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(-) Description

Title :  CRYSTAL STRUCTURE OF AN RNA DOMAIN FROM HEPATITIS C VIRUS.
 
Authors :  S. M. Dibrov, H. Johnston-Cos, Y. H. Weng
Date :  25 Oct 06  (Deposition) - 13 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Mg Binding Site, Bent Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Dibrov, H. Johnston-Cox, Y. H. Weng, T. Hermann
Functional Architecture Of Hcv Ires Domain Ii Stabilized By Divalent Metal Ions In The Crystal And In Solution.
Angew. Chem. Int. Ed. Engl. V. 46 226 2007
PubMed-ID: 17131443  |  Reference-DOI: 10.1002/ANIE.200603807
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP *AP*CP*GP*CP*C)-3'
    Chains: A, C
    Engineered: YES
    Other Details: THE SEQUENCE OF THIS RNA NATURALLY EXISTS IN HEPATITIS C VIRUS.
    Synthetic: YES
 
Molecule 2 - 5'- R(*GP*CP*GP*UP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*CP*GP *G)-3'
    Chains: B, D
    Engineered: YES
    Other Details: THE SEQUENCE OF THIS RNA NATURALLY EXISTS IN HEPATITIS C VIRUS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1MG8Ligand/IonMAGNESIUM ION
2MN5Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG D:107BINDING SITE FOR RESIDUE MG D 121
02AC2SOFTWAREG B:105 , G B:107BINDING SITE FOR RESIDUE MG B 122
03AC3SOFTWAREC B:111BINDING SITE FOR RESIDUE MG B 124
04AC4SOFTWAREA A:57BINDING SITE FOR RESIDUE MG D 125
05AC5SOFTWAREG B:98 , G D:117BINDING SITE FOR RESIDUE MG B 129
06AC6SOFTWAREG B:117 , G D:98BINDING SITE FOR RESIDUE MG B 130
07AC7SOFTWAREC A:55 , C C:55BINDING SITE FOR RESIDUE MN C 118
08AC8SOFTWAREC A:55BINDING SITE FOR RESIDUE MN A 119
09AC9SOFTWAREC C:55BINDING SITE FOR RESIDUE MN C 120
10BC1SOFTWAREG C:52BINDING SITE FOR RESIDUE MN C 123
11BC2SOFTWAREG A:52BINDING SITE FOR RESIDUE MN A 128

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NOK)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:RNA  Length:24
                                                        
                 2nok A  47 CGGAGGAACUACUGUCUUCACGCC  70
                                    56        66    


Chain B from PDB  Type:RNA  Length:20
                                                    
                 2nok B  98 GCGUGUCGUGCAGCCUCCGG 117
                                   107       117


Chain C from PDB  Type:RNA  Length:24
                                                        
                 2nok C  47 CGGAGGAACUACUGUCUUCACGCC  70
                                    56        66    


Chain D from PDB  Type:RNA  Length:20
                                                    
                 2nok D  98 GCGUGUCGUGCAGCCUCCGG 117
                                   107       117
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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