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. Author manuscript; available in PMC: 2011 Apr 5.
Published in final edited form as: Biochemistry. 2011 Mar 9;50(13):2672–2682. doi: 10.1021/bi2000164

Figure 3.

Figure 3

Molecular dynamics simulations of reverse G•U wobble in the product and precleaved forms of HDV ribozyme. (A) Schematic depiction of reverse G•U wobble observed in the crystal structure of the precleaved form (42). Color-coding of the hydrogen bonds is maintained in panel B. (B) Hydrogen-bonding distances in MD trajectory of product C75° state (upper panel). At neutral pH, C75 is deprotonated in the product state. (43). Hydrogen-bonding distances in MD trajectory of precleaved C75+ state (lower panel). In the precleaved state, C75 has a pKa near neutrality and is largely protonated. Distances plotted are between N and O atoms of each hydrogen bond. See Supporting Information for additional independent MD trajectories.