ ion in the Form 2 Mn²⁺ bound structure of SgrAI. Simulated annealing omit 2Fo−Fc electron density shown in blue (1σ) and red (8σ). SP, 3′P, nuc defined as in Figure 6A, arrow, direction of nucleophilic attack. The Mn²⁺ is shown as a pink sphere and ligated water molecules as red spheres. Ligations to the Mn²⁺ are shown as dashed lines. (D) Schematic of the interactions around the Mn²⁺ ions of the Form 2 Mn²⁺ bound structure of SgrAI, shown in Figure 6A. Dashed lines indicate ligation to the Mn²⁺ ions. Water molecules ligated to the Mn²⁺ ions are shown as light blue circles.