Crystal structure of the human 2-oxoglutarate oxygenase LOC390245

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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Structural and Evolutionary Basis for the Dual Substrate Selectivity of Human Kdm4 Histone Demethylase Family.

Hillringhaus, L.Yue, W.W.Rose, N.R.Ng, S.S.Gileadi, C.Loenarz, C.Bello, S.H.Bray, J.E.Schofield, C.J.Oppermann, U.

(2011) J Biol Chem 286: 41616

  • DOI: https://doi.org/10.1074/jbc.M111.283689
  • Primary Citation of Related Structures:  
    2W2I, 2XML

  • PubMed Abstract: 

    N(ε)-Methylations of histone lysine residues play critical roles in cell biology by "marking" chromatin for transcriptional activation or repression. Lysine demethylases reverse N(ε)-methylation in a sequence- and methylation-selective manner. The determinants of sequence selectivity for histone demethylases have been unclear. The human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone. Kinetic, crystallographic, and mutagenetic studies in vitro and in cells on KDM4A-E reveal that selectivity is determined by multiple interactions within the catalytic domain but outside the active site. Structurally informed phylogenetic analyses reveal that KDM4A-C orthologues exist in all genome-sequenced vertebrates with earlier animals containing only a single KDM4 enzyme. KDM4D orthologues only exist in eutherians (placental mammals) where they are conserved, including proposed substrate sequence-determining residues. The results will be useful for the identification of inhibitors for specific histone demethylases.

  • Organizational Affiliation

    Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
358Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for B2RXH2 (Homo sapiens)
Explore B2RXH2 
Go to UniProtKB:  B2RXH2
GTEx:  ENSG00000235268 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RXH2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PD2

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
N [auth C]
C7 H5 N O4
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
C3 H8 O3
Query on NI

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
M [auth C]
Binding Affinity Annotations 
IDSourceBinding Affinity
PD2 PDBBind:  2W2I Ki: 914 (nM) from 1 assay(s)
BindingDB:  2W2I Ki: 9.14e+5 (nM) from 1 assay(s)
IC50: min: 1400, max: 6310 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.904α = 90
b = 111.009β = 90
c = 224.199γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2015-05-13
    Changes: Database references, Non-polymer description, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description