Hammerhead ribozyme scissile phosphate

Figure 1 Schematic view of the coordination sites in the hammerhead ribozyme active site. Upper left The coordination pattern of Mg2 in the C-site coordinated to G10.1 N7 and k9 Ow. Upper right The coordination pattern of Mg2 in the B-site bridging A9 02p and Cl.LO of the scissile phosphate. Lower Coordination sites for Na in the hammerhead ribozyme 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). M, involves direct binding to A9 02P and C.1 02P and indirect binding to G10.1 N 7 through a water molecule. M2 involves direct binding to CT7 02- and C.l 02p M3 involves direct binding to CI7 02 and is positioned toward the outside of the active site. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this book.)...

The core of the hairpin ribozyme comprises two formally unpaired loops carried on adjacent arms of a four-way helical junction. The junction is not essential to the activity, but provides efficient folding to create a local structure that approximates in-line geometry for the attacking 2 -OH of the adenosine residue. In common with the structure of the hammerhead, the scissile bond, which is cleaved to a 2, 3 -cyclic phosphate, is unpaired and is bounded by helical regions. 

---