Nickel in PDB 2ybk: JMJD2A Complexed with R-2-Hydroxyglutarate

The structure of JMJD2A Complexed with R-2-Hydroxyglutarate, PDB code: 2ybk was solved by R.Chowdhury, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.07 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.127, 149.332, 56.525, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.6

The structure of JMJD2A Complexed with R-2-Hydroxyglutarate also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Nickel atom in the JMJD2A Complexed with R-2-Hydroxyglutarate (pdb code 2ybk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the JMJD2A Complexed with R-2-Hydroxyglutarate, PDB code: 2ybk:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the JMJD2A Complexed with R-2-Hydroxyglutarate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of JMJD2A Complexed with R-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:38.6 occ:1.00 O5 A:2HG601 1.9 49.0 1.0 O4 A:2HG601 1.9 43.8 1.0 OE2 A:GLU190 2.1 29.3 1.0 C5 A:2HG601 2.1 45.5 1.0 NE2 A:HIS276 2.2 26.4 1.0 NE2 A:HIS188 2.4 28.8 1.0 O A:HOH2094 2.7 18.8 0.5 CD A:GLU190 2.9 23.2 1.0 CE1 A:HIS276 3.1 24.3 1.0 OE1 A:GLU190 3.1 21.3 1.0 CE1 A:HIS188 3.2 30.5 1.0 CD2 A:HIS276 3.3 25.2 1.0 CD2 A:HIS188 3.4 28.5 1.0 C4 A:2HG601 3.7 41.1 1.0 ND1 A:HIS276 4.2 26.6 1.0 ND1 A:HIS188 4.4 30.4 1.0 CG A:GLU190 4.4 23.1 1.0 CG A:HIS276 4.4 25.8 1.0 O A:HOH2095 4.4 30.8 1.0 CG A:HIS188 4.5 28.4 1.0 C3 A:2HG601 4.5 44.9 1.0 OG A:SER196 4.5 39.5 1.0 NZ A:LYS241 4.8 45.8 1.0 CB A:SER196 4.8 33.0 1.0 N A:GLU190 4.9 26.7 1.0 O A:HIS188 5.0 16.9 1.0 OG1 A:THR270 5.0 28.6 1.0

Nickel binding site 2 out of 2 in the JMJD2A Complexed with R-2-Hydroxyglutarate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of JMJD2A Complexed with R-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:34.6 occ:1.00 O1 B:2HG601 2.2 34.9 0.8 O B:HOH2052 2.2 30.5 1.0 OE2 B:GLU190 2.2 31.2 1.0 NE2 B:HIS188 2.2 31.4 1.0 O3 B:2HG601 2.3 29.8 1.0 NE2 B:HIS276 2.3 28.1 1.0 C1 B:2HG601 2.9 35.4 0.8 CE1 B:HIS188 3.0 30.0 1.0 C2 B:2HG601 3.1 28.4 1.0 CD B:GLU190 3.1 26.4 1.0 CE1 B:HIS276 3.2 29.6 1.0 CD2 B:HIS188 3.3 30.0 1.0 OE1 B:GLU190 3.4 24.5 1.0 CD2 B:HIS276 3.4 25.8 1.0 O2 B:2HG601 3.9 42.5 0.8 ND1 B:HIS188 4.2 30.1 1.0 C3 B:2HG601 4.3 44.5 1.0 ND1 B:HIS276 4.3 27.4 1.0 CG B:HIS188 4.4 29.1 1.0 OG B:SER196 4.5 33.4 1.0 CG B:HIS276 4.5 27.2 1.0 CG B:GLU190 4.5 24.0 1.0 NZ B:LYS241 4.8 52.6 1.0 CB B:SER196 5.0 28.0 1.0

R.Chowdhury, K.K.Yeoh, Y.M.Tian, L.Hillringhaus, E.A.Bagg, N.R.Rose, I.K.Leung, X.S.Li, E.C.Woon, M.Yang, M.A.Mcdonough, O.N.King, I.J.Clifton, R.J.Klose, T.D.Claridge, P.J.Ratcliffe, C.J.Schofield, A.Kawamura. The Oncometabolite 2-Hydroxyglutarate Inhibits Histone Lysine Demethylases. Embo Rep. V. 12 463 2011.
ISSN: ESSN 1469-3178
PubMed: 21460794
DOI: 10.1038/EMBOR.2011.43