Zinc in PDB 5fyy: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map), PDB code: 5fyy was solved by R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, N.Pearce, 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)	46.41 / 2.18
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.790, 141.790, 152.300, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.2

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map) 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 Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map) (pdb code 5fyy). 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 Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map), PDB code: 5fyy:
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 Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map)


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 Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:34.8 occ:1.00 ND1 A:HIS718 2.1 42.5 1.0 SG A:CYS692 2.2 30.4 1.0 SG A:CYS715 2.2 33.2 1.0 SG A:CYS695 2.4 36.9 1.0 CB A:CYS692 3.0 31.5 1.0 CE1 A:HIS718 3.0 37.8 1.0 CG A:HIS718 3.2 42.5 1.0 CB A:CYS715 3.4 34.1 1.0 CB A:CYS695 3.4 33.8 1.0 CB A:HIS718 3.6 30.8 1.0 N A:CYS695 3.8 37.7 1.0 N A:CYS715 3.9 31.2 1.0 CA A:CYS715 4.2 33.6 1.0 CA A:CYS695 4.2 35.9 1.0 NE2 A:HIS718 4.2 51.1 1.0 CG2 A:THR697 4.3 34.1 1.0 CD2 A:HIS718 4.3 43.2 1.0 CA A:CYS692 4.5 29.9 1.0 N A:HIS718 4.6 34.0 1.0 CD A:ARG619 4.6 39.4 1.0 CB A:LYS694 4.6 31.7 1.0 C A:CYS715 4.7 36.2 1.0 O A:CYS715 4.7 33.1 1.0 CA A:HIS718 4.8 32.6 1.0 CB A:HIS717 4.9 34.2 1.0 C A:CYS695 4.9 36.2 1.0 C A:LYS694 4.9 43.9 1.0 CG A:ARG619 5.0 46.1 1.0 C A:VAL714 5.0 28.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map)


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 Maybridge Fragment 3-Pyridin-3-Ylaniline (N05798A) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:91.3 occ:1.00 CB A:CYS708 2.4 64.2 1.0 SG A:CYS723 2.6 52.1 1.0 SG A:CYS706 2.7 57.1 1.0 SG A:CYS725 2.9 57.9 1.0 SG A:CYS708 3.3 0.2 1.0 CB A:CYS723 3.3 49.4 1.0 CB A:CYS725 3.4 41.5 1.0 CA A:CYS708 3.5 63.5 1.0 CB A:CYS706 3.6 44.5 1.0 N A:CYS708 3.8 47.2 1.0 C A:CYS708 3.9 68.4 1.0 N A:LYS709 4.0 60.4 1.0 N A:CYS725 4.3 54.8 1.0 CA A:CYS725 4.4 45.2 1.0 CG A:LYS709 4.5 60.6 1.0 CA A:CYS723 4.7 40.3 1.0 O A:CYS708 4.7 62.8 1.0 CE1 A:TYR730 4.8 58.1 1.0 C A:CYS706 4.8 47.5 1.0 CA A:CYS706 4.9 36.2 1.0 N A:SER724 4.9 52.9 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 N05798A To Be Published.