Equivalence class NR_2.5_16232.4 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 8VAW|1|A+ 8VAW|1|B (rep) | Magnesium catalyzed nonenzymatic RNA primer extension product | synthetic construct | Magnesium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer | X-ray diffraction | 1.25 | 30 | 2024-04-17 | |||
| 2 | 8VAX|1|AAA+ 8VAX|1|BBB | Cadmium catalyzed nonenzymatic RNA primer extension product | synthetic construct | Cadmium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer | X-ray diffraction | 1.417 | 30 | 2024-04-17 | |||
| 3 | 5L00|1|A+ 5L00|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | synthetic construct | Self-complimentary RNA 15mer binding with GMP monomers | X-ray diffraction | 1.25 | 30 | 2016-12-07 | |||
| 4 | 5L00|1|C+ 5L00|1|D | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | synthetic construct | Self-complimentary RNA 15mer binding with GMP monomers | X-ray diffraction | 1.25 | 30 | 2016-12-07 | |||
| 5 | 5KRG|1|C+ 5KRG|1|D | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | synthetic construct | RNA 15mer duplex binding with PZG monomer | X-ray diffraction | 1.6 | 30 | 2016-12-07 | |||
| 6 | 5KRG|1|A+ 5KRG|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | synthetic construct | RNA 15mer duplex binding with PZG monomer | X-ray diffraction | 1.6 | 30 | 2016-12-07 | |||
| 7 | 7U87|1|A+ 7U87|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(G46)P*(G46))-3') | synthetic construct | Product of 13mer primer with activated G monomer diastereomer 1 | X-ray diffraction | 1.701 | 30 | 2023-03-15 | |||
| 8 | 6U6J|1|A+ 6U6J|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(DPG))-3') | synthetic construct | RNA-monomer complex containing pyrophosphate linkage | X-ray diffraction | 1.6 | 30 | 2019-11-20 | |||
| 9 | 6C8O|1|A+ 6C8O|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | synthetic construct | RNA-activated 2-AIpG monomer, 3h soaking | X-ray diffraction | 1.85 | 30 | 2018-05-30 | |||
| 10 | 5V0H|1|A+ 5V0H|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | synthetic construct | RNA duplex with 2-MeImpG analogue bound-one binding site | X-ray diffraction | 1.9 | 30 | 2017-03-08 | |||
| 11 | 7U89|1|A+ 7U89|1|B | RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*(G46))-3') | synthetic construct | Product of 14mer primer with activated G monomer diastereomer 1 | X-ray diffraction | 1.65 | 30 | 2023-03-15 | |||
| 12 | 6C8N|1|A+ 6C8N|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | synthetic construct | RNA-activated 2-AIpG monomer complex, 2h soaking | X-ray diffraction | 1.9 | 30 | 2018-05-30 | |||
| 13 | 7U8A|1|A+ 7U8A|1|B | RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*(G46))-3') | synthetic construct | Product of 14mer primer with activated G monomer diastereomer 2 | X-ray diffraction | 2.1 | 30 | 2023-03-15 | |||
| 14 | 6C8M|1|A+ 6C8M|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3'), RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | synthetic construct | RNA-activated 2-AIpG monomer, 1.5h soaking | X-ray diffraction | 2.4 | 29 | 2018-05-30 | |||
| 15 | 7U88|1|A+ 7U88|1|B | RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(G46)P*(G46))-3') | synthetic construct | Product of 13mer primer with activated G monomer diastereomer 2 | X-ray diffraction | 2.14 | 30 | 2023-03-15 |
Release history
| Release | 3.331 | 3.332 | 3.333 | 3.334 | 3.335 | 3.336 | 3.337 | 3.338 | 3.339 | 3.340 | 3.341 | 3.342 | 3.343 | 3.344 | 3.345 | 3.346 | 3.347 | 3.348 | 3.349 | 3.350 | 3.351 | 3.352 | 3.353 | 3.354 | 3.355 | 3.356 | 3.357 | 3.358 | 3.359 | 3.360 | 3.361 | 3.362 | 3.363 | 3.364 | 3.365 | 3.366 | 3.367 | 3.368 | 3.369 | 3.370 | 3.371 | 3.372 | 3.373 | 3.374 | 3.375 | 3.376 | 3.377 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2024-04-17 | 2024-04-24 | 2024-05-01 | 2024-05-08 | 2024-05-15 | 2024-05-22 | 2024-05-29 | 2024-06-05 | 2024-06-12 | 2024-06-19 | 2024-06-26 | 2024-07-03 | 2024-07-10 | 2024-07-17 | 2024-07-25 | 2024-07-31 | 2024-08-07 | 2024-08-14 | 2024-08-21 | 2024-08-28 | 2024-09-04 | 2024-09-11 | 2024-09-18 | 2024-09-25 | 2024-10-02 | 2024-10-09 | 2024-10-16 | 2024-10-23 | 2024-10-30 | 2024-11-06 | 2024-11-13 | 2024-11-20 | 2024-11-27 | 2024-12-04 | 2024-12-11 | 2024-12-18 | 2024-12-25 | 2025-01-01 | 2025-01-08 | 2025-01-15 | 2025-01-22 | 2025-01-29 | 2025-02-05 | 2025-02-12 | 2025-02-19 | 2025-02-26 | 2025-03-05 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.
| #S | View | PDB | Title | Method | Resolution | #NTs |
|---|---|---|---|---|---|---|
| 1 | 5KRG|1|A+ 5KRG|1|B | RNA 15mer duplex binding with PZG monomer | X-RAY DIFFRACTION | 1.6 | 30 | |
| 2 | 5KRG|1|C+ 5KRG|1|D | RNA 15mer duplex binding with PZG monomer | X-RAY DIFFRACTION | 1.6 | 30 | |
| 3 | 6U6J|1|A+ 6U6J|1|B | RNA-monomer complex containing pyrophosphate linkage | X-RAY DIFFRACTION | 1.6 | 30 | |
| 4 | 5L00|1|A+ 5L00|1|B | Self-complimentary RNA 15mer binding with GMP monomers | X-RAY DIFFRACTION | 1.25 | 30 | |
| 5 | 5L00|1|C+ 5L00|1|D | Self-complimentary RNA 15mer binding with GMP monomers | X-RAY DIFFRACTION | 1.25 | 30 | |
| 6 | 7U89|1|A+ 7U89|1|B | Product of 14mer primer with activated G monomer diastereomer 1 | X-RAY DIFFRACTION | 1.65 | 30 | |
| 7 | 7U88|1|A+ 7U88|1|B | Product of 13mer primer with activated G monomer diastereomer 2 | X-RAY DIFFRACTION | 2.14 | 30 | |
| 8 | 5V0H|1|A+ 5V0H|1|B | RNA duplex with 2-MeImpG analogue bound-one binding site | X-RAY DIFFRACTION | 1.9 | 30 | |
| 9 | 7U87|1|A+ 7U87|1|B | Product of 13mer primer with activated G monomer diastereomer 1 | X-RAY DIFFRACTION | 1.701 | 30 | |
| 10 | 7U8A|1|A+ 7U8A|1|B | Product of 14mer primer with activated G monomer diastereomer 2 | X-RAY DIFFRACTION | 2.1 | 30 | |
| 11 | 8VAX|1|AAA+ 8VAX|1|BBB | Cadmium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer | X-RAY DIFFRACTION | 1.417 | 30 | |
| 12 | 8VAW|1|A+ 8VAW|1|B | Magnesium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer | X-RAY DIFFRACTION | 1.25 | 30 | |
| 13 | 6C8O|1|A+ 6C8O|1|B | RNA-activated 2-AIpG monomer, 3h soaking | X-RAY DIFFRACTION | 1.85 | 30 | |
| 14 | 6C8N|1|A+ 6C8N|1|B | RNA-activated 2-AIpG monomer complex, 2h soaking | X-RAY DIFFRACTION | 1.9 | 30 | |
| 15 | 6C8M|1|A+ 6C8M|1|B | RNA-activated 2-AIpG monomer, 1.5h soaking | X-RAY DIFFRACTION | 2.4 | 29 |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.
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