Zinc in PDB 5fy0: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate, PDB code: 5fy0 was solved by R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, 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)	70.59 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.610, 110.740, 120.750, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.5

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate (pdb code 5fy0). 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 in Complex with L-Malate, PDB code: 5fy0:
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 in Complex with L-Malate


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 in Complex with L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4002 b:33.0 occ:1.00 SG A:CYS1278 2.2 31.7 1.0 SG A:CYS1305 2.3 30.1 1.0 SG A:CYS1281 2.4 34.8 1.0 SG A:CYS1308 2.5 32.3 1.0 CB A:CYS1278 3.1 39.1 1.0 CB A:CYS1308 3.2 29.4 1.0 CB A:CYS1281 3.3 33.0 1.0 CB A:CYS1305 3.4 30.4 1.0 N A:CYS1281 3.8 36.5 1.0 N A:CYS1305 3.9 26.0 1.0 CA A:CYS1281 4.1 30.0 1.0 CA A:CYS1305 4.2 33.9 1.0 N A:CYS1308 4.3 30.3 1.0 CA A:CYS1308 4.3 32.5 1.0 CG1 A:VAL1283 4.3 37.0 1.0 O A:HOH2280 4.4 36.7 1.0 CA A:CYS1278 4.6 35.9 1.0 O A:HOH2275 4.7 36.6 1.0 CB A:ILE1280 4.7 42.9 1.0 C A:CYS1281 4.8 35.9 1.0 N A:GLU1282 4.8 34.7 1.0 C A:CYS1305 4.8 33.5 1.0 O A:CYS1305 4.8 31.7 1.0 C A:ILE1280 4.9 42.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate


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 in Complex with L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4002 b:32.6 occ:1.00 SG B:CYS1278 2.3 30.7 1.0 SG B:CYS1305 2.3 30.3 1.0 SG B:CYS1281 2.4 35.2 1.0 SG B:CYS1308 2.4 39.1 1.0 CB B:CYS1278 3.2 30.8 1.0 CB B:CYS1308 3.2 32.0 1.0 CB B:CYS1281 3.3 32.1 1.0 CB B:CYS1305 3.4 33.0 1.0 N B:CYS1281 3.8 34.9 1.0 N B:CYS1305 4.0 28.5 1.0 CA B:CYS1281 4.1 34.5 1.0 O B:HOH2235 4.2 41.7 1.0 CA B:CYS1305 4.3 31.7 1.0 N B:CYS1308 4.3 37.3 1.0 CA B:CYS1308 4.3 38.0 1.0 CG1 B:VAL1283 4.3 37.3 1.0 CB B:ILE1280 4.6 33.4 1.0 CA B:CYS1278 4.6 38.2 1.0 O B:HOH2260 4.7 43.2 1.0 C B:CYS1281 4.8 39.6 1.0 C B:ILE1280 4.8 37.6 1.0 N B:GLU1282 4.9 35.9 1.0 C B:CYS1305 4.9 40.4 1.0 O B:CYS1305 4.9 35.9 1.0 O B:HOH2257 4.9 37.0 1.0

R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann. Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate To Be Published.