Zinc 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:

Chlorine	(Cl)	1 atom
Nickel	(Ni)	2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of JMJD2A Complexed with R-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:53.2 occ:1.00 SG A:CYS306 2.3 50.6 1.0 NE2 A:HIS240 2.4 45.0 1.0 SG A:CYS234 2.5 46.3 1.0 SG A:CYS308 2.6 56.5 1.0 CD2 A:HIS240 3.2 43.1 1.0 CE1 A:HIS240 3.4 45.0 1.0 CB A:CYS234 3.4 51.2 1.0 CB A:CYS306 3.5 50.5 1.0 CB A:CYS308 3.8 61.2 1.0 N A:CYS308 3.8 62.0 1.0 CA A:CYS306 4.0 50.5 1.0 N A:SER307 4.1 56.4 1.0 CA A:CYS308 4.2 63.1 1.0 N A:ARG309 4.2 69.7 1.0 CG A:ARG309 4.2 73.5 1.0 C A:CYS306 4.3 53.2 1.0 CG A:HIS240 4.4 43.3 1.0 ND1 A:HIS240 4.5 44.5 1.0 C A:CYS308 4.5 66.3 1.0 CD A:ARG309 4.6 73.4 1.0 O A:ALA236 4.6 44.5 1.0 CA A:CYS234 4.8 53.6 1.0 CB A:ARG309 4.8 73.1 1.0 C A:SER307 4.8 61.0 1.0 NE A:ARG309 4.9 74.0 1.0 CA A:PHE237 4.9 40.9 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of JMJD2A Complexed with R-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:49.9 occ:1.00 SG B:CYS234 2.3 50.7 1.0 NE2 B:HIS240 2.4 43.5 1.0 SG B:CYS306 2.4 55.0 1.0 SG B:CYS308 2.5 54.6 1.0 CD2 B:HIS240 3.2 41.8 1.0 CB B:CYS306 3.4 53.0 1.0 CB B:CYS234 3.4 56.6 1.0 CE1 B:HIS240 3.5 45.3 1.0 N B:CYS308 3.6 62.3 1.0 CB B:CYS308 3.7 61.1 1.0 CA B:CYS306 3.8 53.5 1.0 N B:SER307 4.0 58.1 1.0 CA B:CYS308 4.0 62.3 1.0 C B:CYS306 4.1 55.8 1.0 CG B:ARG309 4.3 69.3 1.0 N B:ARG309 4.3 66.5 1.0 C B:CYS308 4.4 63.9 1.0 CG B:HIS240 4.4 42.2 1.0 O B:ALA236 4.5 47.5 1.0 ND1 B:HIS240 4.5 43.4 1.0 CD B:ARG309 4.6 69.7 1.0 C B:SER307 4.6 62.4 1.0 CA B:CYS234 4.7 59.1 1.0 NE B:ARG309 4.8 70.3 1.0 CB B:ARG309 4.8 68.3 1.0 CA B:SER307 4.9 61.0 1.0 O B:CYS306 4.9 55.4 1.0 CA B:PHE237 4.9 44.3 1.0 C B:ALA236 5.0 48.9 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