Figure 3. Example of a tRNA where stacking between two non-collinear stems occurs (PDB id 4WJ4 ³²).

Green cylinders were fitted to stems, blue cylinders represent hairpins and the pink cylinder the unpaired nucleotides at the 3’ end. Red cylinders connect stems and indicate single-stranded connections between these stems (multi loop segments). Left: The stems of the anticodon arm (top) and the D-arm stack (according to DSSR) despite being at an angle of 143°. Right: View along the axis of the anticodon arm’s stem. The red nucleotide is the unpaired multi loop segment which mediates stacking to the stem of the D-arm. This illustration was generated using PyMol ³³ via the visualize_rna.py wrapper in forgi.