Nickel in PDB 4qx8: Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 Complex with Alpha-Kg

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

The structure of Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 Complex with Alpha-Kg, PDB code: 4qx8 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)	85.04 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.797, 84.615, 170.077, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.7

The binding sites of Nickel atom in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 Complex with Alpha-Kg (pdb code 4qx8). 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 Complex with Alpha-Kg, PDB code: 4qx8:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 Complex with Alpha-Kg


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 Complex with Alpha-Kg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni601 b:16.5 occ:0.50 O A:HOH927 1.9 36.7 1.0 OD1 A:ASP214 2.0 30.1 1.0 NE2 A:HIS212 2.1 24.6 1.0 O5 A:AKG602 2.1 31.6 1.0 O1 A:AKG602 2.2 33.6 1.0 NE2 A:HIS284 2.3 24.4 1.0 C2 A:AKG602 2.8 32.2 1.0 C1 A:AKG602 2.9 32.5 0.1 CG A:ASP214 3.0 28.8 1.0 CE1 A:HIS284 3.0 23.9 1.0 CD2 A:HIS212 3.0 23.9 1.0 CE1 A:HIS212 3.1 23.9 1.0 CD2 A:HIS284 3.3 23.1 1.0 OD2 A:ASP214 3.3 33.6 1.0 O A:HOH982 3.9 51.7 1.0 O2 A:AKG602 4.1 33.3 0.4 ND1 A:HIS212 4.2 23.8 1.0 ND1 A:HIS284 4.2 22.3 1.0 CG A:HIS212 4.2 22.4 1.0 C3 A:AKG602 4.3 31.0 1.0 O A:HOH860 4.3 41.4 1.0 CB A:ASP214 4.3 24.6 1.0 CG A:HIS284 4.3 21.7 1.0 CM1 E:M3L36 4.6 31.4 1.0 N A:ASP214 4.8 21.3 1.0 CA A:ASP214 4.8 22.2 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Histone Demethylase KDM2A-H3K36ME3 Complex with Alpha-Kg


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 Complex with Alpha-Kg within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:13.1 occ:0.50 O C:HOH712 2.0 30.5 1.0 OD1 C:ASP214 2.1 25.3 1.0 NE2 C:HIS212 2.1 22.7 1.0 O1 C:AKG602 2.1 32.1 1.0 O5 C:AKG602 2.1 28.1 1.0 NE2 C:HIS284 2.2 20.5 1.0 C1 C:AKG602 2.8 28.8 0.2 C2 C:AKG602 2.8 28.5 1.0 CE1 C:HIS284 3.0 19.6 1.0 CE1 C:HIS212 3.0 21.8 1.0 CG C:ASP214 3.1 24.5 1.0 CD2 C:HIS212 3.1 21.8 1.0 CD2 C:HIS284 3.2 19.6 1.0 OD2 C:ASP214 3.3 27.3 1.0 O C:HOH802 4.0 30.7 1.0 OH C:TYR222 4.0 32.4 1.0 O2 C:AKG602 4.0 28.3 0.3 ND1 C:HIS212 4.1 20.7 1.0 ND1 C:HIS284 4.1 19.4 1.0 O C:HOH854 4.2 47.6 1.0 CG C:HIS212 4.2 20.3 1.0 CG C:HIS284 4.3 18.1 1.0 C3 C:AKG602 4.3 27.5 1.0 CB C:ASP214 4.5 21.9 1.0 CM1 F:M3L36 4.7 38.9 1.0 CA C:ASP214 4.8 20.8 1.0 N C:ASP214 4.9 19.3 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