Nickel in PDB 5ceh: Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor

The structure of Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor, PDB code: 5ceh was solved by J.R.Kiefer, M.Vinogradova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.83 / 3.14
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	159.306, 159.306, 92.462, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 23.8

The structure of Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor (pdb code 5ceh). 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 Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor, PDB code: 5ceh:

Nickel binding site 1 out of 1 in the Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:61.8 occ:1.00 O A:HOH1001 1.9 18.8 1.0 OE2 A:GLU485 1.9 23.4 1.0 N16 A:50P904 2.0 35.3 1.0 NE2 A:HIS483 2.0 39.4 1.0 NE2 A:HIS571 2.0 45.4 1.0 CE1 A:HIS483 2.7 42.8 1.0 CE1 A:HIS571 2.8 57.0 1.0 C15 A:50P904 3.1 23.6 1.0 CD A:GLU485 3.1 23.6 1.0 CD2 A:HIS483 3.2 50.2 1.0 CD2 A:HIS571 3.2 54.8 1.0 OE1 A:GLU485 3.7 23.6 1.0 ND1 A:HIS483 3.9 26.1 1.0 ND1 A:HIS571 4.0 63.0 1.0 CG A:HIS483 4.2 26.6 1.0 CG A:HIS571 4.2 29.1 1.0 CG A:GLU485 4.3 24.1 1.0 C9 A:50P904 4.5 30.4 1.0 OG A:SER491 4.6 27.0 1.0

M.Vinogradova, V.S.Gehling, A.Gustafson, S.Arora, C.A.Tindell, C.Wilson, K.E.Williamson, G.D.Guler, P.Gangurde, W.Manieri, J.Busby, E.M.Flynn, F.Lan, H.J.Kim, S.Odate, A.G.Cochran, Y.Liu, M.Wongchenko, Y.Yang, T.K.Cheung, T.M.Maile, T.Lau, M.Costa, G.V.Hegde, E.Jackson, R.Pitti, D.Arnott, C.Bailey, S.Bellon, R.T.Cummings, B.K.Albrecht, J.C.Harmange, J.R.Kiefer, P.Trojer, M.Classon. An Inhibitor of KDM5 Demethylases Reduces Survival of Drug-Tolerant Cancer Cells. Nat.Chem.Biol. V. 12 531 2016.
ISSN: ESSN 1552-4469
PubMed: 27214401
DOI: 10.1038/NCHEMBIO.2085