Fig. 3: Overview and active site features of the Top6^(A:E342Q)•mcDNA•ADPNP cleavage-complex structure.

a CryoEM density map of the complex (EMD-49972). b Cartoon representation of the atomic model derived from the map (PDB ID: 9O0G). The DNA is shown with a semitransparent atomic surface. c Detail of the ADPNP- and metal-binding region of GHKL and transducer domains in a B-subunit monomer. CryoEM density for ADPNP, metals, and the K435 side chain is shown in semitransparent gray. d Top-down view of the cleaved DNA with the following active-site constituents shown in atomic representations (magenta): phosphotyrosine (residue 106 and the DNA backbone phosphate) (spheres), the metal-binding tetrad (E202, D254, D256, and Q342, sticks); and calcium ion (bright green sphere). e View of the DNA bend and angle, measured as degrees deviated from a straight duplex (“Methods”). The WH domain position is measured as the angle of helix 1 from the horizontal. f Close up of active site constituents in the cleavage state, including the catalytic tyrosine (Y106), the electrostatic clasp (R102 and Q342, mutated from glutamate), the TOPRIM metal-binding site (E202/D254/D256), and the associated calcium ion. The cryoEM density map is shown in semitransparent gray. Distances from the carboxylic oxygens of E202 and D256 to the associated metal are too great to represent inner shell contacts (~ 4 Å) and may be mediated by water molecules that are not evident at the overall resolution of the Coulomb potential maps.