Zinc in PDB 5fzd: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with L-2-Hydroxyglutarate

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with L-2-Hydroxyglutarate, PDB code: 5fzd was solved by R.Nowak, J.Kopec, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.69 / 2.05
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.800, 141.800, 151.410, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.5

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with L-2-Hydroxyglutarate also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with L-2-Hydroxyglutarate (pdb code 5fzd). 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 the Catalytic Domain of Human JARID1B in Complex with L-2-Hydroxyglutarate, PDB code: 5fzd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with L-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 the Catalytic Domain of Human JARID1B in Complex with L-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:57.1 occ:1.00 SG A:CYS723 2.3 48.1 1.0 CB A:CYS708 2.4 56.9 1.0 SG A:CYS706 2.5 43.6 1.0 SG A:CYS708 2.6 69.0 1.0 SG A:CYS725 2.6 52.7 1.0 CB A:CYS725 3.2 38.0 1.0 CB A:CYS723 3.3 45.7 1.0 CB A:CYS706 3.3 42.9 1.0 CA A:CYS708 3.8 50.2 1.0 N A:CYS725 4.1 49.2 1.0 N A:CYS708 4.2 42.9 1.0 CA A:CYS725 4.2 44.5 1.0 CE1 A:TYR730 4.4 43.0 1.0 C A:CYS708 4.5 60.6 1.0 CA A:CYS723 4.6 42.8 1.0 CA A:CYS706 4.7 39.5 1.0 N A:LYS709 4.7 50.8 1.0 N A:SER724 4.8 46.5 1.0 C A:CYS706 4.9 42.7 1.0 C A:CYS723 4.9 47.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with L-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 the Catalytic Domain of Human JARID1B in Complex with L-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:35.0 occ:1.00 SG A:CYS692 2.2 32.7 1.0 ND1 A:HIS718 2.2 36.7 1.0 SG A:CYS715 2.3 34.8 1.0 SG A:CYS695 2.4 34.6 1.0 CE1 A:HIS718 3.0 42.6 1.0 CB A:CYS692 3.1 29.9 1.0 CG A:HIS718 3.3 44.0 1.0 CB A:CYS695 3.4 32.4 1.0 CB A:CYS715 3.5 35.7 1.0 CB A:HIS718 3.7 37.5 1.0 N A:CYS695 3.8 36.4 1.0 N A:CYS715 3.8 33.1 1.0 CA A:CYS695 4.1 35.5 1.0 CA A:CYS715 4.2 33.8 1.0 NE2 A:HIS718 4.2 46.8 1.0 CD2 A:HIS718 4.4 42.8 1.0 CG2 A:THR697 4.4 32.4 1.0 CB A:LYS694 4.5 31.4 1.0 N A:HIS718 4.5 36.5 1.0 CD A:ARG619 4.5 39.8 0.6 CA A:CYS692 4.5 33.1 1.0 O A:CYS715 4.7 32.6 1.0 C A:CYS715 4.7 34.6 1.0 CB A:HIS717 4.8 33.9 1.0 CA A:HIS718 4.8 36.7 1.0 C A:CYS695 4.8 37.8 1.0 C A:LYS694 4.9 44.7 1.0 CD A:ARG619 4.9 38.4 0.4 CG A:ARG619 4.9 41.7 0.6 N A:LYS696 5.0 32.8 1.0 C A:VAL714 5.0 32.3 1.0

R.Nowak, J.Kopec, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with L-2-Hydroxyglutarate To Be Published.