Kink-turn Worked Example
Stage 1 retrieves candidates by tandem non-Watson-Crick topology; Stage 2 applies the motif-specific sheared G.A geometry criteria. Graph matches are candidates, not confirmed kink-turns.
Geometry-confirmed Representatives
| PDB | Context | Sheared G.A pairs | Loop nucleotides | Structure |
|---|---|---|---|---|
| 2GIS | SAM-I riboswitch kink-turn (anchor; Montange & Batey 2006) | A18-A37, A19-A36, A20-A35 | A17,A38,A18,A19,A20,A21,A31,A32,A33,A34,A35,A36,A37 | PDB |
| 1E7K | U4 snRNA kink-turn bound to 15.5K protein (Vidovic et al. 2000) | D32-D44, D33-D43 | D34,D42,D28,D29,D30,D31,D32,D33,D43,D44,D45 | PDB |
| 4BW0 | HMKt-7 kink-turn bound by L7Ae protein (Huang & Lilley 2013) | A4-A22, A5-A21, A6-A20 | A3,A23,A16,A17,A18,A19,A20,A21,A22,A4,A5,A6,A7 | PDB |
| 2OZB | U4 snRNA kink-turn within the human Prp31-15.5K-U4 snRNA complex (Liu et al. 2007) | F32-F44, F33-F43 | F34,F42,F28,F29,F30,F31,F32,F33,F43,F44,F45 | PDB |