Zinc in PDB 5fxx: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with Oxaloacetate

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with Oxaloacetate, PDB code: 5fxx 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)	42.77 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.590, 110.700, 119.740, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.6

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with Oxaloacetate 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 Oxaloacetate (pdb code 5fxx). 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 Oxaloacetate, PDB code: 5fxx:
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 Oxaloacetate


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 Oxaloacetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4002 b:34.0 occ:1.00 SG A:CYS1278 2.2 30.4 1.0 SG A:CYS1305 2.3 33.0 1.0 SG A:CYS1281 2.4 34.0 1.0 SG A:CYS1308 2.4 34.1 1.0 CB A:CYS1278 3.2 36.9 1.0 CB A:CYS1308 3.2 37.3 1.0 CB A:CYS1281 3.2 35.7 1.0 CB A:CYS1305 3.5 26.7 1.0 N A:CYS1281 3.8 40.0 1.0 CA A:CYS1281 4.1 37.5 1.0 O A:HOH2261 4.1 45.5 1.0 N A:CYS1305 4.1 24.9 1.0 N A:CYS1308 4.2 33.1 1.0 CA A:CYS1308 4.3 36.2 1.0 CA A:CYS1305 4.4 30.9 1.0 CG1 A:VAL1283 4.4 32.3 1.0 CA A:CYS1278 4.6 37.2 1.0 O A:HOH2257 4.7 39.5 1.0 C A:CYS1281 4.8 37.0 1.0 CB A:ILE1280 4.8 40.4 1.0 O A:CYS1305 4.9 28.6 1.0 C A:CYS1305 4.9 30.8 1.0 N A:GLU1282 4.9 33.6 1.0 C A:ILE1280 4.9 45.0 1.0

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


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 Oxaloacetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4002 b:30.8 occ:1.00 SG B:CYS1305 2.3 29.4 1.0 SG B:CYS1278 2.4 27.8 1.0 SG B:CYS1281 2.4 29.0 1.0 SG B:CYS1308 2.5 33.2 1.0 CB B:CYS1308 3.2 33.6 1.0 CB B:CYS1281 3.2 25.8 1.0 CB B:CYS1278 3.2 30.8 1.0 CB B:CYS1305 3.5 34.0 1.0 N B:CYS1281 3.7 31.9 1.0 CA B:CYS1281 4.0 31.2 1.0 N B:CYS1305 4.1 21.9 1.0 N B:CYS1308 4.3 33.4 1.0 CA B:CYS1305 4.3 28.7 1.0 CA B:CYS1308 4.4 32.8 1.0 CG1 B:VAL1283 4.4 25.0 1.0 O B:HOH2239 4.4 41.7 1.0 CB B:ILE1280 4.6 30.5 1.0 CA B:CYS1278 4.7 38.7 1.0 C B:CYS1281 4.7 39.5 1.0 C B:ILE1280 4.8 38.1 1.0 N B:GLU1282 4.9 33.5 1.0 O B:HOH2263 4.9 34.2 1.0 C B:CYS1305 4.9 36.6 1.0 O B:CYS1305 5.0 30.0 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 Oxaloacetate To Be Published.