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(-) Description

Title :  STRUCTURE OF OCEANOBACILLUS IHEYENSIS GROUP II INTRON IN A LIGAND-FREE STATE IN THE PRESENCE OF RB+ AND MG2+
 
Authors :  M. Marcia, A. M. Pyle
Date :  20 Mar 12  (Deposition) - 14 Nov 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.28
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribozyme, Metalloenzymes, Self-Splicing, Retrotransposition, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Marcia, A. M. Pyle
Visualizing Group Ii Intron Catalysis Through The Stages Of Splicing.
Cell(Cambridge, Mass. ) V. 151 497 2012
PubMed-ID: 23101623  |  Reference-DOI: 10.1016/J.CELL.2012.09.033

(-) Compounds

Molecule 1 - GROUP IIC INTRON
    ChainsA
    EngineeredYES
    FragmentDOMAINS 1-5
    Organism ScientificOCEANOBACILLUS IHEYENSIS
    Organism Taxid182710
    Other DetailsIN VITRO TRANSCRIPTION
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 52)

Asymmetric/Biological Unit (4, 52)
No.NameCountTypeFull Name
1EPE6Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2MG27Ligand/IonMAGNESIUM ION
3RB18Ligand/IonRUBIDIUM ION
4SPM1Ligand/IonSPERMINE

(-) Sites  (51, 51)

Asymmetric Unit (51, 51)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREC A:286 , A A:287BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWAREU A:375 , C A:377 , HOH A:924BINDING SITE FOR RESIDUE MG A 402
03AC3SOFTWAREC A:358 , G A:359 , C A:377 , RB A:428 , RB A:437 , HOH A:921 , HOH A:924BINDING SITE FOR RESIDUE MG A 403
04AC4SOFTWAREG A:3 , U A:4BINDING SITE FOR RESIDUE MG A 404
05AC5SOFTWAREA A:290 , G A:386BINDING SITE FOR RESIDUE MG A 405
06AC6SOFTWAREC A:360 , G A:373 , G A:374BINDING SITE FOR RESIDUE MG A 406
07AC7SOFTWAREG A:324 , G A:325BINDING SITE FOR RESIDUE MG A 407
08AC8SOFTWAREG A:46BINDING SITE FOR RESIDUE MG A 408
09AC9SOFTWAREC A:119 , A A:174 , U A:238 , G A:239BINDING SITE FOR RESIDUE MG A 409
10BC1SOFTWAREG A:107BINDING SITE FOR RESIDUE MG A 410
11BC2SOFTWAREU A:379 , HOH A:920BINDING SITE FOR RESIDUE MG A 411
12BC3SOFTWAREA A:105BINDING SITE FOR RESIDUE MG A 412
13BC4SOFTWAREG A:135 , G A:136BINDING SITE FOR RESIDUE MG A 413
14BC5SOFTWAREU A:66 , A A:67BINDING SITE FOR RESIDUE MG A 414
15BC6SOFTWAREG A:284BINDING SITE FOR RESIDUE MG A 415
16BC7SOFTWAREC A:6BINDING SITE FOR RESIDUE MG A 416
17BC8SOFTWAREG A:169 , G A:170BINDING SITE FOR RESIDUE MG A 417
18BC9SOFTWAREA A:184BINDING SITE FOR RESIDUE MG A 418
19CC1SOFTWAREA A:67 , G A:68BINDING SITE FOR RESIDUE MG A 419
20CC2SOFTWAREU A:285BINDING SITE FOR RESIDUE MG A 420
21CC3SOFTWAREA A:355 , A A:356BINDING SITE FOR RESIDUE MG A 421
22CC4SOFTWAREG A:288 , HOH A:915BINDING SITE FOR RESIDUE MG A 422
23CC5SOFTWAREG A:142 , A A:144 , HOH A:923BINDING SITE FOR RESIDUE MG A 423
24CC6SOFTWAREC A:372BINDING SITE FOR RESIDUE MG A 424
25CC7SOFTWAREA A:154 , G A:155 , G A:156 , G A:220 , U A:221 , HOH A:904BINDING SITE FOR RESIDUE MG A 425
26CC8SOFTWAREG A:136 , C A:145BINDING SITE FOR RESIDUE MG A 426
27CC9SOFTWAREA A:283BINDING SITE FOR RESIDUE MG A 427
28DC1SOFTWAREC A:358 , A A:376 , C A:377 , MG A:403 , RB A:437BINDING SITE FOR RESIDUE RB A 428
29DC2SOFTWAREU A:273 , G A:274 , G A:275BINDING SITE FOR RESIDUE RB A 429
30DC3SOFTWAREG A:266 , HOH A:902 , HOH A:903BINDING SITE FOR RESIDUE RB A 430
31DC4SOFTWAREU A:4 , G A:107 , U A:375 , A A:376BINDING SITE FOR RESIDUE RB A 431
32DC5SOFTWAREG A:28BINDING SITE FOR RESIDUE RB A 432
33DC6SOFTWAREC A:86 , G A:87 , A A:95 , U A:96 , G A:97BINDING SITE FOR RESIDUE RB A 433
34DC7SOFTWAREG A:3 , U A:4 , G A:5 , A A:376BINDING SITE FOR RESIDUE RB A 434
35DC8SOFTWAREG A:79 , G A:80BINDING SITE FOR RESIDUE RB A 435
36DC9SOFTWAREG A:32 , A A:33 , G A:34 , A A:50BINDING SITE FOR RESIDUE RB A 436
37EC1SOFTWAREG A:288 , C A:358 , G A:359 , C A:377 , MG A:403 , RB A:428BINDING SITE FOR RESIDUE RB A 437
38EC2SOFTWAREG A:331 , U A:332 , A A:348 , HOH A:917BINDING SITE FOR RESIDUE RB A 438
39EC3SOFTWAREG A:80 , G A:81 , A A:100 , U A:101BINDING SITE FOR RESIDUE RB A 439
40EC4SOFTWAREA A:268 , G A:269 , G A:270 , HOH A:914BINDING SITE FOR RESIDUE RB A 440
41EC5SOFTWAREG A:58BINDING SITE FOR RESIDUE RB A 441
42EC6SOFTWAREG A:15BINDING SITE FOR RESIDUE RB A 442
43EC7SOFTWAREG A:320 , G A:321BINDING SITE FOR RESIDUE RB A 444
44EC8SOFTWAREA A:333 , G A:335 , G A:336BINDING SITE FOR RESIDUE RB A 445
45EC9SOFTWAREU A:47 , G A:58BINDING SITE FOR RESIDUE SPM A 446
46FC1SOFTWAREG A:300 , U A:301 , G A:315 , G A:316 , G A:317BINDING SITE FOR RESIDUE EPE A 447
47FC2SOFTWAREA A:115 , C A:116 , G A:117BINDING SITE FOR RESIDUE EPE A 448
48FC3SOFTWAREC A:38 , C A:39 , G A:242 , G A:243 , G A:244BINDING SITE FOR RESIDUE EPE A 449
49FC4SOFTWAREG A:97 , G A:98BINDING SITE FOR RESIDUE EPE A 450
50FC5SOFTWAREA A:110 , G A:111 , C A:112 , G A:113 , G A:114 , A A:115BINDING SITE FOR RESIDUE EPE A 451
51FC6SOFTWAREC A:76 , A A:77 , G A:104BINDING SITE FOR RESIDUE EPE A 452

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E8P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E8P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E8P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E8P)

(-) Exons   (0, 0)

(no "Exon" information available for 4E8P)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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Chain A from PDB  Type:DNA/RNA  Length:393
                                                                                                                                                                                                                                                                                                                                                                                                                                         
                 4e8p A  -2 GGGGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAACAAGUAUGGCGUUCGCGCCUAAGCUUGAACCGCCGUAUACCGAACGGUACGUACGGUGGUGUG 390
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387   

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4E8P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E8P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E8P)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4E8P)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4e8k 4e8m 4e8n 4e8q 4e8r 4e8t 4e8v