Examples of the direct and indirect stabilization of a TJ arrangement. (A,B) The C-loop motif as an example of a directly stabilized TJ. The tertiary structure (A) and schematic representation (B) of the C-loop motif 2AW4-389, originally defined as 16S C-15 (Lescoute et al. 2005). The motif is extracted from the structure of the E. coli 16S rRNA (PDB 2AW4). For depicting the scheme of internucleotide H-bonding, we use the standard annotation of noncanonical base pairs (Leontis and Westhof 2001). The curved lines show backbone connectivity. (C) An example of indirect TJ stabilization observed in arrangement 2AVY-44. The over-twist between base pairs [+1P;+1R] (black) and [0P; 0Q] (white) is stabilized due to the immediate connection of nucleotides 0R and 0Q to adenosine A397 (gray). The position of A397 is fixed through base-pairing with U37, which comes from another part of the structure.
