Nickel in PDB 4qwn: Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure

All present enzymatic activity of Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure:
1.14.11.27;

The structure of Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure, PDB code: 4qwn 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)	85.84 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.343, 87.568, 171.681, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 26.4

The binding sites of Nickel atom in the Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure (pdb code 4qwn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure, PDB code: 4qwn:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni702 b:54.1 occ:1.00 O5 A:AKG701 2.0 53.9 1.0 NE2 A:HIS212 2.1 39.8 1.0 O1 A:AKG701 2.4 54.2 1.0 NE2 A:HIS284 2.4 37.6 1.0 OD1 A:ASP214 2.4 47.5 1.0 C2 A:AKG701 2.8 50.0 1.0 CE1 A:HIS212 2.9 41.2 1.0 OD2 A:ASP214 2.9 51.3 1.0 C1 A:AKG701 2.9 50.5 0.1 CG A:ASP214 3.0 45.4 1.0 CD2 A:HIS212 3.2 39.6 1.0 CE1 A:HIS284 3.2 33.9 1.0 CD2 A:HIS284 3.3 42.0 1.0 OH A:TYR222 3.4 64.5 1.0 ND1 A:HIS212 4.0 42.1 1.0 O2 A:AKG701 4.1 47.2 0.4 CG A:HIS212 4.2 39.0 1.0 C3 A:AKG701 4.2 48.7 1.0 ND1 A:HIS284 4.3 41.0 1.0 CG A:HIS284 4.4 43.0 1.0 CZ A:TYR222 4.5 73.6 1.0 CE2 A:TYR222 4.5 70.8 1.0 CB A:ASP214 4.5 40.1 1.0

Nickel binding site 2 out of 2 in the Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Histone Demethylase KDM2A-H3K36ME1-Alpha-Kg Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni702 b:45.1 occ:1.00 NE2 C:HIS212 2.1 41.1 1.0 OD1 C:ASP214 2.1 40.8 1.0 O C:HOH809 2.2 30.8 1.0 NE2 C:HIS284 2.3 40.0 1.0 O5 C:AKG701 2.3 48.9 1.0 O1 C:AKG701 2.4 41.9 1.0 CG C:ASP214 2.9 41.9 1.0 CE1 C:HIS212 3.0 38.0 1.0 OD2 C:ASP214 3.0 44.0 1.0 C2 C:AKG701 3.0 47.1 1.0 C1 C:AKG701 3.0 42.5 0.2 CE1 C:HIS284 3.0 39.4 1.0 CD2 C:HIS212 3.1 37.9 1.0 CD2 C:HIS284 3.4 39.0 1.0 OH C:TYR222 4.0 51.9 1.0 ND1 C:HIS212 4.1 40.3 1.0 CG C:HIS212 4.2 37.8 1.0 ND1 C:HIS284 4.2 40.7 1.0 O2 C:AKG701 4.2 37.4 0.3 CG C:HIS284 4.4 40.7 1.0 CB C:ASP214 4.4 39.5 1.0 C3 C:AKG701 4.5 47.5 1.0 CA C:ASP214 4.9 36.7 1.0 N C:ASP214 4.9 34.4 1.0 CE2 C:TYR222 4.9 52.1 1.0 CZ C:TYR222 4.9 51.3 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