Nickel in PDB 4qxc: Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog

All present enzymatic activity of Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog:
1.14.11.27;

The structure of Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog, PDB code: 4qxc was solved by Z.J.Cheng, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.49 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.603, 86.707, 170.973, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.4

The binding sites of Nickel atom in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog (pdb code 4qxc). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog, PDB code: 4qxc:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni601 b:24.6 occ:1.00 O2 A:OGA600 2.0 29.6 1.0 NE2 A:HIS212 2.1 19.7 1.0 O2' A:OGA600 2.2 24.7 1.0 NE2 A:HIS284 2.3 17.4 1.0 OD1 A:ASP214 2.3 20.2 1.0 O A:HOH854 2.3 22.3 1.0 C1 A:OGA600 2.7 30.0 1.0 C2 A:OGA600 2.8 26.1 1.0 CE1 A:HIS212 3.0 20.7 1.0 CE1 A:HIS284 3.2 15.5 1.0 CD2 A:HIS212 3.2 18.4 1.0 CG A:ASP214 3.2 20.7 1.0 CD2 A:HIS284 3.3 16.5 1.0 OD2 A:ASP214 3.4 21.8 1.0 O1 A:OGA600 3.9 33.7 1.0 N1 A:OGA600 4.1 24.0 1.0 ND1 A:HIS212 4.2 16.8 1.0 ND1 A:HIS284 4.3 15.5 1.0 CG A:HIS212 4.3 16.4 1.0 CG A:HIS284 4.3 14.4 1.0 CB A:ASP214 4.5 16.1 1.0 CH1 E:MLY36 4.8 28.4 1.0 N A:ASP214 4.9 14.9 1.0 CA A:ASP214 4.9 15.0 1.0 C4 A:OGA600 5.0 22.0 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Histone Demethylase KDM2A-H3K36ME2 with Nog within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:31.4 occ:1.00 O2 C:OGA600 2.1 37.8 1.0 NE2 C:HIS212 2.2 23.0 1.0 OD1 C:ASP214 2.2 24.3 1.0 NE2 C:HIS284 2.3 24.6 1.0 O2' C:OGA600 2.3 31.9 1.0 O C:HOH825 2.4 28.5 1.0 C1 C:OGA600 2.9 40.1 1.0 C2 C:OGA600 3.0 36.0 1.0 CE1 C:HIS284 3.1 25.7 1.0 CE1 C:HIS212 3.1 25.0 1.0 CG C:ASP214 3.1 23.0 1.0 CD2 C:HIS212 3.2 23.2 1.0 CD2 C:HIS284 3.4 24.5 1.0 OD2 C:ASP214 3.4 26.0 1.0 O1 C:OGA600 4.1 44.8 1.0 ND1 C:HIS212 4.2 20.6 1.0 ND1 C:HIS284 4.2 25.1 1.0 O F:HOH104 4.2 47.7 1.0 CG C:HIS212 4.3 20.5 1.0 N1 C:OGA600 4.3 29.5 1.0 CH1 F:MLY36 4.3 45.0 1.0 CG C:HIS284 4.4 24.9 1.0 CB C:ASP214 4.5 20.5 1.0 N C:ASP214 4.9 17.9 1.0 CA C:ASP214 4.9 18.7 1.0

Z.Cheng, P.Cheung, A.J.Kuo, E.T.Yukl, C.M.Wilmot, O.Gozani, D.J.Patel. A Molecular Threading Mechanism Underlies Jumonji Lysine Demethylase KDM2A Regulation of Methylated H3K36. Genes Dev. V. 28 1758 2014.
ISSN: ISSN 0890-9369
PubMed: 25128496
DOI: 10.1101/GAD.246561.114