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Sequence, Chains, Asymmetric and Biological Units

Title STRUCTURE OF THE TETRAHYMENA RIBOZYME: BASE TRIPLE SANDWICH AND METAL ION AT THE ACTIVE SITE
Keywords CATALYTIC RNA, RIBOZYME, GROUP I INTRON, CRYSTAL STRUCTURE, GUANOSINE BINDING SITE, METAL IONS, ACTIVE SITE, CATALYTIC MECHANISM, BASE TRIPLES, CONFORMATIONAL CHANGES
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   1X8W     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  RNA    A 242 5189 0
2  RNA    B 247 5294 0
3  RNA    C 237 5082 0
4  RNA    D 242 5189 0
5  Ligand   TETRAHYMENA RIBOZYME RNA  C 1 0 1
6  Ligand   TETRAHYMENA RIBOZYME RNA  B 1 0 1
7  Ligand   TETRAHYMENA RIBOZYME RNA  A 1 0 1
8  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
9  Ligand   TETRAHYMENA RIBOZYME RNA  B 2 0 2
10  Ligand   TETRAHYMENA RIBOZYME RNA  C 1 0 1
11  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
12  Ligand   TETRAHYMENA RIBOZYME RNA  A 1 0 1
13  Ligand   TETRAHYMENA RIBOZYME RNA  C 1 0 1
14  Ligand   TETRAHYMENA RIBOZYME RNA  A 1 0 1
15  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
16  Ligand   TETRAHYMENA RIBOZYME RNA  B 1 0 1
17  Ligand   TETRAHYMENA RIBOZYME RNA  A 1 0 1
18  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
19  Ligand   TETRAHYMENA RIBOZYME RNA  B 1 0 1
20  Ligand   TETRAHYMENA RIBOZYME RNA  A 1 0 1
21  Ligand   TETRAHYMENA RIBOZYME RNA  C 1 0 1
22  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
23  Ligand   TETRAHYMENA RIBOZYME RNA  C 1 0 1
24  Ligand   TETRAHYMENA RIBOZYME RNA  B 1 0 1
25  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
26  Ligand   TETRAHYMENA RIBOZYME RNA  A 2 0 2
27  Ligand   TETRAHYMENA RIBOZYME RNA  B 1 0 1
28  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
29  Ligand   TETRAHYMENA RIBOZYME RNA  B 1 0 1
30  Ligand   TETRAHYMENA RIBOZYME RNA  C 1 0 1
31  Ligand   TETRAHYMENA RIBOZYME RNA  A 1 0 1
32  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
33  Ligand   TETRAHYMENA RIBOZYME RNA  B 1 0 1
34  Ligand   TETRAHYMENA RIBOZYME RNA  C 2 0 2
35  Ligand   TETRAHYMENA RIBOZYME RNA  A 1 0 1
36  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
37  Ligand   TETRAHYMENA RIBOZYME RNA  A 1 0 1
38  Ligand   TETRAHYMENA RIBOZYME RNA  D 1 0 1
39  Ligand   TETRAHYMENA RIBOZYME RNA  C 1 0 1
total       1006 20754 38
Nucleic acids
Unit 1 G96 A97 C98 C99 G100 U101 C102 A103 A104 A105 U106 U107 G108 C109 G110 G111 G112 A113 A114 A115 G116 G117 G118 G119 U120 C121 A122 A123 C124 A125 G126 C127 C128 G129 U130 U131 C132 A133 G134 U135 A136 C137 C138 A139 A140 G141 U142 C143 U144 C145 A146 G147 G148 G149 G150 A151 A152 A153 C154 U155 U156 U157 G158 A159 G160 A161 U162 G163 G164 C165 C166 U167 U168 G169 C170 A171 A172 A173 G174 G175 G176 U177 A178 U179 G180 G181 U182 A183 A184 U185 A186 A187 G188 C189 U190 G191 A192 C193 G194 G195 A196 C197 A198 U199 G200 G201 U202 C203 C204 U205 A206 A207 C208 C209 G210 C211 G212 C213 A214 G215 C216 C217 A218 A219 G220 U221 C222 C223 U224 A225 A226 G227 U228 C229 A230 A231 C232 A233 G234 G235 A236 G237 A238 C240 U241 G242 U243 U244 G245 A246 U247 A248 U249 G250 G251 A252 U253 G254 C255 A256 G257 U258 A259 C260 A261 C262 A263 G264 A265 C266 U267 A268 G269 A270 U271 G272 U273 C274 G275 G276 C277 C278 G279 G280 G281 G282 A283 A284 G285 A286 U292 C293 U294 U295 C296 U297 C298 A299 U300 A301 A302 G303 G304 U305 A306 U307 A308 G309 U310 C311 G312 G313 A314 C315 C316 U317 C318 U319 C320 C321 C322 G323 A324 A325 A326 G327 G328 G329 A330 G331 U403 U404 G405 G406 A407 G408 U409 A410 C411 U412 C413 G414
Unit 2 G96 A97 C98 C99 G100 U101 C102 A103 A104 A105 U106 U107 G108 C109 G110 G111 G112 A113 A114 A115 G116 G117 G118 G119 U120 C121 A122 A123 C124 A125 G126 C127 C128 G129 U130 U131 C132 A133 G134 U135 A136 C137 C138 A139 A140 G141 U142 C143 U144 C145 A146 G147 G148 G149 G150 A151 A152 A153 C154 U155 U156 U157 G158 A159 G160 A161 U162 G163 G164 C165 C166 U167 U168 G169 C170 A171 A172 A173 G174 G175 G176 U177 A178 U179 G180 G181 U182 A183 A184 U185 A186 A187 G188 C189 U190 G191 A192 C193 G194 G195 A196 C197 A198 U199 G200 G201 U202 C203 C204 U205 A206 A207 C208 C209 G210 C211 G212 C213 A214 G215 C216 C217 A218 A219 G220 U221 C222 C223 U224 A225 A226 G227 U228 C229 A230 A231 C232 A233 G234 G235 A236 G237 A238 C240 U241 G242 U243 U244 G245 A246 U247 A248 U249 G250 G251 A252 U253 G254 C255 A256 G257 U258 A259 C260 A261 C262 A263 G264 A265 C266 U267 A268 G269 A270 U271 G272 U273 C274 G275 G276 C277 C278 G279 G280 G281 G282 A283 A284 G285 A286 U287 G288 U289 A290 U291 U292 C293 U294 U295 C296 U297 C298 A299 U300 A301 A302 G303 G304 U305 A306 U307 A308 G309 U310 C311 G312 G313 A314 C315 C316 U317 C318 U319 C320 C321 C322 G323 A324 A325 A326 G327 G328 G329 A330 G331 U403 U404 G405 G406 A407 G408 U409 A410 C411 U412 C413 G414
Unit 3 G96 A97 C98 C99 G100 U101 C102 A103 A104 A105 U106 U107 G108 C109 G110 G111 G112 A113 A114 A115 G116 G117 G118 G119 U120 C121 A122 A123 C124 A125 G126 C127 C128 G129 U130 U131 C132 A133 G134 U135 A136 C137 C138 A139 A140 G141 U142 C143 U144 C145 A146 G147 G148 G149 G150 A151 A152 A153 C154 U155 U156 U157 G158 A159 G160 A161 U162 G163 G164 C165 C166 U167 U168 G169 C170 A171 A172 A173 G174 G175 G176 U177 A178 U179 G180 G181 U182 A183 A184 U185 A186 A187 G188 C189 U190 G191 A192 C193 G194 G195 A196 C197 A198 U199 G200 G201 U202 C203 C204 U205 A206 A207 C208 C209 G210 C211 G212 C213 A214 G215 C216 C217 A218 A219 G220 U221 C222 C223 U224 A225 A226 G227 U228 C229 A230 A231 C232 A233 G234 G235 A236 G237 A238 C240 U241 G242 U243 U244 G245 A246 U247 A248 U249 G250 G251 A252 U253 G254 C255 A256 G257 U258 A259 C260 A261 C262 A263 G264 A265 C266 U267 A268 G269 A270 U271 G272 U273 C274 G275 G276 C277 C278 G279 G280 G281 G282 A283 A284 G285 A286 U292 C293 U294 U295 C296 U297 C298 A299 U300 A301 A302 G303 G304 U305 A306 U307 A308 G309 U310 C311 G312 G313 A314 C315 C316 U317 C318 U319 C320 C321 C322 G323 A324 A325 A326 G327 G328 G329 A330 G331 U403 U404 G405 G406 U412 C413 G414
Unit 4 G96 A97 C98 C99 G100 U101 C102 A103 A104 A105 U106 U107 G108 C109 G110 G111 G112 A113 A114 A115 G116 G117 G118 G119 U120 C121 A122 A123 C124 A125 G126 C127 C128 G129 U130 U131 C132 A133 G134 U135 A136 C137 C138 A139 A140 G141 U142 C143 U144 C145 A146 G147 G148 G149 G150 A151 A152 A153 C154 U155 U156 U157 G158 A159 G160 A161 U162 G163 G164 C165 C166 U167 U168 G169 C170 A171 A172 A173 G174 G175 G176 U177 A178 U179 G180 G181 U182 A183 A184 U185 A186 A187 G188 C189 U190 G191 A192 C193 G194 G195 A196 C197 A198 U199 G200 G201 U202 C203 C204 U205 A206 A207 C208 C209 G210 C211 G212 C213 A214 G215 C216 C217 A218 A219 G220 U221 C222 C223 U224 A225 A226 G227 U228 C229 A230 A231 C232 A233 G234 G235 A236 G237 A238 C240 U241 G242 U243 U244 G245 A246 U247 A248 U249 G250 G251 A252 U253 G254 C255 A256 G257 U258 A259 C260 A261 C262 A263 G264 A265 C266 U267 A268 G269 A270 U271 G272 U273 C274 G275 G276 C277 C278 G279 G280 G281 G282 A283 A284 G285 A286 U292 C293 U294 U295 C296 U297 C298 A299 U300 A301 A302 G303 G304 U305 A306 U307 A308 G309 U310 C311 G312 G313 A314 C315 C316 U317 C318 U319 C320 C321 C322 G323 A324 A325 A326 G327 G328 G329 A330 G331 U403 U404 G405 G406 A407 G408 U409 A410 C411 U412 C413 G414
Ligands
Unit 5 MG1
Unit 6 MG2
Unit 7 MG3
Unit 8 MG4
Unit 9 MG5 MG6
Unit 10 MG7
Unit 11 MG8
Unit 12 MG9
Unit 13 MG10
Unit 14 MG11
Unit 15 MG12
Unit 16 MG13
Unit 17 MG14
Unit 18 MG15
Unit 19 MG16
Unit 20 MG17
Unit 21 MG18
Unit 22 MG19
Unit 23 MG20
Unit 24 MG21
Unit 25 MG22
Unit 26 MG1 MG2
Unit 27 MG3
Unit 28 MG415
Unit 29 MG415
Unit 30 MG6
Unit 31 MG7
Unit 32 MG416
Unit 33 MG9
Unit 34 MG11 MG415
Unit 35 MG12
Unit 36 MG13
Unit 37 MG415
Unit 38 MG417
Unit 39 MG16
Chirality of ribose and phosphate atoms

Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany