Zinc in PDB 5fz6: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment N05859B (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 N05859B (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening), PDB code: 5fz6 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)	96.57 / 2.33
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.490, 143.490, 153.430, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21.9

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment N05859B (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 N05859B (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) (pdb code 5fz6). 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 N05859B (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening), PDB code: 5fz6:
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 N05859B (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 N05859B (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:35.3 occ:1.00 ND1 A:HIS718 2.1 43.5 1.0 SG A:CYS692 2.2 32.5 1.0 SG A:CYS715 2.3 34.2 1.0 SG A:CYS695 2.5 37.4 1.0 CE1 A:HIS718 2.9 43.0 1.0 CB A:CYS692 3.1 32.0 1.0 CG A:HIS718 3.2 45.9 1.0 CB A:CYS695 3.4 31.6 1.0 CB A:CYS715 3.5 28.6 1.0 CB A:HIS718 3.7 35.8 1.0 N A:CYS695 3.8 39.7 1.0 N A:CYS715 3.9 32.0 1.0 NE2 A:HIS718 4.1 51.3 1.0 CA A:CYS715 4.2 38.8 1.0 CA A:CYS695 4.2 37.5 1.0 CD2 A:HIS718 4.3 40.3 1.0 CG2 A:THR697 4.4 31.3 1.0 N A:HIS718 4.6 41.9 1.0 CB A:LYS694 4.6 32.6 1.0 CA A:CYS692 4.6 29.1 1.0 C A:CYS715 4.7 33.6 1.0 O A:CYS715 4.7 32.1 1.0 CA A:HIS718 4.8 41.0 1.0 CD A:ARG619 4.8 38.2 0.3 CB A:HIS717 4.8 33.8 1.0 CD A:ARG619 4.9 37.1 0.7 C A:CYS695 4.9 38.3 1.0 C A:LYS694 4.9 43.6 1.0 C A:VAL714 5.0 34.7 1.0 CG A:ARG619 5.0 41.9 0.3

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment N05859B (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 N05859B (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:96.3 occ:1.00 CB A:CYS708 2.4 71.2 1.0 SG A:CYS723 2.6 63.5 1.0 SG A:CYS706 2.7 63.4 1.0 SG A:CYS708 2.8 1.0 1.0 SG A:CYS725 2.9 71.8 1.0 CB A:CYS725 3.3 46.2 1.0 CB A:CYS723 3.5 45.6 1.0 CB A:CYS706 3.7 46.9 1.0 CA A:CYS708 3.7 61.6 1.0 N A:CYS708 4.1 50.9 1.0 N A:CYS725 4.2 56.6 1.0 CA A:CYS725 4.4 54.3 1.0 C A:CYS708 4.4 70.5 1.0 N A:LYS709 4.5 64.5 1.0 CE1 A:TYR730 4.6 57.7 1.0 CG A:LYS709 4.7 62.4 1.0 N A:SER724 4.9 54.5 1.0 CA A:CYS723 4.9 47.3 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 N05859B (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) To Be Published.