Introduction - This script shows the structure of E. coli glutaminyl tRNA synthetase, a protein that binds highly structure RNA. Scroll down until the text corresponding to the view is visible. (Based on 1gts.pdb, Perona et a., Biochemistry 32, 8758 (1993)).
Here is the complex with the protein depicted in cartoons and the RNA in wireframe. Note the extensive interface between the tRNA and the protein. Because the base pairing hydrogen bonds are used to form the secondary structure of the tRNA, the interactions between the tRNA and the protein are rather like those between DNA and proteins, relying on extra hydrogen bonding groups on the edges of the bases and electrostatic interactions with the backbone.
In this view the size of the tRNA-protein interface is better seen.
The function of the enzyme is add an amino acid to the terminal adenine of the tRNA. Note how this base is buried in the active site of the enzyme, while most of the rest of the tRNA is bound to the surface.
Here is another view of the acceptor adenine.