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(-) Description

Title :  THE RARE CRYSTALLOGRAPHIC STRUCTURE OF D(CGCGCG)2: THE NATURAL SPERMIDINE MOLECULE BOUND TO THE MINOR GROOVE OF LEFT-HANDED Z-DNA D(CGCGCG)2 AT 10 DEGREE CELSIUS
 
Authors :  H. Ohishi, Y. Tozuka, D. Y. Zhou, T. Ishida, K. Nakatani
Date :  27 Mar 07  (Deposition) - 01 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  D(Cgcgcg)2, Left-Handed Z-Dna, Spermidine, X-Ray Crystallography, Polyamine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ohishi, Y. Tozuka, Z. Da-Yang, T. Ishida, K. Nakatani
The Rare Crystallographic Structure Of D(Cgcgcg)(2): The Natural Spermidine Molecule Bound To The Minor Groove Of Left-Handed Z-Dna D(Cgcgcg)(2) At 10 Degrees C
Biochem. Biophys. Res. Commun. V. 358 24 2007
PubMed-ID: 17467661  |  Reference-DOI: 10.1016/J.BBRC.2007.04.026
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')
    Chains: A, B
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2NA1Ligand/IonSODIUM ION
3SPD1Ligand/IonSPERMIDINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
3SPD2Ligand/IonSPERMIDINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
3SPD1Ligand/IonSPERMIDINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC A:1 , DC A:5 , DG A:6 , DC B:7 , DG B:8 , DC B:9 , DG B:12BINDING SITE FOR RESIDUE SPD A 120
2AC2SOFTWAREDG A:6BINDING SITE FOR RESIDUE MG A 92

(-) SS Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:6
                                     
                  2elg A  1 CGCGCG  6


Chain B from PDB  Type:DNA  Length:6
                                     
                  2elg B  7 CGCGCG 12
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 Related Entries

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(-) Related Entries Specified in the PDB File

1dj6 DEOXYRIBONUCLEIC ACID
292d DEOXYRIBONUCLEIC ACID
293d DEOXYRIBONUCLEIC ACID
336d DEOXYRIBONUCLEIC ACID