Table 2.
NGNRAG cluster analysis (Figure 3A), corresponding to the well-known GNRA tetraloop family.
| Interactions from literature found in ≥75% of structures in the database15, 31, 36, 54, 55 | Percentage of NGNRAG sequence-representative structures with interaction (n = 29)a, b | Percentage of all other tetraloop sequence-representative structures with interaction |
|---|---|---|
| All nucleotides have an anti glycosidic angle | nt 1 – 100% anti | nt 1 – 100% anti |
| nt 2 – 100% anti | nt 2 – 98% anti | |
| nt 3 – 100% anti | nt 3 – 88% anti | |
| nt 4 – 100% anti | nt 4 – 88% anti | |
| nt 5 – 100% anti | nt 5 – 79% anti | |
| nt 6 – 100% anti | nt 6 – 100% anti | |
| Base pairing between nt 1 and nt 6 | 100% | 98% |
| Base pairing between nt 2 and nt 5 | 100% | 29% |
| Hydrogen bond between N2 of nt 2 and N7 of nt 5 | 79% | 5% |
| All nucleotides have a majority of C3’-endo sugar pucker conformation | nt 1 – 97% C3’-endo | |
| nt 2 – 97% C3’-endo | nt 1 – 95% C3’-endo | |
| nt 3 – 93% C3’-endo | nt 2 – 71% C3’-endo | |
| nt 4 – 93% C3’-endo | nt 3 – 33% C3’-endo | |
| nt 5 – 93% C3’-endo | nt 4 – 36% C3’-endo | |
| nt 6 – 90% C3’-endo | nt 5 – 41% C3’-endo | |
| nt 6 – 93% C3’-endo | ||
| Stacking between nt 3 and nt 4 | 100% | 31% |
| Stacking between nt 4 and nt 5 | 97% | 29% |
| Hydrogen bond between O2’ (hydroxyl) of nt 2 and N7 of nt 4 | 86% | 2% |
| Hydrogen bond between N2 of nt 2 and OP2 of nt 5 | 83% | 5% |
| Interactions from literature not found in ≥75% of structures in the database | ||
| Hydrogen bond between N3 of nt 2 and N6 of nt 5 | 10% | 5% |
| Stacking between nt 2 and nt 6 | 69% | 17% |
| New interactions identified | ||
| Stacking between nt 1 and nt 2 | 90% | 67% |
a
n = number of sequence-representative structures in this cluster.
b
Red values indicate interactions that are found among ≥75% of sequence-representative structures in this cluster and <75% of structures among all other tetraloops.