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. Author manuscript; available in PMC: 2020 Jul 29.
Published in final edited form as: Nat Chem. 2020 Jan 20;12(2):193–201. doi: 10.1038/s41557-019-0391-x

Figure 4. An elaborate network of interactions configures the VS ribozyme for proton transfer and transition state stabilization.

Figure 4.

2D schematic of the transition state configuration developed in this work. The transition state is a “late” transition state, in which the P-O2’ bond is almost fully formed, the P-O5’ bond is mostly broken, and the proton from A756 is partly transferred to the 5’O leaving group, consistent with the LFER data, and suggesting that the proton transfer from G638 likely occurs in a pre-equilibrium step prior to arriving at the rate-controlling transition state. Atoms and dashed line connections highlighted in gold indicate functional linkages established in this study. Dotted line connections indicate forming and breaking O-P bonds and H atom in flight from A756 to O5’.