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(-) Description

Title :  FULL-LENGTH HAMMERHEAD RIBOZYME WITH MN(II) BOUND
 
Authors :  M. Martick, W. G. Scott
Date :  01 Jan 07  (Deposition) - 20 Feb 07  (Release) - 12 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribozyme, Hammerhead Rna, Stem-Loop Interaction, Uridine Turn, A-Form Helix, Manganese, Mn (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Martick, T. S. Lee, D. M. York, W. G. Scott
Solvent Structure And Hammerhead Ribozyme Catalysis.
Chem. Biol. V. 15 332 2008
PubMed-ID: 18420140  |  Reference-DOI: 10.1016/J.CHEMBIOL.2008.03.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HAMMERHEAD RIBOZYME
    Chains: A
    Engineered: YES
    Other Details: ENZYME STRAND WAS OBTAINED BY T7 RNA TRANSCRIPTION
    Synthetic: YES
 
Molecule 2 - 5'-R(*GP*GP*CP*GP*UP*(OMC)P*CP*UP*GP*GP*(5BU) P*AP*UP*CP*CP*AP*AP*UP*CP*(DC))-3'
    Chains: B
    Engineered: YES
    Other Details: SUBSTRATE STRAND WAS OBTAINED BY SOLID- PHASE CHEMICAL SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
15BU1Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3MN5Ligand/IonMANGANESE (II) ION
4OMC1Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA A:21 , G A:22 , HOH A:702 , HOH A:703 , HOH A:704 , HOH A:705BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWAREGTP A:1 , HOH A:706 , HOH A:707 , HOH A:708 , HOH A:709BINDING SITE FOR RESIDUE MN A 401
3AC3SOFTWAREA A:38 , HOH A:710 , HOH A:711 , HOH A:712 , HOH A:713 , HOH A:714BINDING SITE FOR RESIDUE MN A 501
4AC4SOFTWAREA A:27 , HOH A:715 , HOH A:716 , HOH A:717BINDING SITE FOR RESIDUE MN A 601
5AC5SOFTWAREHOH A:718 , HOH A:719 , HOH A:720 , HOH A:721 , HOH A:722BINDING SITE FOR RESIDUE MN A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2OEU)

(-) 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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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:43
                                                                          
                  2oeu A  1 gGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACGAAACGCC 43
                            |       10        20        30        40   
                            |                                          
                            1-GTP                                      


Chain B from PDB  Type:DNA/RNA  Length:20
                                                   
                  2oeu B  1 GGCGUcCUGGuAUCCAAUCC 20
                                 |  10|       20
                                 6-OMC|         
                                     11-5BU
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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 2OEU)

(-) 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 Specified in the PDB File

2goz SAME THING WITHOUT MN(II)