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(-) Description

Title :  STRUCTURE OF O6-BENZYL-2'-DEOXYGUANOSINE OPPOSITE PERIMIDINONE-DERIVED SYNTHETIC NUCLEOSIDE IN DNA DUPLEX
 
Authors :  E. A. Kowal, R. Lad, P. S. Pallan, E. Muffly, Z. Wawrzak, M. Egli, S. J. Stu M. P. Stone
Date :  25 Oct 12  (Deposition) - 10 Jul 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  B-Form Dna, O6-Benzyl-2'-Deoxyguanosine, Dper, Perimidinone-Derived Nucleoside, Dickerson-Drew Dodecamer, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Kowal, R. R. Lad, P. S. Pallan, E. Dhummakupt, Z. Wawrzak, M. Egli, S. J. Sturla, M. P. Stone
Recognition Of O6-Benzyl-2'-Deoxyguanosine By A Perimidinone-Derived Synthetic Nucleoside: A Dna Interstran Stacking Interaction.
Nucleic Acids Res. V. 41 7566 2013
PubMed-ID: 23748954  |  Reference-DOI: 10.1093/NAR/GKT488

(-) Compounds

Molecule 1 - SHORT MODIFIED NUCLEIC ACIDS
    Chains: A, B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICALLY SYNTHESIZED MODIFIED OLIGONUCLEOTIDES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1BZG2Mod. Nucleotide6-(BENZYLOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE
2D3N2Mod. Nucleotide1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-1H-PERIMIDIN-2(3H)-ONE
3SPM1Ligand/IonSPERMINE
4SR1Ligand/IonSTRONTIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:2 , D3N A:9 , DG A:10 , DG B:14 , DG B:22BINDING SITE FOR RESIDUE SPM A 101
2AC2SOFTWAREDG A:12BINDING SITE FOR RESIDUE SR A 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HQI)

(-) 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

Asymmetric/Biological Unit
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Chain A from PDB  Type:DNA  Length:11
                                          
                  4hqi A  2 GCxAATTxGCG 12
                              |    |11 
                              |    |   
                              4-BZG|   
                                   9-D3N


Chain B from PDB  Type:DNA  Length:12
                                           
                  4hqi B 13 CGCxAATTxGCG 24
                               |    22  
                              16-BZG|   
                                   21-D3N
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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  4hqi
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 Related Entries

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