Zinc in PDB 5fyz: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A), PDB code: 5fyz was solved by R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, F.Von Delft, P.E.Brennan, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.58 / 1.75
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.880, 141.880, 152.080, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 23.1

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A) also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A) (pdb code 5fyz). 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 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A), PDB code: 5fyz:
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 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A)


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 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:27.4 occ:1.00 ND1 A:HIS718 2.1 30.1 1.0 SG A:CYS692 2.1 25.6 1.0 SG A:CYS715 2.3 27.0 1.0 SG A:CYS695 2.4 24.3 1.0 CE1 A:HIS718 2.9 30.0 1.0 CB A:CYS692 3.1 21.5 1.0 CG A:HIS718 3.3 33.1 1.0 CB A:CYS695 3.4 25.9 1.0 CB A:CYS715 3.5 26.6 1.0 CB A:HIS718 3.7 28.5 1.0 N A:CYS695 3.8 29.1 1.0 N A:CYS715 4.0 21.7 1.0 NE2 A:HIS718 4.1 31.7 1.0 CA A:CYS695 4.2 27.4 1.0 CA A:CYS715 4.2 24.7 1.0 CD2 A:HIS718 4.3 29.7 1.0 CG2 A:THR697 4.3 25.7 1.0 CA A:CYS692 4.6 21.3 1.0 N A:HIS718 4.6 27.2 1.0 CB A:LYS694 4.6 30.5 1.0 CD A:ARG619 4.6 33.7 1.0 O A:CYS715 4.7 25.7 1.0 C A:CYS715 4.7 23.4 1.0 CB A:HIS717 4.8 28.7 1.0 CA A:HIS718 4.8 30.7 1.0 C A:CYS695 4.8 27.6 1.0 C A:LYS694 4.9 36.6 1.0 CG A:ARG619 5.0 34.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A)


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 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:76.8 occ:1.00 SG A:CYS723 2.4 41.1 1.0 CB A:CYS708 2.4 49.9 1.0 SG A:CYS706 2.6 36.5 1.0 SG A:CYS708 2.7 76.7 1.0 SG A:CYS725 2.7 46.4 1.0 CB A:CYS725 3.1 39.3 1.0 CB A:CYS723 3.3 39.7 1.0 CB A:CYS706 3.6 33.0 1.0 CA A:CYS708 3.7 45.6 1.0 N A:CYS708 4.1 38.6 1.0 N A:CYS725 4.1 41.5 1.0 CA A:CYS725 4.2 35.7 1.0 C A:CYS708 4.3 50.0 1.0 N A:LYS709 4.3 44.4 1.0 CE1 A:TYR730 4.4 38.6 1.0 CG A:LYS709 4.6 53.7 1.0 CA A:CYS723 4.7 35.9 1.0 CA A:CYS706 4.9 33.5 1.0 N A:SER724 4.9 39.6 1.0 C A:CYS723 4.9 35.9 1.0 C A:CYS706 4.9 35.6 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 N10063A To Be Published.