Zinc in PDB 5fzb: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening), PDB code: 5fzb was solved by R.Nowak, T.Krojer, C.Johansson, K.Kupinska, A.Szykowska, N.Pearce, R.Talon, P.Collins, C.Gileadi, C.Strain-Damerell, 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)	96.52 / 2.18
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.410, 143.410, 153.370, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.7

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) 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 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) (pdb code 5fzb). 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 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening), PDB code: 5fzb:
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 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening)


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 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:40.4 occ:1.00 ND1 A:HIS718 2.2 51.7 1.0 SG A:CYS692 2.2 39.0 1.0 SG A:CYS715 2.3 39.6 1.0 SG A:CYS695 2.4 42.6 1.0 CE1 A:HIS718 3.0 47.1 1.0 CB A:CYS692 3.1 39.8 1.0 CG A:HIS718 3.3 48.8 1.0 CB A:CYS695 3.4 39.2 1.0 CB A:CYS715 3.6 40.9 1.0 CB A:HIS718 3.7 46.8 1.0 N A:CYS695 3.8 44.3 1.0 N A:CYS715 3.9 35.1 1.0 CA A:CYS695 4.1 40.6 1.0 NE2 A:HIS718 4.2 54.5 1.0 CA A:CYS715 4.3 40.8 1.0 CD2 A:HIS718 4.3 50.9 1.0 CG2 A:THR697 4.4 38.5 1.0 CB A:LYS694 4.5 40.8 1.0 CA A:CYS692 4.6 36.6 1.0 N A:HIS718 4.6 47.6 1.0 CD A:ARG619 4.7 48.3 1.0 O A:CYS715 4.8 36.3 1.0 C A:CYS715 4.8 36.8 1.0 CA A:HIS718 4.8 46.5 1.0 C A:CYS695 4.8 44.2 1.0 C A:LYS694 4.9 52.0 1.0 CB A:HIS717 4.9 42.0 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 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening)


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 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:0.9 occ:1.00 CB A:CYS708 2.4 78.7 1.0 SG A:CYS723 2.6 73.5 1.0 SG A:CYS706 2.7 68.9 1.0 SG A:CYS708 2.8 99.2 1.0 SG A:CYS725 2.9 73.7 1.0 CB A:CYS725 3.3 58.5 1.0 CB A:CYS723 3.6 52.5 1.0 CB A:CYS706 3.7 54.9 1.0 CA A:CYS708 3.8 68.1 1.0 N A:CYS708 4.1 59.6 1.0 N A:CYS725 4.2 64.9 1.0 CA A:CYS725 4.4 60.4 1.0 C A:CYS708 4.4 76.6 1.0 N A:LYS709 4.5 70.8 1.0 CE1 A:TYR730 4.5 58.7 1.0 CG A:LYS709 4.7 68.4 1.0 N A:SER724 4.9 61.9 1.0 CA A:CYS723 5.0 54.3 1.0 CA A:CYS706 5.0 48.7 1.0

R.Nowak, T.Krojer, C.Johansson, K.Kupinska, A.Szykowska, N.Pearce, R.Talon, P.Collins, C.Gileadi, C.Strain-Damerell, 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 Maybridge Fragment 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc -Diamond I04-1 Fragment Screening) To Be Published.