Zinc 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:

Nickel

(Ni)

1 atom

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor, PDB code: 5ceh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn902 b:72.3 occ:1.00 ND1 A:HIS702 2.1 0.3 1.0 SG A:CYS679 2.3 76.7 1.0 SG A:CYS699 2.4 62.7 1.0 SG A:CYS676 2.5 68.4 1.0 CE1 A:HIS702 3.0 0.3 1.0 CB A:CYS679 3.0 71.7 1.0 CG A:HIS702 3.3 0.5 1.0 CB A:CYS676 3.5 65.1 1.0 CB A:HIS702 3.7 92.5 1.0 CB A:CYS699 3.7 62.4 1.0 O A:ALA678 4.0 82.9 1.0 CA A:CYS679 4.0 84.3 1.0 N A:CYS699 4.1 67.3 1.0 NE2 A:HIS702 4.2 0.9 1.0 OG1 A:THR681 4.2 58.0 1.0 N A:HIS702 4.3 0.6 1.0 CD2 A:HIS702 4.3 0.2 1.0 CA A:CYS699 4.3 65.7 1.0 O A:CYS699 4.4 76.8 1.0 N A:CYS679 4.5 86.0 1.0 C A:ALA678 4.6 81.9 1.0 CB A:TYR701 4.6 98.2 1.0 CA A:HIS702 4.7 0.0 1.0 C A:CYS699 4.7 68.0 1.0 C A:TYR701 4.8 0.5 1.0 CD A:ARG603 4.9 74.6 1.0 CA A:CYS676 4.9 72.5 1.0

Zinc binding site 2 out of 2 in the Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Histone Lysine Demethylase KDM5A in Complex with Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:0.5 occ:1.00 SG A:CYS692 2.2 0.1 1.0 CB A:CYS690 2.3 0.2 1.0 SG A:CYS690 2.4 0.8 1.0 SG A:CYS707 2.6 0.9 1.0 SG A:CYS709 2.7 0.3 1.0 CB A:CYS709 3.1 0.4 1.0 N A:CYS692 3.3 0.0 1.0 CB A:CYS692 3.4 0.0 1.0 N A:SER691 3.5 0.8 1.0 CA A:CYS690 3.6 0.3 1.0 C A:CYS690 3.8 0.4 1.0 CA A:CYS692 3.9 0.4 1.0 C A:SER691 4.3 0.0 1.0 CB A:CYS707 4.3 0.2 1.0 CA A:SER691 4.4 0.5 1.0 CA A:CYS709 4.6 0.1 1.0 N A:CYS690 4.7 0.1 1.0 O A:CYS690 4.9 0.5 1.0 CB A:SER691 5.0 0.8 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