1G6D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1007/s00775-001-0333-z

  • 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 o ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
PEPTIDYL-D(CGCAATTGCG)A10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 27.920α = 90.00
b = 44.090β = 90.00
c = 53.220γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model