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. Author manuscript; available in PMC: 2008 Jan 1.
Published in final edited form as: DNA Repair (Amst). 2007 Jul 12;6(12):1709–1725. doi: 10.1016/j.dnarep.2007.05.009

Figure 9.

Figure 9

Accommodating distorted DNA substrates. (A) Superposition of a gapped substrate with an A-A mismatch at the primer terminus (PDB code 1ZJN, orange) and a normal gapped DNA substrate (PDB code 2FMS, khaki). The identities of the primer terminal and nascent base pairs are indicated (normal ternary in khaki, and mismatched ternary in orange). Identities of the DNA bases in the mismatch structure are shown to the right of each base (orange). (B) Superposition of a normal gapped DNA substrate (PDB code 2FMS, khaki) with canonical G-C base pair and a gapped DNA substrate containing an 8oxodG at the templating position (PDB code 1MQ3, orange), paired with incoming dCTP. (C) Pol λ accommodating an extra base. Superposition of a normal ternary complex of Pol λ (PDB code 1XSN; DNA, orange) with the frameshift intermediate (PDB code 2BCV; DNA khaki). Secondary structural elements for the frameshift structure are shown as blue ribbons. The extrahelical nucleotide is depicted in cyan. β-strand 8 harbors the K544 residue proximal to the extrahelical nucleotide, near the top of the panel.