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(-) Description

Title :  CRYSTAL STRUCTURE OF A MINIMAL, MUTANT ALL-RNA HAIRPIN RIBOZYME (U39C, G8I, 2'DEOXY A-1)
 
Authors :  J. D. Salter, J. E. Wedekind
Date :  19 Oct 05  (Deposition) - 14 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ribozyme, G8, Inosine, , Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Salter, J. Krucinska, S. Alam, V. Grum-Tokars, J. E. Wedekind
Water In The Active Site Of An All-Rna Hairpin Ribozyme And Effects Of Gua8 Base Variants On The Geometry Of Phosphoryl Transfer.
Biochemistry V. 45 686 2006
PubMed-ID: 16411744  |  Reference-DOI: 10.1021/BI051887K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*UP*CP*CP*CP*(DA)P*GP*UP*CP*CP*AP*CP*CP*G)- 3')
    Chains: A
    Engineered: YES
    Mutation: YES
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Mutation: YES
    Synthetic: YES
 
Molecule 3 - 5'- R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - 5'- R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) -3'
    Chains: D
    Engineered: YES
    Mutation: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NCO2Ligand/IonCOBALT HEXAMMINE(III)
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:2 , HOH A:22BINDING SITE FOR RESIDUE SO4 A 21
2AC2SOFTWAREA C:20 , G C:21 , A D:40 , U D:41BINDING SITE FOR RESIDUE NCO D 11
3AC3SOFTWAREG B:12 , G B:13BINDING SITE FOR RESIDUE NCO B 14

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:DNA/RNA  Length:13
                                            
                  2bcz A  1 UCCCAGUCCACCG 13
                                    10   


Chain B from PDB  Type:RNA  Length:11
                                          
                  2bcz B  2 CGGUGAAAGGG 13
                                 || 12 
                                 7|    
                                  9    


Chain C from PDB  Type:RNA  Length:17
                                                
                  2bcz C 15 GGCAGAGAAACACACGA 31
                                    24       


Chain D from PDB  Type:RNA  Length:19
                                                  
                  2bcz D 31 UCGUGGUACAUUACCUGCC 49
                                    40
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1zfr NATIVE HAIRPIN RIBOZYME, 2.05 ANGSTROM RESOLUTION
1zft G8I (A-1 2'O-METHYL) MUTANT HAIRPIN RIBOZYME
1zfv G8A MUTANT HAIRPIN RIBOZYME
1zfx G8U MUTANT HAIRPIN RIBOZYME
2bb1 G8DAP MUTANT HAIRPIN RIBOZYME
2bcy