Chlorine 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
Nickel	(Ni)	2 atoms

The binding sites of Chlorine atom in the JMJD2A Complexed with R-2-Hydroxyglutarate (pdb code 2ybk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the JMJD2A Complexed with R-2-Hydroxyglutarate, PDB code: 2ybk:

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of JMJD2A Complexed with R-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:80.2 occ:1.00 NH1 A:ARG98 3.6 68.0 1.0 O A:TYR59 3.7 73.5 1.0 CE1 A:PHE202 3.9 37.6 1.0 CZ A:PHE202 4.2 36.2 1.0 CD1 A:PHE202 4.2 38.4 1.0 CB A:TYR59 4.4 67.1 1.0 C A:TYR59 4.6 71.8 1.0 OD1 A:ASP60 4.6 75.9 1.0 CE2 A:PHE202 4.6 37.8 1.0 CG A:PHE202 4.6 37.7 1.0 CZ A:ARG98 4.8 67.0 1.0 CD2 A:PHE202 4.8 36.2 1.0 CE2 A:PHE283 4.9 40.8 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