1G6D

STRUCTURE OF PEPTIDYL-D(CGCAATTGCG) IN THE PRESENCE OF ZINC IONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.208 

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This is version 1.4 of the entry. See complete history


Literature

Interaction of zinc ions with d(CGCAATTGCG) in a 2.9 A resolution X-ray structure.

Soler-Lopez, M.Malinina, L.Tereshko, V.Zarytova, V.Subirana, J.A.

(2002) J Biol Inorg Chem 7: 533-538

  • DOI: https://doi.org/10.1007/s00775-001-0333-z
  • Primary Citation of Related Structures:  
    1G6D

  • PubMed Abstract: 

    We have synthesized and crystallized in the presence of Zn(2+) ions the peptidyl-oligonucleotide adduct CH(3)CO-(Arg)(4)-NH-(CH(2))(6)-NH-p-d(CGCAATTGCG). This is the first structure obtained from a deoxyoligonucleotide crystallized in the presence of zinc ions. Zn ions are clearly visible in the 2.9 A resolution map. On the other hand, the peptide tail is not visible in the crystal structure as determined by X-ray diffraction. The terminal bases C1 and G10 are found in extra-helical positions. Their phosphates are ligands of a Zn(2+) ion, located in a special position of the unit cell. This ion plays an important role in the packing arrangement, since it binds four different DNA molecules. Two other Zn(2+) ions are also important for DNA packing. They interact specifically with the N7 atoms of the terminal G2 and G10 bases, but not with the internal G8. This result supports the hypothesis that transition metals do not interact with the bases of duplex DNA in the B form.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble Cedex 9, France.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
PEPTIDYL-D(CGCAATTGCG)10N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.92α = 90
b = 44.09β = 90
c = 53.22γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations