Zinc in PDB 5fz1: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (Ligand Modelled Based on Pandda Event Map)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (Ligand Modelled Based on Pandda Event Map), PDB code: 5fz1 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)	96.35 / 2.39
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.300, 143.300, 152.890, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 22.2

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (Ligand Modelled Based on Pandda Event Map) also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (Ligand Modelled Based on Pandda Event Map) (pdb code 5fz1). 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 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (Ligand Modelled Based on Pandda Event Map), PDB code: 5fz1:
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 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (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 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:37.1 occ:1.00 ND1 A:HIS718 2.1 46.0 1.0 SG A:CYS692 2.2 34.7 1.0 SG A:CYS715 2.3 36.2 1.0 SG A:CYS695 2.4 42.0 1.0 CE1 A:HIS718 2.9 49.0 1.0 CB A:CYS692 3.1 33.1 1.0 CG A:HIS718 3.3 50.4 1.0 CB A:CYS695 3.4 36.3 1.0 CB A:CYS715 3.4 30.7 1.0 CB A:HIS718 3.7 33.4 1.0 N A:CYS695 3.8 45.8 1.0 N A:CYS715 3.8 33.0 1.0 NE2 A:HIS718 4.1 55.1 1.0 CA A:CYS715 4.1 40.3 1.0 CA A:CYS695 4.2 37.5 1.0 CD2 A:HIS718 4.3 39.6 1.0 CG2 A:THR697 4.4 32.3 1.0 CA A:CYS692 4.5 32.0 1.0 N A:HIS718 4.6 43.6 1.0 CB A:LYS694 4.7 35.9 1.0 C A:CYS715 4.7 38.6 1.0 O A:CYS715 4.7 38.1 1.0 CD A:ARG619 4.8 36.7 0.7 CA A:HIS718 4.8 35.2 1.0 C A:CYS695 4.9 41.6 1.0 CB A:HIS717 4.9 37.1 1.0 C A:LYS694 4.9 48.1 1.0 CG A:ARG619 5.0 46.6 0.3 C A:VAL714 5.0 40.1 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 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (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 2,4-Dichloro-N-Pyridin-3-Ylbenzamide (E48115B) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:82.8 occ:1.00 CB A:CYS708 2.4 70.6 1.0 SG A:CYS723 2.5 67.4 1.0 SG A:CYS706 2.6 61.4 1.0 SG A:CYS708 2.8 96.4 1.0 SG A:CYS725 2.8 67.9 1.0 CB A:CYS725 3.4 45.0 1.0 CB A:CYS723 3.5 46.7 1.0 CB A:CYS706 3.6 47.0 1.0 CA A:CYS708 3.7 65.8 1.0 N A:CYS708 4.1 52.6 1.0 N A:CYS725 4.2 56.1 1.0 C A:CYS708 4.4 72.1 1.0 CA A:CYS725 4.4 58.4 1.0 N A:LYS709 4.5 66.7 1.0 CE1 A:TYR730 4.5 55.8 1.0 CG A:LYS709 4.8 64.3 1.0 CA A:CYS723 4.9 45.9 1.0 N A:SER724 4.9 54.5 1.0 CA A:CYS706 4.9 43.1 1.0

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. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with E48115B To Be Published.