Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 50

Figure 2.6 Schematic view of the coordination sites in the HHR active site. Left: The coordination pattern of Mg 2þ in the

“ C-site ” coordinated

to G10.1:N7 and A9:O2p. Middle: The coordination pattern of Mg 2þ in the bridging A9:O2p and C1.1:O2p of the scissile phosphate.

Right: Coordination sites for Na þ in the HHR active site found in the RT-Na and dRT-Na simulations. Red numbers next to the coordination sites
are the scores used to calculate the coordination index (see text). M1 involves direct binding to A9:O2p and C.1:O2p and indirect binding to
G10.1:N7 through a water molecule. M2 involves direct binding to C17:O2 0 and C.1:O2p. M3 involves direct binding to C17:O2 0 and is posi-
tioned toward the outside of the active site.

“ B-site ”