Zinc in PDB 5fz8: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Malate

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Malate, PDB code: 5fz8 was solved by R.Nowak, T.Krojer, 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)	61.57 / 1.86
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.200, 142.200, 152.470, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 23.7

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Malate 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 Malate (pdb code 5fz8). 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 Malate, PDB code: 5fz8:
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 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 the Catalytic Domain of Human JARID1B in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:31.8 occ:1.00 ND1 A:HIS718 2.1 38.4 1.0 SG A:CYS692 2.2 30.9 1.0 SG A:CYS715 2.3 31.5 1.0 SG A:CYS695 2.4 29.2 1.0 CE1 A:HIS718 2.9 38.4 1.0 CB A:CYS692 3.2 23.8 1.0 CG A:HIS718 3.3 39.8 1.0 CB A:CYS695 3.4 29.0 1.0 CB A:CYS715 3.5 29.4 1.0 N A:CYS695 3.8 34.0 1.0 CB A:HIS718 3.8 32.7 1.0 N A:CYS715 3.9 26.1 1.0 NE2 A:HIS718 4.1 43.5 1.0 CA A:CYS695 4.1 30.5 1.0 CA A:CYS715 4.2 30.9 1.0 CD2 A:HIS718 4.3 35.2 1.0 CG2 A:THR697 4.4 33.7 1.0 N A:HIS718 4.6 30.4 1.0 CB A:LYS694 4.6 33.3 1.0 CA A:CYS692 4.6 28.5 1.0 CD A:ARG619 4.6 43.2 1.0 O A:CYS715 4.7 30.8 1.0 C A:CYS715 4.7 27.0 1.0 CB A:HIS717 4.8 30.5 1.0 C A:CYS695 4.8 31.9 1.0 CA A:HIS718 4.9 37.1 1.0 C A:LYS694 4.9 41.4 1.0 N A:LYS696 5.0 32.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 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 the Catalytic Domain of Human JARID1B in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1756 b:55.6 occ:1.00 SG A:CYS723 2.3 46.1 1.0 CB A:CYS708 2.4 54.5 1.0 SG A:CYS706 2.4 39.9 1.0 SG A:CYS725 2.6 50.3 1.0 SG A:CYS708 2.6 64.8 1.0 CB A:CYS725 3.1 39.8 1.0 CB A:CYS723 3.3 38.2 1.0 CB A:CYS706 3.4 40.0 1.0 CA A:CYS708 3.8 46.9 1.0 N A:CYS725 4.1 46.1 1.0 N A:CYS708 4.2 44.1 1.0 CA A:CYS725 4.2 42.5 1.0 CE1 A:TYR730 4.3 39.3 1.0 C A:CYS708 4.5 57.2 1.0 N A:LYS709 4.6 48.0 1.0 CA A:CYS723 4.7 39.0 1.0 CA A:CYS706 4.7 37.0 1.0 C A:CYS706 4.9 41.3 1.0 N A:SER724 4.9 42.3 1.0 C A:CYS723 4.9 39.3 1.0 CD1 A:TYR730 5.0 37.0 1.0

R.Nowak, T.Krojer, 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 Malate To Be Published.