Zinc in PDB 5kjh: Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State

The structure of Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State, PDB code: 5kjh was solved by L.Jiao, X.Liu, 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 (%)	16.8 / 21.3

The binding sites of Zinc atom in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State (pdb code 5kjh). 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 An Active Polycomb Repressive Complex 2 in the Stimulated State, PDB code: 5kjh:
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 An Active Polycomb Repressive Complex 2 in the Stimulated State


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 An Active Polycomb Repressive Complex 2 in the Stimulated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8001 b:33.9 occ:1.00 SG B:CYS760 2.3 40.9 1.0 SG B:CYS755 2.3 35.3 1.0 SG B:CYS748 2.4 32.3 1.0 SG B:CYS727 2.4 37.4 1.0 CB B:CYS755 3.2 30.5 1.0 CB B:CYS727 3.3 33.6 1.0 CB B:CYS760 3.3 38.5 1.0 CB B:CYS748 3.4 28.0 1.0 CA B:CYS755 3.6 28.7 1.0 N B:CYS727 3.7 33.5 1.0 ZN B:ZN8003 3.7 36.6 1.0 ZN B:ZN8002 3.9 37.7 1.0 CA B:CYS727 4.1 34.3 1.0 O B:HOH8239 4.2 25.2 1.0 SG B:CYS746 4.3 38.2 1.0 N B:ASP756 4.5 29.2 1.0 SG B:CYS736 4.5 38.4 1.0 N B:CYS755 4.5 26.8 1.0 CA B:CYS760 4.6 40.1 1.0 C B:CYS755 4.6 32.1 1.0 SG B:CYS763 4.7 48.2 1.0 C B:GLY726 4.7 36.8 1.0 CA B:CYS748 4.7 28.4 1.0 N B:CYS748 4.9 28.6 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State


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 An Active Polycomb Repressive Complex 2 in the Stimulated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8002 b:37.7 occ:1.00 SG B:CYS736 2.2 38.4 1.0 SG B:CYS763 2.3 48.2 1.0 SG B:CYS784 2.3 39.1 1.0 SG B:CYS755 2.5 35.3 1.0 CB B:CYS784 3.2 37.1 1.0 CB B:CYS736 3.2 34.6 1.0 CB B:CYS763 3.3 46.8 1.0 CB B:CYS755 3.3 30.5 1.0 ZN B:ZN8003 3.8 36.6 1.0 ZN B:ZN8001 3.9 33.9 1.0 CA B:CYS784 3.9 38.9 1.0 SG B:CYS727 4.1 37.4 1.0 CB B:ALA765 4.4 37.0 1.0 CA B:CYS763 4.6 48.7 1.0 CB B:CYS760 4.6 38.5 1.0 CA B:CYS736 4.6 36.5 1.0 C B:CYS763 4.7 51.0 1.0 N B:ALA765 4.8 39.2 1.0 CA B:CYS755 4.8 28.7 1.0 CB B:ASN786 4.8 28.5 1.0 O B:CYS763 4.9 54.0 1.0 N B:CYS784 4.9 42.6 1.0 C B:CYS784 4.9 39.8 1.0 CA B:ALA765 5.0 37.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State


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 An Active Polycomb Repressive Complex 2 in the Stimulated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8003 b:36.6 occ:1.00 SG B:CYS746 2.3 38.2 1.0 SG B:CYS736 2.4 38.4 1.0 SG B:CYS729 2.4 43.5 1.0 SG B:CYS727 2.4 37.4 1.0 CB B:CYS729 3.1 41.3 1.0 CB B:CYS736 3.2 34.6 1.0 CB B:CYS727 3.2 33.6 1.0 CB B:CYS746 3.3 35.5 1.0 CA B:CYS736 3.5 36.5 1.0 ZN B:ZN8001 3.7 33.9 1.0 ZN B:ZN8002 3.8 37.7 1.0 SG B:CYS755 4.0 35.3 1.0 CA B:CYS746 4.1 36.3 1.0 N B:CYS736 4.1 39.3 1.0 CA B:CYS729 4.4 43.7 1.0 N B:CYS729 4.5 44.2 1.0 CA B:CYS727 4.6 34.3 1.0 CB B:CYS763 4.8 46.8 1.0 C B:CYS736 4.9 43.3 1.0 C B:CYS746 4.9 37.8 1.0 SG B:CYS748 4.9 32.3 1.0 CB B:CYS748 4.9 28.0 1.0 C B:CYS727 5.0 40.8 1.0 SG B:CYS763 5.0 48.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State


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 An Active Polycomb Repressive Complex 2 in the Stimulated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8004 b:31.9 occ:1.00 NE2 B:HIS687 2.0 34.2 1.0 SG B:CYS697 2.2 33.3 1.0 SG B:CYS691 2.3 31.1 1.0 SG B:CYS685 2.4 33.8 1.0 CE1 B:HIS687 2.9 34.8 1.0 CD2 B:HIS687 3.1 34.0 1.0 CB B:CYS691 3.1 28.2 1.0 CB B:CYS685 3.1 30.0 1.0 CB B:CYS697 3.2 31.0 1.0 CA B:CYS691 3.6 29.6 1.0 ZN B:ZN8006 3.8 29.2 1.0 ZN B:ZN8005 3.9 31.9 1.0 ND1 B:HIS687 4.0 36.1 1.0 CG B:HIS687 4.1 34.0 1.0 SG B:CYS709 4.1 34.1 1.0 CA B:CYS697 4.2 30.9 1.0 O B:HOH8323 4.3 34.5 0.9 N B:CYS691 4.4 31.2 1.0 CA B:CYS685 4.6 30.0 1.0 C B:CYS691 4.7 33.4 1.0 SG B:CYS699 4.7 31.3 1.0 O B:PRO690 4.9 34.3 1.0 CB B:CYS699 5.0 28.0 1.0 C B:CYS697 5.0 33.1 1.0 SG B:CYS715 5.0 33.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State


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 An Active Polycomb Repressive Complex 2 in the Stimulated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8005 b:31.9 occ:1.00 SG B:CYS715 2.3 33.4 1.0 SG B:CYS709 2.3 34.1 1.0 SG B:CYS691 2.4 31.1 1.0 SG B:CYS720 2.4 40.4 1.0 CB B:CYS709 3.1 29.3 1.0 CB B:CYS691 3.3 28.2 1.0 CB B:CYS715 3.3 31.5 1.0 CB B:CYS720 3.4 37.8 1.0 ZN B:ZN8006 3.9 29.2 1.0 ZN B:ZN8004 3.9 31.9 1.0 SG B:CYS685 4.0 33.8 1.0 O B:HOH8265 4.5 42.4 0.9 CA B:CYS709 4.6 28.2 1.0 CB B:LEU722 4.7 29.3 1.0 CA B:CYS691 4.7 29.6 1.0 CA B:CYS715 4.8 32.8 1.0 CA B:CYS720 4.8 39.4 1.0 N B:LYS723 4.9 27.7 1.0 CB B:CYS713 4.9 27.5 1.0 CD B:LYS723 5.0 33.1 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State


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 An Active Polycomb Repressive Complex 2 in the Stimulated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8006 b:29.2 occ:1.00 SG B:CYS699 2.2 31.3 1.0 SG B:CYS713 2.3 30.2 1.0 SG B:CYS709 2.3 34.1 1.0 SG B:CYS685 2.5 33.8 1.0 CB B:CYS709 3.2 29.3 1.0 CB B:CYS713 3.2 27.5 1.0 CB B:CYS699 3.3 28.0 1.0 CB B:CYS685 3.3 30.0 1.0 CA B:CYS709 3.6 28.2 1.0 N B:CYS685 3.8 29.6 1.0 ZN B:ZN8004 3.8 31.9 1.0 ZN B:ZN8005 3.9 31.9 1.0 CA B:CYS685 4.1 30.0 1.0 O B:HOH8218 4.3 26.1 1.0 SG B:CYS697 4.3 33.3 1.0 SG B:CYS715 4.4 33.4 1.0 CA B:CYS713 4.5 27.5 1.0 SG B:CYS691 4.6 31.1 1.0 N B:CYS709 4.6 28.7 1.0 C B:CYS709 4.6 32.8 1.0 CA B:CYS699 4.7 28.1 1.0 N B:GLU710 4.7 28.1 1.0 N B:CYS699 4.9 28.6 1.0 O B:HOH8213 4.9 20.7 0.6 C B:CYS685 5.0 35.8 1.0 O B:CYS685 5.0 35.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State


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 An Active Polycomb Repressive Complex 2 in the Stimulated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8007 b:26.4 occ:1.00 ND1 B:HIS518 2.1 26.5 1.0 SG B:CYS511 2.3 25.3 1.0 SG B:CYS516 2.3 21.4 1.0 SG B:CYS508 2.3 24.8 1.0 CE1 B:HIS518 3.0 25.6 1.0 CG B:HIS518 3.0 25.5 1.0 CB B:CYS508 3.1 21.8 1.0 CB B:CYS516 3.2 18.1 1.0 CB B:HIS518 3.4 23.2 1.0 CB B:CYS511 3.4 22.2 1.0 N B:CYS511 3.8 23.0 1.0 O B:HOH8317 3.9 28.4 0.9 N B:HIS518 4.0 24.0 1.0 CA B:CYS511 4.1 23.6 1.0 NE2 B:HIS518 4.2 25.4 1.0 CD2 B:HIS518 4.2 25.4 1.0 CA B:HIS518 4.3 23.3 1.0 N B:GLU517 4.5 24.2 1.0 O B:HOH8244 4.5 23.9 1.0 CA B:CYS508 4.5 23.3 1.0 CA B:CYS516 4.6 18.3 1.0 CB B:ILE510 4.8 25.7 1.0 C B:CYS511 4.8 30.7 1.0 C B:CYS516 4.9 25.9 1.0 N B:PHE512 4.9 27.1 1.0 O B:HOH8120 4.9 20.2 1.0 C B:ILE510 4.9 28.4 1.0 O B:SER513 4.9 30.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Stimulated State


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 An Active Polycomb Repressive Complex 2 in the Stimulated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8008 b:79.8 occ:1.00 SG B:CYS570 2.3 82.7 1.0 SG B:CYS574 2.4 78.8 1.0 SG B:CYS615 2.6 72.6 1.0 SG B:CYS625 2.7 74.3 1.0 CB B:CYS570 2.9 78.2 1.0 CB B:CYS574 3.2 76.5 1.0 CB B:CYS615 3.3 66.2 1.0 CB B:CYS625 3.3 71.1 1.0 CA B:CYS574 3.5 76.9 1.0 N B:CYS570 3.6 82.5 1.0 CA B:CYS615 3.7 65.3 1.0 CA B:CYS570 3.8 79.9 1.0 N B:CYS615 4.2 66.0 1.0 N B:TYR575 4.4 77.2 1.0 N B:CYS574 4.5 78.3 1.0 C B:CYS574 4.5 82.3 1.0 CD1 B:TYR575 4.6 93.6 1.0 C B:CYS570 4.6 84.3 1.0 CA B:CYS625 4.8 71.1 1.0 O B:CYS570 4.8 86.3 1.0 C B:PRO569 4.8 90.0 1.0 CE1 B:TYR575 5.0 93.0 1.0

L.Jiao, X.Liu. Response to 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: 28008038
DOI: 10.1126/SCIENCE.AAJ2335