Figure 5.

Recognition mechanism of the WOPR domain with its specific DNA. (A) DNA is shown with a surface model in light blue. The R loop is colored in magenta and strands β3 and β4 in green. The five key residues of the WOPR domain (Arg65, Ser75, Arg76, Ile77, and Leu82) involved in the recognition of the DNA are shown with side chains. The specific interactions between WOPR and DNA can be divided into two regions. In region I, the side chain of Arg65 of the R loop is inserted into the narrow minor groove and recognizes the first three bases of the core motif via the local shape readout mechanism. In region II, the last three bases of the core motif in the major groove are recognized by the side chains of Ser75 and Arg76 of the R loop and Ile77 and Leu82 of the β-sheet via the base readout mechanism. (B) Graphs showing the width and depth of the minor groove of the dsDNA. The binding site of Arg65 in the minor groove is indicated. The geometrical parameters of the DNA were calculated using Curves+³⁸.