Zinc in PDB 3zpo: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1, PDB code: 3zpo was solved by M.Vollmar, C.Gileadi, L.Shrestha, S.Goubin, C.Johansson, T.Krojer, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.51 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.158, 110.755, 119.492, 90.00, 90.00, 90.00
R / Rfree (%)	17.745 / 20.977

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1 also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1 (pdb code 3zpo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1, PDB code: 3zpo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1901 b:28.4 occ:1.00 SG A:CYS1278 2.2 26.7 1.0 SG A:CYS1305 2.3 27.5 1.0 SG A:CYS1281 2.4 30.0 1.0 SG A:CYS1308 2.4 28.7 1.0 CB A:CYS1308 3.1 27.1 1.0 CB A:CYS1278 3.2 26.4 1.0 CB A:CYS1281 3.3 31.9 1.0 CB A:CYS1305 3.5 24.8 1.0 N A:CYS1281 3.8 31.9 1.0 N A:CYS1305 4.0 25.2 1.0 CA A:CYS1281 4.1 32.5 1.0 N A:CYS1308 4.2 27.5 1.0 CA A:CYS1308 4.3 27.3 1.0 CA A:CYS1305 4.3 25.0 1.0 O A:HOH2260 4.3 37.8 1.0 CG1 A:VAL1283 4.3 31.1 1.0 O A:HOH2258 4.4 39.5 1.0 CB A:ILE1280 4.5 36.7 1.0 O A:HOH2239 4.5 44.8 1.0 CA A:CYS1278 4.6 26.3 1.0 C A:CYS1281 4.8 32.6 1.0 C A:ILE1280 4.9 34.6 1.0 C A:CYS1305 4.9 24.6 1.0 O A:CYS1305 4.9 23.5 1.0 N A:GLU1282 4.9 30.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty with Bound Gsk J1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1902 b:27.3 occ:1.00 SG B:CYS1305 2.2 25.2 1.0 SG B:CYS1278 2.3 25.2 1.0 SG B:CYS1281 2.4 28.0 1.0 SG B:CYS1308 2.4 26.7 1.0 CB B:CYS1308 3.2 25.2 1.0 CB B:CYS1278 3.2 25.3 1.0 CB B:CYS1281 3.3 28.2 1.0 CB B:CYS1305 3.4 25.4 1.0 N B:CYS1281 3.8 29.0 1.0 N B:CYS1305 4.0 25.3 1.0 CA B:CYS1281 4.1 30.0 1.0 N B:CYS1308 4.2 24.9 1.0 CA B:CYS1305 4.3 25.1 1.0 CA B:CYS1308 4.3 25.3 1.0 CG1 B:VAL1283 4.3 27.6 1.0 O B:HOH2229 4.4 39.5 1.0 O B:HOH2247 4.5 40.0 1.0 CB B:ILE1280 4.5 33.3 1.0 CA B:CYS1278 4.7 25.2 1.0 C B:CYS1281 4.8 29.9 1.0 C B:CYS1305 4.9 24.6 1.0 C B:ILE1280 4.9 31.3 1.0 O B:CYS1305 4.9 22.7 1.0 N B:GLU1282 5.0 29.2 1.0

L.J.Walport, R.J.Hopkinson, M.Vollmar, S.K.Madden, C.Gileadi, U.Oppermann, C.J.Schofield, C.Johansson. Human Uty(KDM6C) Is A Male-Specific Nepislon-Methyl Lysyl Demethylase. J.Biol.Chem. V. 289 18302 2014.
ISSN: ISSN 0021-9258
PubMed: 24798337
DOI: 10.1074/JBC.M114.555052