Zinc in PDB 5fz3: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 3,6-Dihydroxybenzonorbornane (N08776B) (Ligand Modelled Based on Pandda Event Map)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 3,6-Dihydroxybenzonorbornane (N08776B) (Ligand Modelled Based on Pandda Event Map), PDB code: 5fz3 was solved by R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, N.Pearce, R.Talon, P.Collins, 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)	71.59 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.170, 143.170, 153.530, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 21.7

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Maybridge Fragment 3,6-Dihydroxybenzonorbornane (N08776B) (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 3,6-Dihydroxybenzonorbornane (N08776B) (Ligand Modelled Based on Pandda Event Map) (pdb code 5fz3). 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 3,6-Dihydroxybenzonorbornane (N08776B) (Ligand Modelled Based on Pandda Event Map), PDB code: 5fz3:
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 3,6-Dihydroxybenzonorbornane (N08776B) (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 3,6-Dihydroxybenzonorbornane (N08776B) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:34.5 occ:1.00 ND1 A:HIS718 2.1 45.1 1.0 SG A:CYS715 2.2 33.1 1.0 SG A:CYS692 2.3 34.2 1.0 SG A:CYS695 2.5 39.5 1.0 CE1 A:HIS718 2.9 49.9 1.0 CB A:CYS692 3.1 33.7 1.0 CG A:HIS718 3.2 52.0 1.0 CB A:CYS695 3.4 35.3 1.0 CB A:CYS715 3.4 31.1 1.0 CB A:HIS718 3.7 34.7 1.0 N A:CYS695 3.8 45.9 1.0 N A:CYS715 3.8 32.6 1.0 NE2 A:HIS718 4.1 47.8 1.0 CA A:CYS695 4.1 36.3 1.0 CA A:CYS715 4.1 38.9 1.0 CD2 A:HIS718 4.3 46.0 1.0 CG2 A:THR697 4.4 28.8 1.0 N A:HIS718 4.5 36.9 1.0 CA A:CYS692 4.6 32.4 1.0 CB A:LYS694 4.6 40.2 1.0 CD A:ARG619 4.7 48.7 1.0 C A:CYS715 4.7 36.1 1.0 O A:CYS715 4.7 35.1 1.0 CA A:HIS718 4.8 36.6 1.0 C A:CYS695 4.8 39.0 1.0 C A:LYS694 4.9 48.5 1.0 CB A:HIS717 4.9 39.3 1.0 N A:LYS696 5.0 36.0 1.0 C A:VAL714 5.0 34.9 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 3,6-Dihydroxybenzonorbornane (N08776B) (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 3,6-Dihydroxybenzonorbornane (N08776B) (Ligand Modelled Based on Pandda Event Map) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:0.7 occ:1.00 CB A:CYS708 2.4 71.7 1.0 SG A:CYS723 2.5 67.9 1.0 SG A:CYS725 2.7 66.6 1.0 SG A:CYS708 2.7 0.5 1.0 SG A:CYS706 2.7 62.6 1.0 CB A:CYS725 3.2 45.6 1.0 CB A:CYS723 3.5 48.1 1.0 CA A:CYS708 3.7 61.4 1.0 CB A:CYS706 3.8 46.8 1.0 N A:CYS725 4.1 56.4 1.0 N A:CYS708 4.1 52.6 1.0 CA A:CYS725 4.3 51.4 1.0 C A:CYS708 4.4 71.6 1.0 N A:LYS709 4.5 67.1 1.0 CE1 A:TYR730 4.5 56.3 1.0 N A:SER724 4.8 51.4 1.0 CA A:CYS723 4.9 47.1 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 N08776B To Be Published.