Zinc in PDB 5fym: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate, PDB code: 5fym 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)	36.82 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.480, 109.340, 117.300, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.5

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate 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 D-2-Hydroxyglutarate (pdb code 5fym). 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 D-2-Hydroxyglutarate, PDB code: 5fym:
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 D-2-Hydroxyglutarate


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 D-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4002 b:35.9 occ:1.00 SG A:CYS1199 2.2 29.3 1.0 SG A:CYS1226 2.2 33.2 1.0 SG A:CYS1202 2.4 34.4 1.0 SG A:CYS1229 2.4 35.4 1.0 CB A:CYS1229 3.1 32.0 1.0 CB A:CYS1199 3.1 35.0 1.0 CB A:CYS1202 3.3 33.7 1.0 CB A:CYS1226 3.5 27.6 1.0 N A:CYS1202 3.7 32.4 1.0 CA A:CYS1202 4.1 39.5 1.0 N A:CYS1226 4.1 27.9 1.0 O A:HOH3293 4.1 47.1 1.0 CG1 A:VAL1204 4.2 33.1 1.0 N A:CYS1229 4.3 32.9 1.0 CA A:CYS1229 4.3 36.0 1.0 CA A:CYS1226 4.3 31.8 1.0 O A:HOH3289 4.4 43.0 1.0 CA A:CYS1199 4.6 40.5 1.0 CB A:ILE1201 4.7 39.8 1.0 C A:CYS1202 4.7 38.1 1.0 C A:ILE1201 4.8 43.2 1.0 N A:GLU1203 4.8 37.1 1.0 C A:CYS1226 4.9 31.6 1.0 O A:CYS1226 4.9 28.6 1.0

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


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 D-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4002 b:31.2 occ:1.00 SG B:CYS1226 2.2 29.4 1.0 SG B:CYS1199 2.3 28.6 1.0 SG B:CYS1229 2.3 35.0 1.0 SG B:CYS1202 2.4 30.3 1.0 CB B:CYS1199 3.1 30.7 1.0 CB B:CYS1229 3.1 31.4 1.0 CB B:CYS1202 3.3 25.2 1.0 CB B:CYS1226 3.5 28.0 1.0 N B:CYS1202 3.7 25.2 1.0 N B:CYS1226 4.0 23.9 1.0 CA B:CYS1202 4.1 33.3 1.0 O B:HOH3266 4.2 44.6 1.0 N B:CYS1229 4.2 31.6 1.0 CA B:CYS1229 4.3 32.8 1.0 CA B:CYS1226 4.3 30.4 1.0 CG1 B:VAL1204 4.4 24.1 1.0 O B:HOH3295 4.4 45.9 1.0 CB B:ILE1201 4.5 32.1 1.0 CA B:CYS1199 4.6 33.9 1.0 C B:CYS1202 4.8 34.0 1.0 N B:GLU1203 4.8 32.4 1.0 C B:ILE1201 4.9 34.5 1.0 O B:HOH3287 4.9 34.6 1.0 C B:CYS1226 4.9 33.8 1.0 O B:CYS1226 4.9 30.5 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 D-2- Hydroxyglutarate To Be Published.