Nickel 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:

Zinc

(Zn)

2 atoms

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

Nickel 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 Nickel with other atoms in the Ni 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:Ni1356 b:29.3 occ:1.00 OE2 A:GLU190 2.2 27.0 1.0 NE2 A:HIS276 2.2 23.3 1.0 O3 A:2HG1359 2.3 29.7 1.0 O1 A:2HG1359 2.3 34.7 0.8 O A:HOH2168 2.3 35.2 1.0 NE2 A:HIS188 2.3 20.9 1.0 C1 A:2HG1359 3.0 36.7 0.8 CE1 A:HIS188 3.1 21.6 1.0 C2 A:2HG1359 3.1 34.6 1.0 CE1 A:HIS276 3.2 22.9 1.0 CD2 A:HIS276 3.2 22.5 1.0 CD A:GLU190 3.2 25.7 1.0 CD2 A:HIS188 3.4 22.0 1.0 OE1 A:GLU190 3.5 26.1 1.0 O A:HOH2296 4.0 32.0 1.0 O2 A:2HG1359 4.2 40.8 0.8 ND1 A:HIS188 4.3 21.8 1.0 O A:HOH2206 4.3 42.0 1.0 ND1 A:HIS276 4.3 21.6 1.0 CG A:HIS276 4.3 23.1 1.0 C3 A:2HG1359 4.4 36.9 1.0 OG A:SER196 4.5 25.6 1.0 CG A:HIS188 4.5 20.7 1.0 CG A:GLU190 4.6 23.4 1.0 CM2 C:M3L36 4.7 31.3 1.0 CG2 A:THR270 4.9 17.7 1.0 CB A:SER196 4.9 23.9 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni1356 b:28.1 occ:1.00 NE2 B:HIS276 2.1 22.0 1.0 O B:HOH2178 2.2 35.3 1.0 OE2 B:GLU190 2.2 22.7 1.0 O3 B:2HG1358 2.3 27.1 1.0 NE2 B:HIS188 2.3 21.9 1.0 O1 B:2HG1358 2.3 36.8 0.8 CD2 B:HIS276 3.1 21.4 1.0 C1 B:2HG1358 3.1 37.1 0.8 CE1 B:HIS276 3.1 22.3 1.0 CE1 B:HIS188 3.1 21.5 1.0 CD B:GLU190 3.2 22.5 1.0 C2 B:2HG1358 3.2 34.6 1.0 CD2 B:HIS188 3.4 23.8 1.0 OE1 B:GLU190 3.4 22.1 1.0 O B:HOH2298 3.9 34.3 1.0 ND1 B:HIS276 4.2 22.1 1.0 CG B:HIS276 4.2 20.5 1.0 ND1 B:HIS188 4.3 23.4 1.0 O2 B:2HG1358 4.3 40.0 0.8 OG B:SER196 4.4 26.6 1.0 O B:HOH2212 4.4 38.6 1.0 CG B:HIS188 4.4 22.5 1.0 C3 B:2HG1358 4.4 37.0 1.0 CG B:GLU190 4.5 21.2 1.0 CM2 D:M3L36 4.7 29.1 1.0 CG2 B:THR270 4.8 22.4 1.0 CB B:SER196 4.9 23.3 1.0 OG1 B:THR270 4.9 21.2 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