1ZAA

ZINC FINGER-DNA RECOGNITION: CRYSTAL STRUCTURE OF A ZIF268-DNA COMPLEX AT 2.1 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A.

Pavletich, N.P.Pabo, C.O.

(1991) Science 252: 809-817


  • PubMed Abstract: 
  • The zinc finger DNA-binding motif occurs in many proteins that regulate eukaryotic gene expression. The crystal structure of a complex containing the three zinc fingers from Zif268 (a mouse immediate early protein) and a consensus DNA-binding site ha ...

    The zinc finger DNA-binding motif occurs in many proteins that regulate eukaryotic gene expression. The crystal structure of a complex containing the three zinc fingers from Zif268 (a mouse immediate early protein) and a consensus DNA-binding site has been determined at 2.1 angstroms resolution and refined to a crystallographic R factor of 18.2 percent. In this complex, the zinc fingers bind in the major groove of B-DNA and wrap part way around the double helix. Each finger has a similar relation to the DNA and makes its primary contacts in a three-base pair subsite. Residues from the amino-terminal portion of an alpha helix contact the bases, and most of the contracts are made with the guanine-rich strand of the DNA. This structure provides a framework for understanding how zinc fingers recognize DNA and suggests that this motif may provide a useful basis for the design of novel DNA-binding proteins.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ZIF268)
C
87Mus musculusGene Names: Egr1 (Egr-1, Krox-24)
Find proteins for P08046 (Mus musculus)
Go to UniProtKB:  P08046
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3')A11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3')B11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 45.400α = 90.00
b = 56.200β = 90.00
c = 130.800γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance