2OQ7

The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 2OQ7

Classification: OXIDOREDUCTASE

Total Structure Weight: 89194.92

Macromolecule Entities
Molecule Chains Length Organism Details
JmjC domain-containing histone demethylation protein 3A A, B 381 Homo sapiens Gene Name(s): KDM4A Gene View JHDM3A JMJD2 JMJD2A KIAA0677
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.177
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 101.12 α = 90.00
b = 148.53 β = 90.00
c = 57.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-01-31
  • Released Date: 2007-03-13
  • Deposition author(s): Kavanagh, K.L., Ng, S.S., Pilka, E., McDonough, M.A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History

  • Version 1_0: 2007-03-13

    Type: Initial release

  • Version 1_1: 2007-10-15

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Refinement description, Version format compliance

  • Version 1_3: 2017-10-18

    Type: Refinement description