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

The structure of JMJD2A Complexed with S-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41), PDB code: 2ybs was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.14 / 2.32
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.924, 149.354, 57.271, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 23.7

The structure of JMJD2A Complexed with S-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 S-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41) (pdb code 2ybs). 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 S-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41), PDB code: 2ybs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the JMJD2A Complexed with S-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 S-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1357 b:38.7 occ:1.00 SG A:CYS306 2.3 37.3 1.0 SG A:CYS234 2.4 41.4 1.0 SG A:CYS308 2.4 41.8 1.0 NE2 A:HIS240 2.4 31.8 1.0 CD2 A:HIS240 3.3 29.1 1.0 CB A:CYS308 3.4 46.8 1.0 CB A:CYS306 3.4 40.6 1.0 CB A:CYS234 3.5 44.7 1.0 CE1 A:HIS240 3.5 31.0 1.0 N A:CYS308 3.8 48.7 1.0 O A:HOH2200 4.1 55.0 1.0 CA A:CYS308 4.1 48.7 1.0 CA A:CYS306 4.1 41.8 1.0 O A:ALA236 4.3 33.0 1.0 CG A:ARG309 4.3 54.5 1.0 N A:SER307 4.4 45.4 1.0 N A:ARG309 4.4 52.0 1.0 C A:CYS306 4.5 43.4 1.0 CG A:HIS240 4.5 30.4 1.0 C A:CYS308 4.5 50.0 1.0 ND1 A:HIS240 4.5 31.7 1.0 CD A:ARG309 4.7 54.2 1.0 C A:ALA236 4.8 34.3 1.0 CA A:PHE237 4.8 30.9 1.0 NE A:ARG309 4.8 54.4 1.0 CA A:CYS234 4.9 46.2 1.0 CB A:ARG309 4.9 53.9 1.0 C A:SER307 5.0 48.8 1.0

Zinc binding site 2 out of 2 in the JMJD2A Complexed with S-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 S-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1357 b:37.9 occ:1.00 SG B:CYS306 2.2 37.9 1.0 NE2 B:HIS240 2.4 33.6 1.0 SG B:CYS234 2.4 36.4 1.0 SG B:CYS308 2.5 42.7 1.0 CB B:CYS234 3.3 40.1 1.0 CD2 B:HIS240 3.3 31.1 1.0 CE1 B:HIS240 3.4 32.4 1.0 CB B:CYS306 3.4 37.4 1.0 N B:CYS308 3.6 45.6 1.0 CB B:CYS308 3.7 44.6 1.0 CA B:CYS306 4.0 39.3 1.0 N B:SER307 4.0 43.7 1.0 CG B:ARG309 4.1 50.8 1.0 CA B:CYS308 4.1 46.1 1.0 N B:ARG309 4.1 48.9 1.0 C B:CYS306 4.3 41.3 1.0 CG B:HIS240 4.5 31.8 1.0 C B:CYS308 4.5 47.3 1.0 ND1 B:HIS240 4.5 34.0 1.0 C B:SER307 4.7 46.8 1.0 CA B:CYS234 4.7 42.6 1.0 O B:ALA236 4.7 31.3 1.0 CB B:ARG309 4.8 50.4 1.0 CD B:ARG309 4.9 51.0 1.0 CA B:SER307 4.9 47.0 1.0 CA B:PHE237 4.9 28.8 1.0 O B:HOH2064 5.0 54.8 1.0 CE B:MET312 5.0 49.1 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