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(-) Description

Title :  CO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION
 
Authors :  S. T. Hoehn, H. -D. Junker, R. C. Bunt, C. J. Turner, J. Stubbe
Date :  01 Nov 00  (Deposition) - 06 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C
Keywords :  Damaged Dna, Dna-Drug Complex, Intercalation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. T. Hoehn, H. D. Junker, R. C. Bunt, C. J. Turner, J. Stubbe
Solution Structure Of Co(Iii)-Bleomycin-Ooh Bound To A Phosphoglycolate Lesion Containing Oligonucleotide: Implications For Bleomycin-Induced Double-Strand Dna Cleavage.
Biochemistry V. 40 5894 2001
PubMed-ID: 11352724  |  Reference-DOI: 10.1021/BI002635G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*CP*AP*AP*AP*G)-3'
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(P*AP*CP*TP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

NMR Structure (5, 5)
No.NameCountTypeFull Name
13CO1Ligand/IonCOBALT (III) ION
2BLB1Ligand/IonBLEOMYCIN B2
3O1Ligand/IonOXYGEN ATOM
4PEO1Ligand/IonHYDROGEN PEROXIDE
5PGA1Ligand/Ion2-PHOSPHOGLYCOLIC ACID

(-) Sites  (5, 5)

NMR Structure (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:6 , BLB C:1BINDING SITE FOR RESIDUE PGA A 7
2AC2SOFTWAREBLB C:1 , PEO C:11BINDING SITE FOR RESIDUE 3CO B 14
3AC3SOFTWAREDA B:8BINDING SITE FOR RESIDUE O B 15
4AC4SOFTWAREDG A:6 , PGA A:7 , DA B:8 , DC B:9 , DT B:10 , DG B:11 , DG B:12 , DG B:13 , 3CO B:14 , PEO C:11 , DG C:18 , DT C:19 , DA C:20BINDING SITE FOR RESIDUE BLB C 1
5AC5SOFTWARE3CO B:14 , BLB C:1 , DT C:19BINDING SITE FOR RESIDUE PEO C 11

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GJ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GJ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GJ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GJ2)

(-) Exons   (0, 0)

(no "Exon" information available for 1GJ2)

(-) Sequences/Alignments

NMR Structure
   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:DNA  Length:6
                                     
                  1gj2 A  1 CCAAAG  6


Chain B from PDB  Type:DNA  Length:6
                                     
                  1gj2 B  8 ACTGGG 13


Chain C from PDB  Type:DNA  Length:13
                                            
                  1gj2 C 14 CCCAGTACTTTGG 26
                                    23
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1GJ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1GJ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GJ2)

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1GJ2)

(-) Related Entries Specified in the PDB File

1g5d ENSEMBLE: 1G5D HAS THE SAME SEQUENCE AND CONTAINS AN ABASIC SITE (ALPHA ANOMER) INSTEAD OF THE PHOSPHOGLYCOLATE LESION
1g5e ENSEMBLE: 1G5E HAS THE SAME SEQUENCE AND CONTAINS AN ABASIC SITE (BETA ANOMER) INSTEAD OF THE PHOSPHOGLYCOLATE LESION
1g5k ENSEMBLE: 1G5K IS THE STRUCTURE OF THE OLIGONUCLEOTIDE CONTAINING THE PHOSPHOGLYCOLATE LESION WITHOUT THE BLEOMYCIN BOUND.
1g5l ENSEMBLE: 1G5L IS CO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION
1giz MINIMIZED AVERAGE STRUCTURE: 1GIZ HAS THE SAME SEQUENCE AND CONTAINS AN ABASIC SITE (ALPHA ANOMER) INSTEAD OF THE PHOSPHOGLYCOLATE LESION
1gj0 MINIMIZED AVERAGE STRUCTURE: 1GJ0 HAS THE SAME SEQUENCE AND CONTAINS AN ABASIC SITE (BETA ANOMER) INSTEAD OF THE PHOSPHOGLYCOLATE LESION
1gj1 MINIMIZED AVERAGE STRUCTURE: 1GJ1 IS THE STRUCTURE OF THE OLIGONUCLEOTIDE CONTAINING THE PHOSPHOGLYCOLATE LESION WITHOUT THE BLEOMYCIN BOUND.