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. 2008 Nov 26;37(1):215–230. doi: 10.1093/nar/gkn911

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© 2008 The Author(s)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Examples of typical UA_handle interactions involving the bulging nucleotides N(4.n). (A) Schematic highlighting the various bulge mediated tertiary interactions in UA_handle motifs. (B) UA_h_turn motifs: (top) Hm 23S rRNA U1116 (PDB_ID:1JJ2), (middle) Tt 23S rRNA U1621 (PDB_ID:2J01), (bottom) Hm 23S rRNA U1696 (PDB_ID:1JJ2). (C) UA_h A-minor junction motifs: (top) Tt 23S rRNA U2562 (PDB_ID:2J01), (bottom) from TPP riboswitch (PDB_ID:2GDI). (D) UA_h 3WJ motifs: (top) Ec 16S rRNA U652 (PDB_ID:2AW7), (bottom) Ec 23S rRNA U1991 (PDB_ID:2AWB). (E) UA_h_PK motifs: (top) Hm 23S rRNA U1676 (PDB_ID:1JJ2), (bottom) from Diels-alderase (PDB_ID:1YKV). (F) UAA/GAN motif: Hm 23S rRNA U1457 (PDB_ID:1JJ2). (G) UGA/gAN motif; Tt 23S rRNA U1621 (PDB_ID:2J01). (H) Nested double T-loop: Tt 23S rRNA U475 (PDB_ID:2J01). (I) T-loop motif: Hm 23S rRNA U1388 (PDB_ID:1JJ2). For each examples displayed, the type of interactions involved is indicated in the upper left corner. Conserved and semi-conserved interactions are circled with continuous or dashed lines, respectively. For annotations, see Figures 2 and S3.