Zinc in PDB 2ybp: JMJD2A Complexed with R-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41)

The structure of JMJD2A Complexed with R-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41), PDB code: 2ybp 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)	45.51 / 2.02
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.291, 149.668, 57.319, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.5

The structure of JMJD2A Complexed with R-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41) also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the JMJD2A Complexed with R-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41) (pdb code 2ybp). 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 and Histone H3K36ME3 Peptide (30-41), PDB code: 2ybp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the JMJD2A Complexed with R-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41)


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 and Histone H3K36ME3 Peptide (30-41) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1357 b:32.2 occ:1.00 SG A:CYS306 2.3 30.7 1.0 NE2 A:HIS240 2.3 29.8 1.0 SG A:CYS234 2.3 33.5 1.0 SG A:CYS308 2.4 37.7 1.0 CD2 A:HIS240 3.2 28.1 1.0 CE1 A:HIS240 3.3 30.2 1.0 CB A:CYS234 3.3 35.4 1.0 CB A:CYS306 3.3 32.0 1.0 CB A:CYS308 3.6 41.9 1.0 N A:CYS308 4.0 41.8 1.0 CA A:CYS306 4.0 34.5 1.0 CA A:CYS308 4.3 42.5 1.0 O A:HOH2253 4.3 39.8 1.0 CG A:HIS240 4.4 28.2 1.0 ND1 A:HIS240 4.4 28.7 1.0 CG A:ARG309 4.4 45.3 1.0 N A:SER307 4.5 38.1 1.0 C A:CYS306 4.5 36.2 1.0 O A:HOH2075 4.5 41.4 1.0 N A:ARG309 4.6 42.9 1.0 C A:CYS308 4.6 42.8 1.0 O A:ALA236 4.7 27.2 1.0 CD A:ARG309 4.7 44.4 1.0 CA A:CYS234 4.7 37.0 1.0 CA A:PHE237 4.8 29.1 1.0 C A:ALA236 4.9 30.0 1.0 N A:PHE237 5.0 28.5 1.0 CB A:ARG309 5.0 43.5 1.0

Zinc binding site 2 out of 2 in the JMJD2A Complexed with R-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41)


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 and Histone H3K36ME3 Peptide (30-41) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1357 b:24.9 occ:1.00 NE2 B:HIS240 2.3 25.2 1.0 SG B:CYS234 2.3 31.5 1.0 SG B:CYS306 2.3 29.1 1.0 SG B:CYS308 2.3 32.0 1.0 CB B:CYS234 3.1 32.7 1.0 CD2 B:HIS240 3.2 23.7 1.0 CE1 B:HIS240 3.3 24.3 1.0 CB B:CYS306 3.3 29.1 1.0 CB B:CYS308 3.5 36.3 1.0 N B:CYS308 3.8 38.3 1.0 CA B:CYS306 4.1 29.9 1.0 CA B:CYS308 4.1 37.2 1.0 N B:SER307 4.3 34.9 1.0 O B:HOH2261 4.4 38.7 1.0 ND1 B:HIS240 4.4 23.0 1.0 N B:ARG309 4.4 39.4 1.0 CG B:HIS240 4.4 24.4 1.0 CG B:ARG309 4.4 42.6 1.0 C B:CYS308 4.5 38.6 1.0 C B:CYS306 4.5 31.6 1.0 O B:ALA236 4.6 21.7 1.0 CA B:CYS234 4.6 34.9 1.0 CA B:PHE237 4.8 22.4 1.0 O B:HOH2077 4.8 34.8 1.0 C B:ALA236 4.8 23.3 1.0 CB B:ARG309 4.8 40.2 1.0 CD B:ARG309 4.9 41.1 1.0 N B:PHE237 4.9 21.8 1.0 C B:SER307 5.0 39.7 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