Figure 5.

The model of the structure of the DT region for clone K31 (red) superimposed on the corresponding region in yeast tRNA^Phe (green). The figure also includes the T-stem and the tertiary base pair 15-48. For both tRNAs, the ribbon follows the sugar–phosphate backbone. Explicitly shown are base pairs 15-48 and 54-58 and nucleotide 59 in tRNA^Phe, as well as all nucleotides of the DT region and pair 15-48 in K31. Comparison of the modeled structure with tRNA^Phe demonstrates a good superposition of the T-stem and base pairs RH and 15-48, as well as nucleotide 59. The proper arrangements of the nucleotides in the RH base pair thus guarantees the proper position of nucleotide 59, whose stacking to base pair 15-48 would fix the juxtaposition of the two helical domains known as the L-form. Still, one can notice a difference in the conformation of the backbone in the two structures, which is highest between nucleotides 58 and 59. Such a difference makes a universal interaction of this region with a particular protein factor unlikely.