Zinc in PDB 5wfd: Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126

The structure of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126, PDB code: 5wfd was solved by M.A.Bratkowski, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.15 / 2.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.534, 136.971, 223.583, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 24

The binding sites of Zinc atom in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 (pdb code 5wfd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126, PDB code: 5wfd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8001 b:34.6 occ:1.00 SG B:CYS755 2.3 32.5 1.0 SG B:CYS748 2.3 38.2 1.0 SG B:CYS760 2.4 33.7 1.0 SG B:CYS727 2.5 35.7 1.0 CB B:CYS755 3.1 32.5 1.0 CB B:CYS727 3.1 50.3 1.0 CB B:CYS760 3.2 34.5 1.0 N B:CYS727 3.4 36.1 1.0 CB B:CYS748 3.4 32.4 1.0 CA B:CYS755 3.6 30.7 1.0 CA B:CYS727 3.8 36.9 1.0 ZN B:ZN8002 4.0 34.0 1.0 ZN B:ZN8003 4.0 42.5 1.0 SG B:CYS763 4.4 34.9 1.0 C B:GLY726 4.4 36.4 1.0 CA B:CYS760 4.5 35.5 1.0 N B:ASP756 4.5 31.0 1.0 N B:CYS755 4.6 29.8 1.0 C B:CYS755 4.6 30.3 1.0 SG B:CYS746 4.6 39.2 1.0 SG B:CYS736 4.7 34.9 1.0 CA B:GLY726 4.7 35.6 1.0 CA B:CYS748 4.7 32.7 1.0 C B:CYS727 4.8 38.2 1.0 N B:CYS748 4.9 34.9 1.0

Zinc binding site 2 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8002 b:34.0 occ:1.00 SG B:CYS763 2.3 34.9 1.0 SG B:CYS736 2.4 34.9 1.0 SG B:CYS755 2.4 32.5 1.0 CB B:CYS763 3.0 36.0 1.0 CB B:CYS736 3.3 34.1 1.0 CB B:CYS755 3.3 32.5 1.0 ZN B:ZN8001 4.0 34.6 1.0 SG B:CYS727 4.0 35.7 1.0 ZN B:ZN8003 4.0 42.5 1.0 CB B:ALA765 4.5 32.5 1.0 CA B:CYS763 4.5 37.1 1.0 CB B:ASN786 4.5 30.7 1.0 CA B:CYS755 4.7 30.7 1.0 CA B:CYS736 4.7 34.8 1.0 CB B:CYS760 4.7 34.5 1.0 N B:ASN786 4.8 30.8 1.0 N B:GLN785 5.0 32.6 1.0 C B:CYS763 5.0 48.3 1.0

Zinc binding site 3 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8003 b:42.5 occ:1.00 SG B:CYS746 2.1 39.2 1.0 SG B:CYS729 2.2 41.7 1.0 SG B:CYS727 2.3 35.7 1.0 SG B:CYS736 2.3 34.9 1.0 CB B:CYS727 3.1 50.3 1.0 CB B:CYS746 3.2 35.8 1.0 CB B:CYS736 3.3 34.1 1.0 CB B:CYS729 3.5 38.7 1.0 CA B:CYS736 3.7 34.8 1.0 ZN B:ZN8002 4.0 34.0 1.0 ZN B:ZN8001 4.0 34.6 1.0 SG B:CYS755 4.0 32.5 1.0 CA B:CYS746 4.0 38.6 1.0 N B:CYS729 4.3 39.6 1.0 N B:CYS736 4.3 35.9 1.0 CA B:CYS729 4.5 39.9 1.0 CA B:CYS727 4.5 36.9 1.0 C B:CYS746 4.7 36.0 1.0 CB B:CYS763 4.9 36.0 1.0 N B:ALA728 4.9 49.2 1.0 CB B:CYS748 4.9 32.4 1.0 SG B:CYS763 4.9 34.9 1.0 N B:ILE747 5.0 36.4 1.0 C B:CYS727 5.0 38.2 1.0 SG B:CYS748 5.0 38.2 1.0

Zinc binding site 4 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8004 b:43.5 occ:1.00 NE2 B:HIS687 2.0 39.3 1.0 SG B:CYS691 2.1 39.2 1.0 SG B:CYS697 2.3 44.2 1.0 SG B:CYS685 2.4 37.4 1.0 CB B:CYS685 2.7 44.6 1.0 CD2 B:HIS687 2.9 38.9 1.0 CE1 B:HIS687 3.0 40.6 1.0 CB B:CYS697 3.2 49.4 1.0 CB B:CYS691 3.3 40.2 1.0 CA B:CYS691 3.8 47.5 1.0 ZN B:ZN8006 3.8 44.8 1.0 CA B:CYS697 4.0 47.3 1.0 ND1 B:HIS687 4.1 41.1 1.0 CG B:HIS687 4.1 40.0 1.0 ZN B:ZN8005 4.1 44.2 1.0 SG B:CYS709 4.2 36.5 1.0 CA B:CYS685 4.2 38.6 1.0 N B:CYS691 4.7 48.7 1.0 C B:CYS697 4.8 43.1 1.0 SG B:CYS699 4.8 44.0 1.0 SG B:CYS715 4.8 44.2 1.0 CD B:PRO698 4.8 43.9 1.0 C B:CYS685 4.9 37.6 1.0 C B:CYS691 4.9 45.9 1.0 CB B:CYS699 5.0 38.6 1.0 N B:CYS685 5.0 39.7 1.0

Zinc binding site 5 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8005 b:44.2 occ:1.00 SG B:CYS715 2.1 44.2 1.0 SG B:CYS720 2.1 41.9 1.0 SG B:CYS709 2.3 36.5 1.0 SG B:CYS691 2.6 39.2 1.0 CB B:CYS720 3.0 41.2 1.0 CB B:CYS715 3.1 39.5 1.0 CB B:CYS691 3.4 40.2 1.0 CB B:CYS709 3.4 44.6 1.0 ZN B:ZN8006 3.9 44.8 1.0 ZN B:ZN8004 4.1 43.5 1.0 SG B:CYS685 4.2 37.4 1.0 CA B:CYS720 4.5 51.1 1.0 CB B:LEU722 4.6 43.0 1.0 CA B:CYS715 4.6 44.8 1.0 CA B:CYS691 4.8 47.5 1.0 CA B:CYS709 4.9 40.0 1.0 N B:LYS723 4.9 44.0 1.0 N B:CYS715 5.0 38.3 1.0

Zinc binding site 6 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8006 b:44.8 occ:1.00 SG B:CYS685 2.2 37.4 1.0 SG B:CYS709 2.3 36.5 1.0 SG B:CYS699 2.3 44.0 1.0 SG B:CYS713 2.4 47.5 1.0 CB B:CYS709 2.8 44.6 1.0 CB B:CYS699 3.2 38.6 1.0 CB B:CYS713 3.4 39.6 1.0 CA B:CYS709 3.5 40.0 1.0 CB B:CYS685 3.6 44.6 1.0 ZN B:ZN8004 3.8 43.5 1.0 N B:CYS685 3.9 39.7 1.0 ZN B:ZN8005 3.9 44.2 1.0 SG B:CYS715 4.2 44.2 1.0 SG B:CYS697 4.2 44.2 1.0 SG B:CYS691 4.3 39.2 1.0 CA B:CYS685 4.4 38.6 1.0 N B:CYS709 4.4 34.9 1.0 CA B:CYS699 4.6 45.4 1.0 C B:CYS709 4.7 39.4 1.0 CA B:CYS713 4.8 42.7 1.0 N B:CYS699 4.8 44.5 1.0 N B:GLU710 4.8 37.0 1.0

Zinc binding site 7 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8007 b:28.3 occ:1.00 ND1 B:HIS518 2.0 29.0 1.0 SG B:CYS516 2.2 23.2 1.0 SG B:CYS508 2.3 29.1 1.0 SG B:CYS511 2.4 28.2 1.0 CE1 B:HIS518 2.8 31.9 1.0 CB B:CYS516 3.0 31.5 1.0 CG B:HIS518 3.1 27.1 1.0 CB B:CYS508 3.2 24.3 1.0 CB B:CYS511 3.4 24.6 1.0 CB B:HIS518 3.5 25.7 1.0 N B:CYS511 3.8 27.8 1.0 NE2 B:HIS518 4.0 28.1 1.0 N B:HIS518 4.1 37.2 1.0 CD2 B:HIS518 4.1 26.6 1.0 CA B:CYS511 4.1 30.0 1.0 CA B:CYS516 4.4 26.5 1.0 N B:GLU517 4.4 36.1 1.0 CA B:HIS518 4.5 33.3 1.0 CB B:ILE510 4.6 24.7 1.0 C B:CYS511 4.6 31.3 1.0 CA B:CYS508 4.7 26.4 1.0 C B:CYS516 4.8 28.4 1.0 N B:PHE512 4.8 27.5 1.0 CG2 B:ILE510 4.9 24.2 1.0 C B:ILE510 4.9 34.2 1.0

Zinc binding site 8 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK126 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8008 b:88.1 occ:1.00 SG B:CYS570 2.1 76.7 1.0 SG B:CYS625 2.4 54.2 1.0 SG B:CYS615 2.5 92.0 1.0 SG B:CYS574 2.6 89.3 1.0 CB B:CYS570 3.2 75.4 1.0 CB B:CYS615 3.2 64.2 1.0 CB B:CYS625 3.5 55.2 1.0 CB B:CYS574 3.6 77.8 1.0 CA B:CYS574 3.7 72.8 1.0 CA B:CYS615 3.7 48.1 1.0 N B:CYS570 3.8 95.8 1.0 CA B:CYS570 4.0 85.4 1.0 N B:TYR575 4.2 89.2 1.0 N B:CYS615 4.3 55.6 1.0 CD1 B:TYR575 4.4 0.5 1.0 C B:CYS574 4.5 81.7 1.0 O B:CYS570 4.6 86.7 1.0 N B:CYS574 4.7 67.3 1.0 C B:CYS570 4.7 85.4 1.0 CA B:CYS625 4.9 59.7 1.0 C B:CYS615 5.0 72.4 1.0 CE1 B:TYR575 5.0 0.6 1.0

M.Bratkowski, X.Yang, X.Liu. An Evolutionarily Conserved Structural Platform For PRC2 Inhibition By A Class of EZH2 Inhibitors. Sci Rep V. 8 9092 2018.
ISSN: ESSN 2045-2322
PubMed: 29904056
DOI: 10.1038/S41598-018-27175-W