Figure 4.

Quantitative determination of 3°γ (HBN) effect induced by metal ion binding in VSr, HHr, Psr, and 8-17dz. One-dimensional probability distribution functions (1D PDFs) constructed from the unbiased and reweighted umbrella sampling simulations (see Supporting Information for full details) are shown for VSr (A), HHr (B), Psr (C), and 8-17dz (D). The 1D PDFs are constructed along the coordinates d_HO2′–G that correspond to the distance of the HO2′ from the WC edge of the catalytic N1-deprotonated guanine (minimal distance to either N1 or O6 positions). 1D PDFs obtained in the presence of the metal ion are shown in purple and 1D PDFs obtained in absence of metal ion are shown in cyan. The 3°γ (HBN) factor is defined as the ratio of the areas under the 1D PDFs obtained in the presence and absence of the metal ion that reside below a threshold value (2.5 Å marked by gold line) of the HO2′–guanine distance (shaded region).