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(-) Description

Title :  CRYSTAL STRUCTURE OF A MINIMAL, ALL RNA HAIRPIN RIBOZYME WITH MODIFICATIONS (G8DAP, U39C) AT PH 8.6
 
Authors :  J. D. Salter, J. E. Wedekind
Date :  22 Dec 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, Diaminopurine, In-Line Geometry, Mutant, 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*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'
    Chains: A
    Engineered: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*GP*GP*UP*GP*AP*(N6G)P*AP*AP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Mutation: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    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
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    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
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1N6G1Mod. Nucleotide((2R,3S,4R,5S)-5-(2,6-DIAMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGENPHOSPHATE
2NCO1Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG C:19 , A C:20 , G C:21 , A D:40 , U D:41BINDING SITE FOR RESIDUE NCO C 11

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:RNA  Length:13
                                            
                  2fgp A  1 UCCCAGUCCACCG 13
                                    10   


Chain B from PDB  Type:RNA  Length:12
                                           
                  2fgp B  2 CGGUGAgAAGGG 13
                                  | 11  
                                  8-N6G 


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


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

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(-) Gene Ontology  (0, 0)

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  2fgp
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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 PRECATALYTIC G8 NATIVE MINIMAL ALL-RNA HAIRPIN RIBOZYME WITH AN A-1 2'-OME MODIFICATION
1zft MINIMAL ALL-RNA HAIRPIN RIBOZYME WITH THE G8I/A-1 2'-OME MODIFICATIONS
1zfv GROUND STATE MINIMAL ALL-RNA HAIRPIN RIBOZYME WITH THE G8A/ A-1 2'-OH MODIFICATIONS
1zfx GROUND STATE MINIMAL ALL-RNA HAIRPIN RIBOZYME WITH THE G8U/ A-1 2'-OH MODIFICATIONS
2bcy MINIMAL ALL-RNA HAIRPIN RIBOZYME WITH THE G8AP/A-1 2'-OH MODIFICATIONS AT PH 8.8
2bcz MINIMAL ALL-RNA HAIRPIN RIBOZYME WITH THE G8I/A-1 2'-DEOXY MODIFICATIONS