Structure Gallery:

The malachite green - RNA aptamer complex shows the ligand deeply embedded in the core of the RNA. The complex is stabilized by electrostatic forces and stacking interactions. Adenines are shown in red, guanines in blue, cytosin in yellow and uridines in green.

• structure: Flinders, J. et al ChemBioChem 5(2004): 62-72.
• coordinates: PDB/RCSB entry 1Q8N

Substrate stem-loop of the VS ribozyme. The structure illustrates how the internal loop around the cleavage site forms a completely base paired bulge that contains tandem G:A base pairs and an A+:C base pair (the A is protonated). Further studies of the structure revealed a pH dependent conformational switch that causes the A in the A+:C pair to loop out of the helix at high pH.

• structure: Flinders, J. et al J. Mol.Biol. 308(2001): 665-679.
• coordinates: PDB/RCSB entry 1HWQ

The active site loop (Loop VI) of the VS ribozyme contains the nucleotides that are most likely involved in the chemical catalysis step. The structure of the loop shows a high degree of dynamics within the RNA backbone. We assume that this is related to the transition between active and inactive conformations of the ribozyme.

• structure: Flinders, J. et al J. Mol. Biol. 341(2004): 935-949.
• coordinates: PDB/RCSB entry 1TJZ