Fig. 6.

A-configuration and B-configuration metal coordination. (A) Left panel: The 2.1-Å structure of GSK299423 (PDB code: 2XCS) has a Mn²⁺ ion at the A (or 3′) site. For clarity, only the DNA, compound, catalytic tyrosine (mutated to Phe), metal and coordinating residues and waters (small red spheres) are shown. View is similar to Fig. 4B. The dotted lines show approximate positions of Asp 508 and Mn²⁺ ion for B-configuration metal. Right panel: Density around the modeled Mn²⁺ in 2XCS (blue cage, contoured at 8.4 rmsd). The coordinating oxygens were omitted, and the difference map (light green cage, contoured at 5.4 rmsd) is shown around the modeled coordinating oxygen. (B) Left panel: The 2.5-Å structure of QPT-1 (PDB code: 5CDM) has a Mn²⁺ ion in the B-configuration (similar view to Fig. 4A). The DNA has been cleaved by the catalytic tyrosine. Carbon atoms in DNA covalently attached to the catalytic tyrosines are colored as in tyrosine A123 (slate-blue) or C123 (gray). The position of an A-configuration metal is shown (broken circle) as in panel A, left panel. Right panel: Density around the modeled B-configuration Mn²⁺ for 5NPP (the highest-resolution B-configuration metal structure) is shown as in panel A, right panel (contoured at 5.1 rmsd). The omit map for coordinating oxygen is shown as above in a lighter-green cage (contoured at 4.1 rmsd).