Nickel in PDB 3u78: E67-2 Selectively Inhibits KIAA1718, A Human Histone H3 Lysine 9 Jumonji Demethylase

The structure of E67-2 Selectively Inhibits KIAA1718, A Human Histone H3 Lysine 9 Jumonji Demethylase, PDB code: 3u78 was solved by A.K.Upadhyay, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.59 / 2.69
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.429, 77.429, 289.685, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 26.5

The structure of E67-2 Selectively Inhibits KIAA1718, A Human Histone H3 Lysine 9 Jumonji Demethylase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the E67-2 Selectively Inhibits KIAA1718, A Human Histone H3 Lysine 9 Jumonji Demethylase (pdb code 3u78). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the E67-2 Selectively Inhibits KIAA1718, A Human Histone H3 Lysine 9 Jumonji Demethylase, PDB code: 3u78:

Nickel binding site 1 out of 1 in the E67-2 Selectively Inhibits KIAA1718, A Human Histone H3 Lysine 9 Jumonji Demethylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of E67-2 Selectively Inhibits KIAA1718, A Human Histone H3 Lysine 9 Jumonji Demethylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni702 b:40.3 occ:1.00 O5 A:AKG701 2.2 39.6 1.0 O1 A:AKG701 2.2 42.2 1.0 NE2 A:HIS282 2.2 35.6 1.0 OD1 A:ASP284 2.3 34.4 1.0 O A:HOH801 2.3 38.8 1.0 NE2 A:HIS354 2.3 36.2 1.0 C2 A:AKG701 2.8 46.1 1.0 C1 A:AKG701 2.8 46.1 1.0 CD2 A:HIS282 3.1 36.8 1.0 CG A:ASP284 3.2 32.8 1.0 CE1 A:HIS354 3.2 32.6 1.0 CE1 A:HIS282 3.3 32.7 1.0 CD2 A:HIS354 3.4 32.0 1.0 OD2 A:ASP284 3.4 37.8 1.0 O2 A:AKG701 4.1 44.8 1.0 C3 A:AKG701 4.3 39.0 1.0 OH A:TYR292 4.3 44.7 1.0 CG A:HIS282 4.3 34.8 1.0 ND1 A:HIS354 4.3 30.9 1.0 ND1 A:HIS282 4.3 34.2 1.0 CG A:HIS354 4.4 30.2 1.0 CB A:ASP284 4.5 27.5 1.0 CBF A:E67707 4.6 51.2 1.0 CBE A:E67707 4.8 59.9 1.0 CA A:ASP284 4.9 30.8 1.0 CE1 A:TYR292 4.9 38.6 1.0 C4 A:AKG701 4.9 38.1 1.0

A.K.Upadhyay, D.Rotili, J.W.Han, R.Hu, Y.Chang, D.Labella, X.Zhang, Y.S.Yoon, A.Mai, X.Cheng. An Analog of Bix-01294 Selectively Inhibits A Family of Histone H3 Lysine 9 Jumonji Demethylases. J.Mol.Biol. V. 416 319 2012.
ISSN: ISSN 0022-2836
PubMed: 22227394
DOI: 10.1016/J.JMB.2011.12.036