Zinc in PDB 5fzf: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3962

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3962, PDB code: 5fzf 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, 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)	70.86 / 1.97
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.710, 141.710, 150.910, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21.1

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3962 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 MC3962 (pdb code 5fzf). 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 MC3962, PDB code: 5fzf:
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 MC3962


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 MC3962 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:32.3 occ:1.00 ND1 A:HIS718 2.0 38.8 1.0 SG A:CYS692 2.2 30.2 1.0 SG A:CYS715 2.3 32.4 1.0 SG A:CYS695 2.4 30.6 1.0 CE1 A:HIS718 2.9 39.6 1.0 CB A:CYS692 3.1 27.8 1.0 CG A:HIS718 3.2 40.1 1.0 CB A:CYS695 3.4 30.8 1.0 CB A:CYS715 3.4 29.2 1.0 CB A:HIS718 3.6 32.2 1.0 N A:CYS695 3.8 36.5 1.0 N A:CYS715 3.9 28.2 1.0 NE2 A:HIS718 4.0 42.1 1.0 CA A:CYS695 4.1 34.7 1.0 CA A:CYS715 4.2 29.2 1.0 CD2 A:HIS718 4.2 41.8 1.0 CG2 A:THR697 4.3 29.5 1.0 CB A:LYS694 4.6 32.2 1.0 CA A:CYS692 4.6 32.5 1.0 N A:HIS718 4.6 33.0 1.0 CD A:ARG619 4.6 38.1 1.0 O A:CYS715 4.7 30.1 1.0 C A:CYS715 4.7 27.1 1.0 CB A:HIS717 4.8 32.0 1.0 CA A:HIS718 4.8 36.7 1.0 C A:CYS695 4.8 34.0 1.0 C A:LYS694 4.9 45.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3962


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 MC3962 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1756 b:59.3 occ:1.00 CB A:CYS708 2.4 51.1 1.0 SG A:CYS723 2.4 45.1 1.0 SG A:CYS706 2.5 45.2 1.0 SG A:CYS725 2.6 50.1 1.0 SG A:CYS708 2.7 76.9 1.0 CB A:CYS725 3.1 37.1 1.0 O A:HOH2243 3.4 66.4 1.0 CB A:CYS706 3.4 37.0 1.0 CB A:CYS723 3.4 40.1 1.0 CA A:CYS708 3.7 52.9 1.0 N A:CYS708 4.0 41.4 1.0 N A:CYS725 4.2 46.5 1.0 CA A:CYS725 4.3 39.4 1.0 CE1 A:TYR730 4.4 46.7 1.0 C A:CYS708 4.4 58.0 1.0 N A:LYS709 4.4 47.9 1.0 CG A:LYS709 4.7 54.8 1.0 CA A:CYS706 4.7 32.6 1.0 CA A:CYS723 4.8 40.4 1.0 C A:CYS706 4.9 37.1 1.0 N A:SER724 5.0 47.0 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, D.Rotili, A.Mai, U.Oppermann. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with MC3962 To Be Published.