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. Author manuscript; available in PMC: 2018 Jul 17.
Published in final edited form as: Biochem J. 2018 Feb 9;475(3):571–585. doi: 10.1042/BCJ20170787

Figure 3.

Figure 3

Ternary structure of Asn279Ala polβ with the dG:dTTP* mismatch and active-site Mn2+ (PDB ID 4Z6E). (A) Overall structure of the Asn279Ala polβ-dG:dTTP*-Mn2+ ternary complex. Polβ adopts a closed conformation. (B) Close-up view of the active site of the Asn279Ala polβ-dG:dTTP*-Mn2+ ternary structure. Mn2+ ions are shown as cyan spheres. (C) dG:dTTP* base pairing observed in the Asn279Ala polβ active site. Distances for N1(dTTP*)-O6(dG) and O2(dTTP*)-N1(dG) are indicated by dashed lines. Distances for O6(dTTP*)-O6(dG), N1(dTTP*)-N1(dG), and O2(dTTP*)-N2(dG) are 3.8Å, 3.4Å, and 3.1Å, respectively. The λ angles for dG and dTTP* are 45.8° and 65.8°, respectively, indicating a wobble base pair geometry. A 2Fo-Fc map contoured at 1σ around dG:dTTP* is shown. (D) Comparison of the Asn279Ala polβ-dG:dTTP*-Mg2+ (green) and the Asn279Ala polβ-dG:dTTP*-Mn2+ (purple) structures. (E) Published ternary structure of wild-type polβ with the dG:dTTP* mismatch and active-site Mn2+ (PDB ID 4PGX). Hydrogen bond contacts by Asn279 are indicated by dotted lines. O2 of dTTP* and the backbone carbonyl oxygen of Tyr271 engage in hydrogen bond interactions with Asn279. (F) Base pairing properties of dG:dTTP* in the published structure with the wild-type polβ and Mn2+ (PDB ID 4PGX)19. The λ angles for dG and dTTP* are 50.1° and 56.2°, respectively, indicating Watson-Crick-like base pair geometry. A 2Fo-Fc map contoured at 1σ around dG:dTTP* is shown. Distances of N1(dTTP*)-O6(dG) and O2(dTTP*)-N1(dG) are 3.1Å and 3.2Å, respectively. (G) Comparison of the Asn279Ala polβ-dG:dTTP*-Mn2+ (green) and the polβ-dG:dTTP*-Mn2+ (black) structures. Both structures contain two Mn2+ ions at the insertion site. (H). Comparison of dG:dTTP base pairing in the active site of wild-type polβ (black) and Asn279Ala polβ (green). Hydrogen bonds are indicated by dashed lines.