Figure 8
Protein-DNA interactions involving Arg77 in the PAM-absent (a) and PAM-present (b) systems, and the average distances of relevant atomic pairs (c). The Cas2/Cas2′ (green/cyan), DNA (α strand: pink; β strand: light blue) are depicted with ribbon and tube models, respectively. Atoms involved in protein-DNA interactions are shown in CPK. In the PAM-absent system (a), the side chain of Arg77 swings in the surface of DNA minor groove. In the PAM-present system (b), the side chain of Arg77 always orientates toward the DNA backbone and forms more arginine-DNA interactions. So the two systems have different atomic pair distance distributions (c). Ad3/Ad4 stands for the distance between Arg77 NH2/Arg77 NH1 in Cas2′ and C13 O3′/G12 O1P along α strand, which is not shown in (a) for clarity. Values represent mean ± S.D. (error bars) from the equilibrium trajectories. *Indicating the bond length of two bonded atoms labeled in (a,b).
