Nickel 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:

Zinc

(Zn)

2 atoms

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the JMJD2A Complexed with S-2-Hydroxyglutarate and Histone H3K36ME3 Peptide (30-41), PDB code: 2ybs:
Jump to Nickel binding site number: 1; 2;

Nickel 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 Nickel with other atoms in the Ni 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:Ni1356 b:42.6 occ:1.00 O3 A:S2G1359 2.2 38.7 1.0 NE2 A:HIS188 2.3 25.4 1.0 OE2 A:GLU190 2.3 29.8 1.0 NE2 A:HIS276 2.3 25.1 1.0 O2 A:S2G1359 2.4 42.6 1.0 O A:HOH2229 2.4 41.3 1.0 C2 A:S2G1359 2.8 42.0 1.0 C1 A:S2G1359 3.0 43.5 1.0 CE1 A:HIS188 3.0 23.8 1.0 CD2 A:HIS276 3.2 24.6 1.0 CD A:GLU190 3.2 25.9 1.0 CE1 A:HIS276 3.4 25.3 1.0 OE1 A:GLU190 3.4 23.9 1.0 CD2 A:HIS188 3.4 25.3 1.0 O A:HOH2231 4.0 42.8 1.0 ND1 A:HIS188 4.2 26.4 1.0 O1 A:S2G1359 4.2 45.1 1.0 C3 A:S2G1359 4.3 43.8 1.0 CG A:HIS188 4.4 24.2 1.0 CG A:HIS276 4.4 22.9 1.0 ND1 A:HIS276 4.4 22.6 1.0 OG A:SER196 4.6 29.1 1.0 CG A:GLU190 4.6 26.2 1.0 CM2 C:M3L36 4.8 51.7 1.0 C4 A:S2G1359 4.9 43.6 1.0 CB A:SER196 5.0 25.8 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni1356 b:38.4 occ:1.00 OE2 B:GLU190 2.2 26.4 1.0 NE2 B:HIS276 2.3 20.9 1.0 O B:HOH2235 2.3 46.5 1.0 O2 B:S2G1358 2.4 47.9 1.0 O3 B:S2G1358 2.5 37.6 1.0 NE2 B:HIS188 2.5 28.3 1.0 C2 B:S2G1358 2.9 44.7 1.0 C1 B:S2G1358 3.0 47.6 1.0 CD B:GLU190 3.2 24.1 1.0 CD2 B:HIS276 3.2 23.4 1.0 CE1 B:HIS188 3.2 27.2 1.0 CE1 B:HIS276 3.3 24.1 1.0 OE1 B:GLU190 3.4 24.7 1.0 CD2 B:HIS188 3.6 27.4 1.0 O B:HOH2163 4.1 46.9 1.0 O1 B:S2G1358 4.2 51.3 1.0 OG B:SER196 4.3 27.6 1.0 ND1 B:HIS188 4.4 26.7 1.0 CG B:HIS276 4.4 23.1 1.0 ND1 B:HIS276 4.4 26.3 1.0 C3 B:S2G1358 4.4 44.9 1.0 CG B:GLU190 4.5 25.1 1.0 CG B:HIS188 4.6 27.8 1.0 CM2 D:M3L36 4.6 35.2 1.0 CB B:SER196 4.7 22.3 1.0 CG2 B:THR270 4.8 25.7 1.0 OG1 B:THR270 4.9 25.6 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