Fig. 7

a, overlay of the structures (PRN-GLU-C model) illustrating the retraction of the intercalating side chain of Phe111. The structure with carbons colored green is the starting structure after minimization (0 ns); the structure with carbons colored cyan is at 8 ns. The protein backbone (residues 109–113) is shown in the cartoon representation, colored in the same way, with Phe111 presented as a stick model. The N, O, and P atoms are colored blue, red, and orange, respectively. In DNA, only the non-damaged strand is colored. Note the protein backbone movement, accompanied with ~90° Phe111 ring turn, and the corresponding turn of A⁽⁺¹⁾ to keep the phenyl ring stacked with the purine heterocycle. b, propeller twist angle (ω) of the pair T^–1:A⁽⁺¹⁾. In B-DNA (PDB ID 355D) [80], ω = 13° ± 4°