Zinc in PDB 5m5g: Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)

The structure of Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2), PDB code: 5m5g was solved by Y.Zhang, N.Justin, J.Wilson, S.Gamblin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.84 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.554, 74.612, 128.508, 90.00, 107.70, 90.00
R / Rfree (%)	17.1 / 22.1

The binding sites of Zinc atom in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) (pdb code 5m5g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2), PDB code: 5m5g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)


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 Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8001 b:31.7 occ:1.00 SG B:CYS760 2.2 34.3 1.0 SG B:CYS748 2.3 28.4 1.0 SG B:CYS755 2.3 33.0 1.0 SG B:CYS727 2.4 36.4 1.0 CB B:CYS755 3.1 29.4 1.0 CB B:CYS727 3.3 33.4 1.0 CB B:CYS760 3.3 36.5 1.0 CB B:CYS748 3.3 27.7 1.0 CA B:CYS755 3.5 28.8 1.0 N B:CYS727 3.6 34.6 1.0 ZN B:ZN8003 3.7 34.7 1.0 ZN B:ZN8002 3.9 35.6 1.0 CA B:CYS727 4.0 35.0 1.0 O B:HOH8217 4.2 23.9 1.0 SG B:CYS746 4.3 31.7 1.0 N B:ASP756 4.5 31.0 1.0 C B:CYS755 4.5 30.8 1.0 CA B:CYS760 4.5 37.1 1.0 N B:CYS755 4.5 25.5 1.0 SG B:CYS736 4.6 33.8 1.0 C B:GLY726 4.7 31.7 1.0 CA B:CYS748 4.7 30.1 1.0 SG B:CYS763 4.7 36.3 1.0 N B:CYS748 4.9 28.0 1.0 C B:CYS727 5.0 37.3 1.0 CA B:GLY726 5.0 31.1 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)


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 Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8002 b:35.6 occ:1.00 SG B:CYS736 2.2 33.8 1.0 SG B:CYS763 2.3 36.3 1.0 SG B:CYS784 2.3 37.1 1.0 SG B:CYS755 2.4 33.0 1.0 CB B:CYS784 3.2 39.0 1.0 CB B:CYS763 3.2 41.4 1.0 CB B:CYS736 3.3 37.5 1.0 CB B:CYS755 3.3 29.4 1.0 ZN B:ZN8003 3.8 34.7 1.0 ZN B:ZN8001 3.9 31.7 1.0 CA B:CYS784 4.0 39.4 1.0 SG B:CYS727 4.1 36.4 1.0 CB B:ALA765 4.4 39.0 1.0 CB B:CYS760 4.6 36.5 1.0 CA B:CYS763 4.6 44.3 1.0 CA B:CYS736 4.7 39.6 1.0 N B:ALA765 4.7 38.8 1.0 C B:CYS763 4.8 38.7 1.0 O B:CYS763 4.8 54.4 1.0 CA B:CYS755 4.8 28.8 1.0 CB B:ASN786 4.9 32.7 1.0 C B:CYS784 5.0 34.7 1.0 CA B:ALA765 5.0 39.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8003 b:34.7 occ:1.00 SG B:CYS746 2.3 31.7 1.0 SG B:CYS727 2.3 36.4 1.0 SG B:CYS736 2.3 33.8 1.0 SG B:CYS729 2.4 40.9 1.0 CB B:CYS727 3.1 33.4 1.0 CB B:CYS736 3.2 37.5 1.0 CB B:CYS729 3.2 39.3 1.0 CB B:CYS746 3.3 34.9 1.0 CA B:CYS736 3.6 39.6 1.0 ZN B:ZN8001 3.7 31.7 1.0 ZN B:ZN8002 3.8 35.6 1.0 SG B:CYS755 3.9 33.0 1.0 CA B:CYS746 4.1 34.4 1.0 N B:CYS736 4.2 46.5 1.0 N B:CYS729 4.4 48.1 1.0 CA B:CYS729 4.4 44.6 1.0 CA B:CYS727 4.5 35.0 1.0 SG B:CYS748 4.8 28.4 1.0 CB B:CYS748 4.8 27.7 1.0 CB B:CYS763 4.9 41.4 1.0 C B:CYS736 4.9 41.3 1.0 C B:CYS746 4.9 34.2 1.0 C B:CYS727 4.9 37.3 1.0 SG B:CYS763 5.0 36.3 1.0 OE1 B:GLN740 5.0 71.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8004 b:28.9 occ:1.00 NE2 B:HIS687 2.0 33.8 1.0 SG B:CYS697 2.2 30.1 1.0 SG B:CYS691 2.3 28.4 1.0 SG B:CYS685 2.4 30.4 1.0 CE1 B:HIS687 2.9 32.0 1.0 CD2 B:HIS687 3.1 31.8 1.0 CB B:CYS685 3.1 28.5 1.0 CB B:CYS691 3.2 27.6 1.0 CB B:CYS697 3.2 30.8 1.0 CA B:CYS691 3.6 31.4 1.0 ZN B:ZN8006 3.8 27.6 1.0 ZN B:ZN8005 3.9 29.4 1.0 ND1 B:HIS687 4.1 32.0 1.0 SG B:CYS709 4.2 32.0 1.0 CA B:CYS697 4.2 31.8 1.0 CG B:HIS687 4.2 31.9 1.0 O B:HOH8330 4.3 26.3 0.9 N B:CYS691 4.5 31.0 1.0 CA B:CYS685 4.6 30.4 1.0 SG B:CYS699 4.7 27.8 1.0 C B:CYS691 4.8 27.2 1.0 C B:CYS697 4.9 28.7 1.0 O B:HOH8322 4.9 42.1 1.0 CB B:CYS699 4.9 26.2 1.0 O B:PRO690 5.0 30.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8005 b:29.4 occ:1.00 SG B:CYS715 2.3 30.2 1.0 SG B:CYS691 2.3 28.4 1.0 SG B:CYS720 2.3 34.8 1.0 SG B:CYS709 2.4 32.0 1.0 CB B:CYS709 3.2 30.4 1.0 CB B:CYS691 3.2 27.6 1.0 CB B:CYS715 3.4 33.1 1.0 CB B:CYS720 3.4 38.4 1.0 ZN B:ZN8006 3.9 27.6 1.0 ZN B:ZN8004 3.9 28.9 1.0 SG B:CYS685 4.1 30.4 1.0 O B:HOH8251 4.6 35.9 0.9 CA B:CYS709 4.7 31.1 1.0 CB B:LEU722 4.7 28.5 1.0 CA B:CYS691 4.7 31.4 1.0 CA B:CYS715 4.8 35.4 1.0 CA B:CYS720 4.8 39.5 1.0 N B:LYS723 4.9 27.5 1.0 CB B:CYS713 5.0 30.2 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8006 b:27.6 occ:1.00 SG B:CYS699 2.3 27.8 1.0 SG B:CYS709 2.3 32.0 1.0 SG B:CYS713 2.3 26.7 1.0 SG B:CYS685 2.4 30.4 1.0 CB B:CYS709 3.2 30.4 1.0 CB B:CYS699 3.3 26.2 1.0 CB B:CYS713 3.3 30.2 1.0 CB B:CYS685 3.4 28.5 1.0 CA B:CYS709 3.6 31.1 1.0 ZN B:ZN8004 3.8 28.9 1.0 ZN B:ZN8005 3.9 29.4 1.0 N B:CYS685 3.9 27.2 1.0 CA B:CYS685 4.2 30.4 1.0 O B:HOH8229 4.2 25.1 1.0 SG B:CYS697 4.3 30.1 1.0 SG B:CYS715 4.5 30.2 1.0 SG B:CYS691 4.5 28.4 1.0 CA B:CYS713 4.5 29.2 1.0 N B:CYS709 4.6 28.6 1.0 CA B:CYS699 4.7 26.6 1.0 C B:CYS709 4.7 33.1 1.0 N B:GLU710 4.7 31.8 1.0 N B:CYS699 4.9 24.8 1.0 O B:HOH8162 5.0 19.4 0.6

Zinc binding site 7 out of 8 in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8007 b:24.9 occ:1.00 ND1 B:HIS518 2.0 23.9 1.0 SG B:CYS516 2.3 19.2 1.0 SG B:CYS511 2.3 21.5 1.0 SG B:CYS508 2.3 22.9 1.0 CE1 B:HIS518 3.0 27.5 1.0 CG B:HIS518 3.0 24.2 1.0 CB B:CYS508 3.1 24.0 1.0 CB B:CYS516 3.2 20.5 1.0 CB B:HIS518 3.4 24.6 1.0 CB B:CYS511 3.4 23.4 1.0 O B:HOH8328 3.8 29.6 0.9 N B:CYS511 3.9 22.6 1.0 N B:HIS518 4.0 25.9 1.0 NE2 B:HIS518 4.1 23.8 1.0 CD2 B:HIS518 4.1 22.8 1.0 CA B:CYS511 4.2 24.1 1.0 CA B:HIS518 4.3 25.9 1.0 N B:GLU517 4.5 25.5 1.0 O B:HOH8226 4.5 22.6 1.0 CA B:CYS516 4.6 21.3 1.0 CA B:CYS508 4.6 25.2 1.0 C B:CYS511 4.7 26.3 1.0 CB B:ILE510 4.8 26.0 1.0 N B:PHE512 4.8 25.6 1.0 C B:CYS516 4.9 23.5 1.0 O B:HOH8146 4.9 21.8 1.0 O B:SER513 4.9 28.3 1.0 C B:ILE510 4.9 25.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Chaetomium Thermophilum Polycomb Repressive Complex 2 (PRC2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8008 b:73.3 occ:1.00 SG B:CYS625 2.3 57.0 1.0 SG B:CYS570 2.3 67.6 1.0 SG B:CYS574 2.3 84.8 1.0 SG B:CYS615 2.4 68.2 1.0 CB B:CYS570 3.2 76.1 1.0 CB B:CYS625 3.3 60.6 1.0 CB B:CYS615 3.3 62.5 1.0 CB B:CYS574 3.4 80.1 1.0 CA B:CYS574 3.6 81.2 1.0 CA B:CYS615 3.7 61.0 1.0 N B:CYS570 3.8 72.5 1.0 CA B:CYS570 4.1 74.2 1.0 N B:CYS615 4.1 62.8 1.0 N B:TYR575 4.3 81.7 1.0 C B:CYS574 4.5 85.1 1.0 CD1 B:TYR575 4.6 77.0 1.0 N B:CYS574 4.6 81.0 1.0 CA B:CYS625 4.7 64.3 1.0 C B:CYS570 4.8 74.9 1.0 CE1 B:TYR575 4.9 75.7 1.0 C B:PRO569 4.9 84.8 1.0 C B:GLU614 5.0 66.2 1.0

Y.Zhang, N.Justin, J.R.Wilson, S.J.Gamblin. Comment on "Structural Basis of Histone H3K27 Trimethylation By An Active Polycomb Repressive Complex 2". Science V. 354 1543 2016.
ISSN: ESSN 1095-9203
PubMed: 28008037
DOI: 10.1126/SCIENCE.AAF6236