Zinc in PDB 5fzg: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3948

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3948, PDB code: 5fzg was solved by R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, V.Srikannathasan, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, D.Rotili, A.Mai, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.96 / 1.96
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.920, 141.920, 151.220, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.4

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3948 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 MC3948 (pdb code 5fzg). 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 MC3948, PDB code: 5fzg:
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 MC3948


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 MC3948 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:33.7 occ:1.00 ND1 A:HIS718 2.1 38.2 1.0 SG A:CYS692 2.1 30.4 1.0 SG A:CYS715 2.3 33.2 1.0 SG A:CYS695 2.4 31.2 1.0 CE1 A:HIS718 2.9 43.2 1.0 CB A:CYS692 3.1 29.4 1.0 CG A:HIS718 3.2 41.3 1.0 CB A:CYS695 3.4 30.8 1.0 CB A:CYS715 3.5 33.6 1.0 CB A:HIS718 3.7 34.3 1.0 N A:CYS695 3.8 36.3 1.0 N A:CYS715 3.9 28.3 1.0 NE2 A:HIS718 4.1 43.6 1.0 CA A:CYS695 4.1 36.6 1.0 CA A:CYS715 4.2 29.3 1.0 CD2 A:HIS718 4.3 42.5 1.0 CG2 A:THR697 4.4 35.2 1.0 CA A:CYS692 4.6 34.5 1.0 CD A:ARG619 4.6 41.6 1.0 CB A:LYS694 4.6 37.8 1.0 N A:HIS718 4.6 31.9 1.0 O A:CYS715 4.7 31.4 1.0 C A:CYS715 4.7 28.7 1.0 CA A:HIS718 4.8 36.6 1.0 C A:CYS695 4.8 33.7 1.0 C A:LYS694 4.9 46.3 1.0 CB A:HIS717 4.9 38.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3948


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 MC3948 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:56.0 occ:1.00 SG A:CYS723 2.4 44.6 1.0 CB A:CYS708 2.5 51.1 1.0 SG A:CYS706 2.5 41.3 1.0 SG A:CYS725 2.6 48.2 1.0 SG A:CYS708 2.6 62.9 1.0 CB A:CYS725 3.1 41.9 1.0 CB A:CYS723 3.4 39.6 1.0 CB A:CYS706 3.5 35.6 1.0 O A:HOH2241 3.8 64.3 1.0 CA A:CYS708 3.8 49.7 1.0 N A:CYS725 4.1 46.6 1.0 N A:CYS708 4.2 38.4 1.0 CA A:CYS725 4.2 44.3 1.0 CE1 A:TYR730 4.4 41.3 1.0 C A:CYS708 4.5 53.3 1.0 N A:LYS709 4.6 44.4 1.0 CG A:LYS709 4.7 54.9 1.0 CA A:CYS723 4.7 41.0 1.0 CA A:CYS706 4.8 34.3 1.0 N A:SER724 4.9 47.4 1.0 C A:CYS706 4.9 33.8 1.0 C A:CYS723 5.0 40.5 1.0

R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, V.Srikannathasan, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, D.Rotili, A.Mai, U.Oppermann. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3948 To Be Published.