Zinc in PDB 5fz4: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (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 3D Fragment (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening), PDB code: 5fz4 was solved by R.Nowak, T.Krojer, N.Pearce, R.Talon, P.Collins, 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)	70.68 / 2.07
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.360, 141.360, 151.960, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 23.4

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (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 3D Fragment (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) (pdb code 5fz4). 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 (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening), PDB code: 5fz4:
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 (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (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 3D Fragment (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (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:37.9 occ:1.00 ND1 A:HIS718 2.1 48.1 1.0 SG A:CYS692 2.2 36.0 1.0 SG A:CYS715 2.3 36.5 1.0 SG A:CYS695 2.4 39.0 1.0 CE1 A:HIS718 2.9 47.0 1.0 CB A:CYS692 3.1 34.5 1.0 CG A:HIS718 3.2 47.0 1.0 CB A:CYS695 3.4 37.4 1.0 CB A:CYS715 3.5 36.3 1.0 CB A:HIS718 3.6 38.4 1.0 N A:CYS695 3.7 44.4 1.0 N A:CYS715 3.8 37.1 1.0 CA A:CYS695 4.1 39.2 1.0 NE2 A:HIS718 4.1 50.7 1.0 CA A:CYS715 4.2 38.4 1.0 CD2 A:HIS718 4.3 42.6 1.0 CG2 A:THR697 4.3 39.6 1.0 CB A:LYS694 4.5 41.9 1.0 N A:HIS718 4.5 43.2 1.0 CA A:CYS692 4.6 36.0 1.0 C A:CYS715 4.7 34.2 1.0 O A:CYS715 4.7 34.3 1.0 CD A:ARG619 4.7 38.2 0.6 CA A:HIS718 4.8 44.5 1.0 C A:CYS695 4.8 38.9 1.0 C A:LYS694 4.8 51.3 1.0 CB A:HIS717 4.9 40.7 1.0 CD A:ARG619 4.9 37.6 0.4 C A:VAL714 5.0 38.4 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 (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (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 3D Fragment (3R)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl) Methyl]Pyrrolidin-3-Ol (N10057A) (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:0.5 occ:1.00 CB A:CYS708 2.4 73.7 1.0 SG A:CYS723 2.4 71.3 1.0 SG A:CYS708 2.6 0.6 1.0 SG A:CYS706 2.7 64.5 1.0 SG A:CYS725 2.7 72.7 1.0 CB A:CYS725 3.1 54.7 1.0 CB A:CYS723 3.3 51.7 1.0 CB A:CYS706 3.6 55.5 1.0 CA A:CYS708 3.8 68.6 1.0 N A:CYS725 3.9 61.3 1.0 CA A:CYS725 4.1 58.5 1.0 N A:CYS708 4.2 54.9 1.0 CE1 A:TYR730 4.4 56.4 1.0 C A:CYS708 4.4 74.6 1.0 N A:LYS709 4.5 70.9 1.0 CA A:CYS723 4.7 50.1 1.0 N A:SER724 4.7 59.4 1.0 CG A:LYS709 4.8 66.5 1.0 C A:CYS723 4.9 52.0 1.0 CA A:CYS706 5.0 48.2 1.0

R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, R.Talon, P.Collins, 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 N10057A To Be Published.