GlnRS-tRNA^Gln

PDB file 1GTR

This file depicts the E. coli glutamine Aminoacyl-tRNA Synthetase (GlnRS) complexed with tRNA^Gln and the substrate ATP. The structure was determined by M. A. Rould, J. J. Perona, & T. A. Steitz in 1995.

Suggested display options:

Select nucleic and change display to sticks to make the tRNA more prominent.
Select protein and color chain.
Select residue atp, display as ball & stick and color CPK. 
Note how the acceptor stem of the tRNA extends into the enzyme active site, where ATP is bound.

Using the command line, enter select 76b.
Display as ball & stick and zoom in to visualize the terminal residue (A) in the acceptor stem of tRNA.
Identify the ribose hydroxyl to which the amino acid would be esterified. Note its proximity to ATP.

To distinguish the 3 residues of the anticodon, select 34-36b, display as ball & stick, and color CPK.
The anticodon is part of an identity element recognized by this enzyme. Anticodon bases are splayed in different directions, due to adjacent modified bases promoting interactions with the protein.
Question: Are identity elements expected to be touching the enzyme?

Now select all and display spacefill.
Separately select HOH and select display as wireframe to eliminate waters.
Note how amino acid residues interdigitate with the anticodon bases.
 

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