293D

INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE-2: THE CRYSTAL STRUCTURE OF THE D(CG)3 AND SPERMIDINE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interaction between the left-handed Z-DNA and polyamine-2. The crystal structure of the d(CG)3 and spermidine complex.

Ohishi, H.Nakanishi, I.Inubushi, K.van der Marel, G.van Boom, J.H.Rich, A.Wang, A.H.Hakoshima, T.Tomita, K.

(1996) FEBS Lett. 391: 153-156


  • PubMed Abstract: 
  • This paper deals with the crystal structure of d(CG)3-spermidine complex. The DNA fragment, d(CG)3, was crystallized with N-(2-amino-propyl)-1,4-diamino-butane, PA(34), spermidine. The results of its X-ray crystallographic analysis showed many interm ...

    This paper deals with the crystal structure of d(CG)3-spermidine complex. The DNA fragment, d(CG)3, was crystallized with N-(2-amino-propyl)-1,4-diamino-butane, PA(34), spermidine. The results of its X-ray crystallographic analysis showed many intermolecular contacts between d(CG)3 and spermidine, but the binding mode of spermidine to the d(CG)3 molecule is different from that of the d(CG)3 and N-(2-amino-ethyl)-1,4-diamino-butane [PA(24)] complex: a spermidine molecule bound to the d(CG)3 and its symmetrically related neighboring d(CG)3 molecules through the water molecules with hydrogen bonds, while one PA(24) molecule connected directly to one d(CG)3 molecule, but not to its neighboring d(CG)3 molecule. In the crystal, the d(CG)3 molecule was the left-handed Z-form, and three magnesium cations and a sodium cation were observed around the d(CG)3 moiety with different binding modes from the case of the d(CG)3-PA(24) complex.


    Organizational Affiliation

    Osaka University of Pharmaceutical Sciences, Japan. ohishi@oysun01.oups.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')A,B6N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

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A
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 17.930α = 90.00
b = 31.230β = 90.00
c = 44.640γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-02
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance