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. 2015 Jun 4;290(29):17923–17934. doi: 10.1074/jbc.M115.648352

FIGURE 2.

FIGURE 2.

D4·DNA and hUNG·DNA contacts. A, structural alignment of the hUNG sequence with the one from VACV D4 (done with PDBeFold (46) and drawn with Espript (48)). Matched residues are printed in bold and black, and positions with similar residues are in red. Residues contacting the cognate DNA strand are boxed in black, residues contacting the complementary strand are boxed and printed in green, and residues marked with a # contact both strands. Residues involved in hydrogen bonds with DNA are printed with a cyan background. An asterisk marks a hydrogen bond to a thymidine base, which is specific to the DNA oligomer used. Residues corresponding to the water-activating loop are underlined in orange, the ones belonging to the 4-Pro loop are underlined in blue, the ones of the Gly-Ser loop are underlined in green, and residues belonging to the intercalation loop are underlined in red. B, sequences of DNA oligomers present in the complexes. Nucleotides involved in van der Waals contacts are underlined, and nucleotides involved in hydrogen bonds are highlighted in yellow. An asterisk marks a hydrogen bond, which is specific to the DNA oligomer used. a, abasic site. The analysis was done with PISA (32).