Nickel in PDB 4qxb: Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 with Nog

All present enzymatic activity of Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 with Nog:
1.14.11.27;

The structure of Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 with Nog, PDB code: 4qxb 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)	85.55 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.604, 86.724, 171.102, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.7

The binding sites of Nickel atom in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 with Nog (pdb code 4qxb). 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-H3K36ME3 with Nog, PDB code: 4qxb:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 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-H3K36ME3 with Nog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni601 b:20.0 occ:1.00 O2 A:OGA600 2.0 20.2 1.0 NE2 A:HIS212 2.1 16.4 1.0 O2' A:OGA600 2.1 20.5 1.0 NE2 A:HIS284 2.2 14.1 1.0 OD1 A:ASP214 2.2 19.0 1.0 O A:HOH835 2.3 18.6 1.0 C1 A:OGA600 2.7 20.8 1.0 C2 A:OGA600 2.7 21.2 1.0 CE1 A:HIS212 3.0 19.3 1.0 CE1 A:HIS284 3.0 14.6 1.0 CD2 A:HIS212 3.1 15.6 1.0 CD2 A:HIS284 3.2 14.1 1.0 CG A:ASP214 3.2 18.5 1.0 OD2 A:ASP214 3.5 18.5 1.0 O1 A:OGA600 3.9 20.5 1.0 N1 A:OGA600 4.1 18.7 1.0 ND1 A:HIS212 4.1 15.5 1.0 ND1 A:HIS284 4.2 14.0 1.0 CG A:HIS212 4.2 13.3 1.0 O E:HOH113 4.2 25.6 1.0 CG A:HIS284 4.3 13.4 1.0 CM3 E:M3L36 4.5 16.6 1.0 CB A:ASP214 4.6 14.9 1.0 C4 A:OGA600 4.9 20.3 1.0 CM1 E:M3L36 5.0 16.4 1.0 N A:ASP214 5.0 12.8 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 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-H3K36ME3 with Nog within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:27.3 occ:1.00 NE2 C:HIS212 2.1 21.2 1.0 O2 C:OGA600 2.1 25.3 1.0 OD1 C:ASP214 2.1 24.8 1.0 NE2 C:HIS284 2.2 20.9 1.0 O C:HOH817 2.2 22.9 1.0 O2' C:OGA600 2.2 24.0 1.0 C1 C:OGA600 2.8 27.7 1.0 C2 C:OGA600 2.9 26.0 1.0 CE1 C:HIS284 3.0 23.1 1.0 CE1 C:HIS212 3.0 24.9 1.0 CD2 C:HIS212 3.1 20.1 1.0 CG C:ASP214 3.2 22.4 1.0 CD2 C:HIS284 3.3 24.7 1.0 OD2 C:ASP214 3.5 22.4 1.0 O1 C:OGA600 4.1 30.2 1.0 ND1 C:HIS212 4.1 20.9 1.0 ND1 C:HIS284 4.1 21.9 1.0 O F:HOH104 4.2 31.7 1.0 N1 C:OGA600 4.2 23.6 1.0 CG C:HIS212 4.2 18.7 1.0 CG C:HIS284 4.3 23.3 1.0 CB C:ASP214 4.5 18.3 1.0 CM3 F:M3L36 4.7 23.8 1.0 N C:ASP214 4.9 15.0 1.0 C4 C:OGA600 4.9 25.6 1.0 CA C:ASP214 5.0 15.6 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