Zinc in PDB 5fyt: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A), PDB code: 5fyt was solved by R.Nowak, T.Krojer, C.Johansson, N.Pearce, 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)	70.91 / 1.87
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.810, 141.810, 151.830, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 22.2

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A) also contains other interesting chemical elements:

Fluorine	(F)	1 atom
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 3D Fragment (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A) (pdb code 5fyt). 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 (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A), PDB code: 5fyt:
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 (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A)


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 (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:29.6 occ:1.00 ND1 A:HIS718 2.1 33.3 1.0 SG A:CYS692 2.1 28.3 1.0 SG A:CYS715 2.3 29.3 1.0 SG A:CYS695 2.4 28.2 1.0 CE1 A:HIS718 2.9 33.8 1.0 CB A:CYS692 3.1 24.0 1.0 CG A:HIS718 3.3 36.4 1.0 CB A:CYS695 3.4 28.9 1.0 CB A:CYS715 3.5 31.6 1.0 CB A:HIS718 3.7 28.5 1.0 N A:CYS695 3.8 29.4 1.0 N A:CYS715 3.9 24.2 1.0 NE2 A:HIS718 4.1 36.4 1.0 CA A:CYS695 4.2 31.7 1.0 CA A:CYS715 4.2 27.7 1.0 CD2 A:HIS718 4.3 34.7 1.0 CG2 A:THR697 4.3 31.6 1.0 CB A:LYS694 4.5 34.5 1.0 CD A:ARG619 4.6 38.5 1.0 CA A:CYS692 4.6 25.9 1.0 N A:HIS718 4.6 27.6 1.0 O A:CYS715 4.6 25.7 1.0 C A:CYS715 4.7 26.4 1.0 CA A:HIS718 4.8 32.8 1.0 CB A:HIS717 4.9 32.8 1.0 C A:CYS695 4.9 27.5 1.0 C A:LYS694 4.9 40.1 1.0 CG A:ARG619 4.9 39.1 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 (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A)


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 (5-Fluoro-2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetic Acid (N09996A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:47.1 occ:0.52 CB A:CYS708 2.2 51.1 1.0 SG A:CYS723 2.4 43.0 1.0 SG A:CYS706 2.5 41.4 1.0 SG A:CYS708 2.5 72.0 1.0 SG A:CYS725 2.7 51.2 1.0 CB A:CYS725 3.1 43.5 1.0 CB A:CYS723 3.4 41.2 1.0 CB A:CYS706 3.5 34.4 1.0 CA A:CYS708 3.6 46.6 1.0 N A:CYS708 4.0 38.5 1.0 N A:CYS725 4.1 43.7 1.0 CA A:CYS725 4.2 37.5 1.0 N A:LYS709 4.2 48.9 1.0 C A:CYS708 4.2 57.0 1.0 CE1 A:TYR730 4.4 45.1 1.0 CA A:CYS723 4.7 39.1 1.0 CA A:CYS706 4.8 36.8 1.0 CG A:LYS709 4.8 52.6 1.0 C A:CYS706 4.8 38.5 1.0 N A:SER724 4.9 44.4 1.0 C A:CYS723 5.0 36.2 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 N09996A To Be Published.