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(-) Description

Title :  DUPLEX DNA CONTAINING AN ABASIC SITE WITH AN OPPOSITE DC (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*CP*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:8 , DT B:23BINDING SITE FOR RESIDUE ORP A 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O80)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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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
                                            
                  2o80 A  1 CCAAAGxACCGGG 13
                                  | 10   
                                  7-ORP  


Chain B from PDB  Type:DNA  Length:13
                                            
                  2o80 B 14 CCCGGTCCTTTGG 26
                                    23
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2O80)

(-) CATH Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
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  2o80
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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 2O80)

(-) Related Entries Specified in the PDB File

2hsl ABASIC SITE WITH AN OPPOSING DA IN THE SAME SEQUENCE CONTEXT
2hsr ABASIC SITE WITH AN OPPOSING DA IN THE SAME SEQUENCE CONTEXT
2o7x ABASIC SITE WITH AN OPPOSING DG IN THE SAME SEQUENCE CONTEXT
2o7y ABASIC SITE WITH AN OPPOSING T IN THE SAME SEQUENCE CONTEXT
2o7z ABASIC SITE WITH AN OPPOSING T IN THE SAME SEQUENCE CONTEXT
2o82
2o7w ABASIC SITE WITH AN OPPOSING DG IN THE SAME SEQUENCE CONTEXT