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(-) Description

Title :  DUPLEX DNA CONTAINING AN ABASIC SITE WITH AN OPPOSITE G (ALPHA ANOMER) IN 5'-G_AC-3' (10 STRUCTURE ENSEMBLE AND AVERAGED STRUCTURE)
 
Authors :  J. Chen, F. Y. Dupradeau, D. A. Case, C. J. Turner, J. Stubbe
Date :  11 Dec 06  (Deposition) - 27 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (11x)
Keywords :  Dna Damage, Ape1, Abasic, Nmr, Amber, Molecular Dynamics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Chen, F. Y. Dupradeau, D. A. Case, C. J. Turner, J. Stubbe
Dna Oligonucleotides With A, T, G Or C Opposite An Abasic Site: Structure And Dynamics.
Nucleic Acids Res. V. 36 253 2008
PubMed-ID: 18025040  |  Reference-DOI: 10.1093/NAR/GKM622
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*CP*AP*AP*AP*GP*(ORP)P*AP*CP*CP*GP*GP*G)- 3'
    Chains: A
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED.
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*CP*CP*GP*GP*TP*GP*CP*TP*TP*TP*GP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (11x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ORP1Mod. Nucleotide2-DEOXY-5-PHOSPHONO-RIBOSE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:6 , DA A:8BINDING SITE FOR RESIDUE ORP A 7

(-) SS Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:13
                                            
                  2o7w A  1 CCAAAGxACCGGG 13
                                  | 10   
                                  7-ORP  


Chain B from PDB  Type:DNA  Length:13
                                            
                  2o7w B 14 CCCGGTGCTTTGG 26
                                    23
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(-) 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)

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(-) Related Entries Specified in the PDB File

2hsl ABASIC SITE DNA WITH AN OPPOSITE A IN THE SAME SEQUENCE CONTEXT
2hsr ABASIC SITE DNA WITH AN OPPOSITE A IN THE SAME SEQUENCE CONTEXT
2o7x
2o7y
2o7z
2o81