Fig. 5.

Opening of β-lobe is sufficient for DNA loading even when the clamp is partially closed. (A) D1 is the distance between center of mass of clamp and β-lobe. The atoms included for the calculation of center of mass is the same as the ones included for PCA. (B) Merging the clustering in A and B results in 12 combinations of clamp and β-lobe conformations. The D1 values for the structure closest to the cluster centers from each combination are shown as bar graph. There are three combinations of clamp and β-lobe conformation that can accommodate dsDNA, which are (C) open and open, (D) open and partially closed, (E) partially closed and open, respectively.