Equivalence class NR_3.5_35054.4 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3IGI|1|A (rep) | 5'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-3', Group IIC intron | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-ray diffraction | 3.12 | 389 | 2009-12-22 | ||||
| 2 | 5J02|1|A | Group II catalytic intron D1-D4-1 | 5' EXON ANALOG (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3'), GROUP II INTRON LARIAT | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon. | X-ray diffraction | 3.49 | 414 | 2016-12-14 |
| 3 | 4FAX|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+ | X-ray diffraction | 3.1 | 392 | 2012-11-14 |
| 4 | 4FAR|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon | X-ray diffraction | 2.86 | 390 | 2012-11-14 |
| 5 | 4E8N|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+ | X-ray diffraction | 2.96 | 393 | 2012-11-14 |
| 6 | 6T3S|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon | X-ray diffraction | 3.28 | 393 | 2020-05-13 |
| 7 | 4FAU|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon | X-ray diffraction | 2.87 | 393 | 2012-11-14 |
| 8 | 4FB0|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+ | X-ray diffraction | 3.22 | 393 | 2012-11-14 |
| 9 | 4E8K|1|A | Group II catalytic intron D1-D4-1 | 5'-R(*CP*G*AP*UP*UP*UP*AP*UP*UP*A)-3', Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate | X-ray diffraction | 3.03 | 388 | 2012-11-14 |
| 10 | 4E8Q|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+ | X-ray diffraction | 2.84 | 393 | 2012-11-14 |
| 11 | 4Y1O|1|A | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 | X-ray diffraction | 2.95 | 258 | 2015-10-14 |
| 12 | 4Y1O|1|B | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 | X-ray diffraction | 2.95 | 256 | 2015-10-14 |
| 13 | 6T3N|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon | X-ray diffraction | 3.22 | 394 | 2020-05-13 |
| 14 | 4E8P|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+ | X-ray diffraction | 3.28 | 393 | 2012-11-14 |
| 15 | 4E8T|1|A | Group II catalytic intron D1-D4-1 | 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3', Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset) | X-ray diffraction | 3.34 | 388 | 2012-11-14 |
| 16 | 5J01|1|A | Group II catalytic intron D1-D4-1 | group II intron lariat | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+. | X-ray diffraction | 3.39 | 414 | 2016-12-14 |
| 17 | 4FAW|1|A | Group II catalytic intron D1-D4-1 | 5'-R(*A*UP*UP*UP*AP*UP*UP*A)-3', Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragment | X-ray diffraction | 2.7 | 390 | 2012-11-14 |
| 18 | 3EOH|1|A | 5'-R(*UP*UP*AP*UP*UP*A)-3', Group IIC intron | Refined group II intron structure | X-ray diffraction | 3.12 | 381 | 2008-10-28 | ||||
| 19 | 4FAQ|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exon | X-ray diffraction | 3.11 | 396 | 2012-11-14 |
| 20 | 4E8R|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+ | X-ray diffraction | 3.36 | 393 | 2012-11-14 |
| 21 | 4Y1N|1|B | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-ray diffraction | 3 | 259 | 2015-10-14 |
| 22 | 3G78|1|A | Group II catalytic intron D1-D4-1 | Group II intron, Ligated EXON product | Oceanobacillus iheyensis | Bacteria | RF01998 | Insight into group II intron catalysis from revised crystal structure | X-ray diffraction | 2.8 | 389 | 2010-02-16 |
| 23 | 4E8M|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+ | X-ray diffraction | 3.5 | 394 | 2012-11-14 |
| 24 | 6T3K|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon | X-ray diffraction | 3.44 | 390 | 2020-05-13 |
| 25 | 4Y1N|1|A | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-ray diffraction | 3 | 249 | 2015-10-14 |
| 26 | 3EOG|1|A | 5'-R(*UP*UP*AP*UP*UP*A)-3', Group IIC intron | Co-crystallization showing exon recognition by a group II intron | X-ray diffraction | 3.39 | 388 | 2008-10-28 | ||||
| 27 | 3BWP|1|A | Group IIC intron | Crystal structure of a self-spliced group II intron | X-ray diffraction | 3.1 | 356 | 2008-04-15 |
Release history
| Release | 3.127 | 3.128 | 3.129 | 3.130 | 3.131 | 3.132 | 3.133 | 3.134 | 3.135 | 3.136 | 3.137 | 3.138 | 3.139 | 3.140 | 3.141 | 3.142 | 3.143 | 3.144 | 3.145 | 3.146 | 3.147 | 3.148 | 3.149 | 3.150 | 3.151 | 3.152 | 3.153 | 3.154 | 3.155 | 3.156 | 3.157 | 3.158 | 3.159 | 3.160 | 3.161 | 3.162 | 3.163 | 3.164 | 3.165 | 3.166 | 3.167 | 3.168 | 3.169 | 3.170 | 3.171 | 3.172 | 3.173 | 3.174 | 3.175 | 3.176 | 3.177 | 3.178 | 3.179 | 3.180 | 3.181 | 3.182 | 3.183 | 3.184 | 3.185 | 3.186 | 3.187 | 3.188 | 3.189 | 3.190 | 3.191 | 3.192 | 3.193 | 3.194 | 3.195 | 3.196 | 3.197 | 3.198 | 3.199 | 3.200 | 3.201 | 3.202 | 3.203 | 3.204 | 3.205 | 3.206 | 3.207 | 3.208 | 3.209 | 3.210 | 3.211 | 3.212 | 3.213 | 3.214 | 3.215 | 3.216 | 3.217 | 3.218 | 3.219 | 3.220 | 3.221 | 3.222 | 3.223 | 3.224 | 3.225 | 3.226 | 3.227 | 3.228 | 3.229 | 3.230 | 3.231 | 3.232 | 3.233 | 3.234 | 3.235 | 3.236 | 3.237 | 3.238 | 3.239 | 3.240 | 3.241 | 3.242 | 3.243 | 3.244 | 3.245 | 3.246 | 3.247 | 3.248 | 3.249 | 3.250 | 3.251 | 3.252 | 3.253 | 3.254 | 3.255 | 3.256 | 3.257 | 3.258 | 3.259 | 3.260 | 3.261 | 3.262 | 3.263 | 3.264 | 3.265 | 3.266 | 3.267 | 3.268 | 3.269 | 3.270 | 3.271 | 3.272 | 3.273 | 3.274 | 3.275 | 3.276 | 3.277 | 3.278 | 3.279 | 3.280 | 3.281 | 3.282 | 3.283 | 3.284 | 3.285 | 3.286 | 3.287 | 3.288 | 3.289 | 3.290 | 3.291 | 3.292 | 3.293 | 3.294 | 3.295 | 3.296 | 3.297 | 3.298 | 3.299 | 3.300 | 3.301 | 3.302 | 3.303 | 3.304 | 3.305 | 3.306 | 3.307 | 3.308 | 3.309 | 3.310 | 3.311 | 3.312 | 3.313 | 3.314 | 3.315 | 3.316 | 3.317 | 3.318 | 3.319 | 3.320 | 3.321 | 3.322 | 3.323 | 3.324 | 3.325 | 3.326 | 3.327 | 3.328 | 3.329 | 3.330 | 3.331 | 3.332 | 3.333 | 3.334 | 3.335 | 3.336 | 3.337 | 3.338 | 3.339 |
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| Date | 2020-05-20 | 2020-05-27 | 2020-06-03 | 2020-06-10 | 2020-06-17 | 2020-06-24 | 2020-07-01 | 2020-07-08 | 2020-07-15 | 2020-07-22 | 2020-07-29 | 2020-08-05 | 2020-08-12 | 2020-08-19 | 2020-08-26 | 2020-09-02 | 2020-09-09 | 2020-09-16 | 2020-09-23 | 2020-09-30 | 2020-10-07 | 2020-10-14 | 2020-10-21 | 2020-10-28 | 2020-11-04 | 2020-11-11 | 2020-11-18 | 2020-11-25 | 2020-12-02 | 2020-12-09 | 2020-12-16 | 2020-12-23 | 2020-12-30 | 2021-01-06 | 2021-01-13 | 2021-01-20 | 2021-01-27 | 2021-02-03 | 2021-02-10 | 2021-02-17 | 2021-02-24 | 2021-03-03 | 2021-03-10 | 2021-03-17 | 2021-03-24 | 2021-03-31 | 2021-04-07 | 2021-04-14 | 2021-04-21 | 2021-04-28 | 2021-05-05 | 2021-05-12 | 2021-05-19 | 2021-05-26 | 2021-06-02 | 2021-06-09 | 2021-06-16 | 2021-06-23 | 2021-06-30 | 2021-07-07 | 2021-07-14 | 2021-07-21 | 2021-07-28 | 2021-08-04 | 2021-08-11 | 2021-08-18 | 2021-08-25 | 2021-09-01 | 2021-09-08 | 2021-09-15 | 2021-09-22 | 2021-09-29 | 2021-10-06 | 2021-10-13 | 2021-10-20 | 2021-10-27 | 2021-11-03 | 2021-11-10 | 2021-11-17 | 2021-11-24 | 2021-12-01 | 2021-12-08 | 2021-12-15 | 2021-12-22 | 2021-12-29 | 2022-01-05 | 2022-01-12 | 2022-01-19 | 2022-01-26 | 2022-02-02 | 2022-02-09 | 2022-02-16 | 2022-02-23 | 2022-03-02 | 2022-03-09 | 2022-03-16 | 2022-03-23 | 2022-03-30 | 2022-04-06 | 2022-04-13 | 2022-04-20 | 2022-04-27 | 2022-05-04 | 2022-05-11 | 2022-05-18 | 2022-05-25 | 2022-06-01 | 2022-06-08 | 2022-06-15 | 2022-06-22 | 2022-06-29 | 2022-07-06 | 2022-07-13 | 2022-07-20 | 2022-07-27 | 2022-08-03 | 2022-08-10 | 2022-08-17 | 2022-08-24 | 2022-08-31 | 2022-09-07 | 2022-09-14 | 2022-09-21 | 2022-09-28 | 2022-10-05 | 2022-10-12 | 2022-10-19 | 2022-10-26 | 2022-11-02 | 2022-11-09 | 2022-11-16 | 2022-11-23 | 2022-11-30 | 2022-12-07 | 2022-12-14 | 2022-12-21 | 2022-12-28 | 2023-01-04 | 2023-01-11 | 2023-01-18 | 2023-01-25 | 2023-02-01 | 2023-02-08 | 2023-02-15 | 2023-02-22 | 2023-03-01 | 2023-03-08 | 2023-03-15 | 2023-03-22 | 2023-03-29 | 2023-04-05 | 2023-04-12 | 2023-04-19 | 2023-04-26 | 2023-05-03 | 2023-05-10 | 2023-05-17 | 2023-05-24 | 2023-05-31 | 2023-06-07 | 2023-06-14 | 2023-06-21 | 2023-06-28 | 2023-07-05 | 2023-07-12 | 2023-07-19 | 2023-07-26 | 2023-08-02 | 2023-08-09 | 2023-08-16 | 2023-08-23 | 2023-08-30 | 2023-09-06 | 2023-09-13 | 2023-09-20 | 2023-09-27 | 2023-10-04 | 2023-10-11 | 2023-10-18 | 2023-10-25 | 2023-11-01 | 2023-11-08 | 2023-11-15 | 2023-11-24 | 2023-11-29 | 2023-12-06 | 2023-12-13 | 2023-12-20 | 2023-12-27 | 2024-01-03 | 2024-01-10 | 2024-01-17 | 2024-01-24 | 2024-01-31 | 2024-02-07 | 2024-02-14 | 2024-02-21 | 2024-02-28 | 2024-03-06 | 2024-03-13 | 2024-03-20 | 2024-03-27 | 2024-04-03 | 2024-04-10 | 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 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_35054.4 | NR_3.5_35054.3 | 3.127 | (24) 3BWP|1|A, 3EOG|1|A, 3EOH|1|A, 3G78|1|A, 3IGI|1|A, 4E8K|1|A, 4E8M|1|A, 4E8N|1|A, 4E8P|1|A, 4E8Q|1|A, 4E8R|1|A, 4E8T|1|A, 4FAQ|1|A, 4FAR|1|A, 4FAU|1|A, 4FAW|1|A, 4FAX|1|A, 4FB0|1|A, 4Y1N|1|A, 4Y1N|1|B, 4Y1O|1|A, 4Y1O|1|B, 5J01|1|A, 5J02|1|A | (3) 6T3K|1|A, 6T3N|1|A, 6T3S|1|A | (0) |
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 | 5J01|1|A | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+. | X-RAY DIFFRACTION | 3.39 | 414 | |
| 2 | 5J02|1|A | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon. | X-RAY DIFFRACTION | 3.49 | 414 | |
| 3 | 6T3N|1|A | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.22 | 394 | |
| 4 | 6T3S|1|A | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.28 | 393 | |
| 5 | 4FAX|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+ | X-RAY DIFFRACTION | 3.1 | 392 | |
| 6 | 4E8R|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+ | X-RAY DIFFRACTION | 3.36 | 393 | |
| 7 | 4E8P|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+ | X-RAY DIFFRACTION | 3.28 | 393 | |
| 8 | 4E8Q|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+ | X-RAY DIFFRACTION | 2.84 | 393 | |
| 9 | 4E8N|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+ | X-RAY DIFFRACTION | 2.96 | 393 | |
| 10 | 4FB0|1|A | Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+ | X-RAY DIFFRACTION | 3.22 | 393 | |
| 11 | 4E8M|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+ | X-RAY DIFFRACTION | 3.5 | 394 | |
| 12 | 4FAW|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragment | X-RAY DIFFRACTION | 2.7 | 390 | |
| 13 | 4FAU|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 2.87 | 393 | |
| 14 | 4FAR|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 2.86 | 390 | |
| 15 | 6T3K|1|A | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.44 | 390 | |
| 16 | 4FAQ|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exon | X-RAY DIFFRACTION | 3.11 | 396 | |
| 17 | 4E8K|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate | X-RAY DIFFRACTION | 3.03 | 388 | |
| 18 | 4E8T|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset) | X-RAY DIFFRACTION | 3.34 | 388 | |
| 19 | 3IGI|1|A | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-RAY DIFFRACTION | 3.12 | 389 | |
| 20 | 3G78|1|A | Insight into group II intron catalysis from revised crystal structure | X-RAY DIFFRACTION | 2.8 | 389 | |
| 21 | 3EOH|1|A | Refined group II intron structure | X-RAY DIFFRACTION | 3.12 | 381 | |
| 22 | 3BWP|1|A | Crystal structure of a self-spliced group II intron | X-RAY DIFFRACTION | 3.1 | 356 | |
| 23 | 3EOG|1|A | Co-crystallization showing exon recognition by a group II intron | X-RAY DIFFRACTION | 3.39 | 388 | |
| 24 | 4Y1O|1|B | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 256 | |
| 25 | 4Y1N|1|A | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 249 | |
| 26 | 4Y1N|1|B | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 259 | |
| 27 | 4Y1O|1|A | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 258 |
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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