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Figure 3.
Figure 3: Proposed mechanism for general acid -base catalysis in
the HDV ribozyme. a, In the ground state, a hinge rotation
along O3'-P bond brings the nucleophilic 2'-OH to the in-line
attack conformation. In the transition state, C75 (the general
base) deprotonates the 2'-OH whereas the bound hydrated metal
ion (the general acid) protonates the 5' oxygen leaving group.
Conformational changes after scissile bond breakage discharge
the catalytic metal ion and down-shift the catalytic base C75 by
2 Å to enable hydrogen bonding with the 5'-OH of G1. b,
Structural models of the HDV ribozyme in the ground state,
transition state and product state. Some metal-chelating groups
and coordinating waters are omitted for clarity.
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