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(-) Description

Title :  EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY JUNCTIONS
 
Authors :  F. A. Hays, J. M. Vargason, P. S. Ho
Date :  24 Apr 03  (Deposition) - 02 Sep 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  B-Dna, Double Helix, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. A. Hays, J. M. Vargason, P. S. Ho
Effect Of Sequence On The Conformation Of Dna Holliday Junctions
Biochemistry V. 42 9586 2003
PubMed-ID: 12911300  |  Reference-DOI: 10.1021/BI0346603

(-) Compounds

Molecule 1 - 5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3'
    Chains: A
    Engineered: YES
    Other Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL- PROTECTING GROUP LEFT INTACT AT THE 5-TERMINAL NUCLEOTIDE, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NA3Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC A:2 , HOH A:25BINDING SITE FOR RESIDUE NA A 12
2AC2SOFTWAREDG A:4BINDING SITE FOR RESIDUE NA A 13
3AC3SOFTWAREDC A:7 , HOH A:42BINDING SITE FOR RESIDUE NA A 24

(-) SS Bonds  (0, 0)

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(-) Sequences/Alignments

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Chain A from PDB  Type:DNA  Length:10
                                         
                  1p4z A  1 CCAGTACTGG 10
                                    10
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 Related Entries

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(-) Related Entries Specified in the PDB File

1p4y EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY JUNCTIONS
1p54 EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY JUNCTIONS