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. 2022 Jul 1;13:3806. doi: 10.1038/s41467-022-31278-4

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2022

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Fig. 8 — a Blunt-ended DSB substrate (DSB.D) co-crystallized with the Polλ catalytic domain. The break site is indicated (red dashed line). Upstream (left) template and primer (pink and blue, respectively) are annealed separately from the downstream (right) template (pale orange) and primer (lavender) strands, and synapsis is mediated entirely by the polymerase. The DSB.D pre-catalytic quaternary complex is formed by addition of the nonhydrolyzable incoming dUMPNPP (cyan) nucleotide. b Global superposition of the pre-catalytic SSB ternary (orange) and blunt-ended DSB quaternary (protein in green, DNA and incoming dUMPNPP colored as in a) complexes. c Structure of the DSB.D substrate bound in the Polλ active site, with the pre- (protein in light green, DNA and incoming nucleotide colored as in a) and partially incorporated (protein and DNA in dark green, unincorporated hydrolyzable incoming dTTP nucleotide in yellow, PDB ID code 7M0A) substrates, with zoomed-in views of each complex included to the right (top, pre-catalytic, with 2F_o-F_c electron density contoured to 1σ; bottom, partially incorporated, with unincorporated primer terminus and dTTP in gray and yellow, respectively). The Ca²⁺ and Mg²⁺ ions are shown as magenta and green spheres, respectively. Though the metal in the B site is modeled at full occupancy, based on geometry and coordination distances, a mixture of metals is observed in the A site. Occupancies for the metal A site mixture and newly incorporated nucleotide are indicated in each case. d Superposition of the pre-catalytic SSB (protein residues in orange, DNA template in transparent pale yellow) and blunt-ended DSB.D substrates (protein in green, DNA template strands colored as in a, water molecule as red sphere) for comparison of interactions surrounding the DSB break site (red arrow). Hydrogen bonding interactions with the DSB or the SSB are drawn as dashed lines (black or yellow, respectively).