2QNC

Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.258

Literature

Macromolecules
Sequence Display for 2QNC

Classification: Hydrolase / DNA

Total Structure Weight: 66135.12


Macromolecule Entities
Molecule Chains Length Organism Details
Recombination endonuclease VII A, B 157 Enterobacteria phage t4 sensu lato Mutation: N62D
Gene Name(s): 49
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*DCP*DG*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DCP*DC)-3') C 24 synthetic
DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3') D 24 synthetic
DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DCP*DCP*DT)-3') E 24 synthetic
DNA (5'-D(*DAP*DGP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DG)-3') F 24 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.258
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 99.20 α = 90.00
b = 99.20 β = 90.00
c = 186.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-18
  • Released Date: 2008-01-29
  • Deposition author(s): Biertumpfel, C., Yang, W., Suck, D.

Revision History

  • Version 1_0: 2008-01-29

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance