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. 2021 Jan 7;49(2):1046–1064. doi: 10.1093/nar/gkaa1248

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© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Structural comparison of ssDNA recognition by Reps and relaxases: (A–D), PCV2 (6WDZ), WDV (6WE0), TraI36 (2A0I), TrwC (2CDM), are illustrated in gray surface display where DNA interactions within 4 Å are highlighted in cyan, green, magenta, and yellow, respectively. Bound single-stranded DNA is represented as a cartoon backbone in orange or as sticks with carbons and phosphates colored in orange. Nucleotides bound inside pockets are solid; other bound nucleotides are transparent. Relaxase ‘clasps’ (TraI36 residues 231–271 and TrwC residues 237–262) are either solid or transparent and outlined in black. Total buried solvent accessible surface area (BASA; Å²) for ssDNA bound to the docking interface was calculated for each structure including values for with, or without, contribution from relaxase clasps.