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

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate, PDB code: 5fys 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)	47.88 / 1.89
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.080, 142.080, 152.470, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 22.1

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

Manganese	(Mn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate (pdb code 5fys). 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 D-2-Hydroxyglutarate, PDB code: 5fys:
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 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 the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:31.1 occ:1.00 ND1 A:HIS718 2.1 39.6 1.0 SG A:CYS692 2.2 29.5 1.0 SG A:CYS715 2.3 31.2 1.0 SG A:CYS695 2.4 28.4 1.0 CE1 A:HIS718 3.0 39.6 1.0 CB A:CYS692 3.2 25.6 1.0 CG A:HIS718 3.3 38.2 1.0 CB A:CYS695 3.3 28.9 1.0 CB A:CYS715 3.5 31.0 1.0 CB A:HIS718 3.7 34.3 1.0 N A:CYS695 3.8 31.8 1.0 N A:CYS715 3.9 26.0 1.0 CA A:CYS695 4.1 30.8 1.0 NE2 A:HIS718 4.2 38.1 1.0 CA A:CYS715 4.2 30.1 1.0 CD2 A:HIS718 4.3 36.3 1.0 CG2 A:THR697 4.4 33.6 1.0 N A:HIS718 4.6 29.7 1.0 CB A:LYS694 4.6 32.8 1.0 CD A:ARG619 4.6 33.3 0.7 CA A:CYS692 4.6 28.2 1.0 O A:CYS715 4.7 27.8 1.0 C A:CYS715 4.7 26.7 1.0 C A:CYS695 4.8 33.0 1.0 CB A:HIS717 4.8 33.5 1.0 CA A:HIS718 4.8 38.2 1.0 CD A:ARG619 4.8 33.1 0.3 C A:LYS694 4.9 40.7 1.0 N A:LYS696 5.0 29.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B 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 the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:52.0 occ:1.00 SG A:CYS723 2.3 43.7 1.0 SG A:CYS706 2.5 40.0 1.0 CB A:CYS708 2.5 52.7 1.0 SG A:CYS708 2.5 60.3 1.0 SG A:CYS725 2.6 48.6 1.0 CB A:CYS725 3.2 37.7 1.0 CB A:CYS723 3.3 38.5 1.0 CB A:CYS706 3.4 35.4 1.0 CA A:CYS708 3.9 47.6 1.0 N A:CYS725 4.1 42.0 1.0 CA A:CYS725 4.3 37.8 1.0 N A:CYS708 4.3 40.7 1.0 CE1 A:TYR730 4.4 36.6 1.0 C A:CYS708 4.6 52.6 1.0 CA A:CYS723 4.7 38.7 1.0 CA A:CYS706 4.7 34.9 1.0 N A:LYS709 4.7 48.2 1.0 CG A:LYS709 4.7 52.3 1.0 N A:SER724 4.9 40.6 1.0 C A:CYS723 4.9 39.8 1.0 C A:CYS706 4.9 39.1 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 D-2-Hydroxyglutarate To Be Published.