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

The structure of Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal State, PDB code: 5kji 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)	47.31 / 2.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.333, 74.619, 127.035, 90.00, 105.63, 90.00
R / Rfree (%)	17.9 / 24.9

The binding sites of Zinc atom in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal State (pdb code 5kji). 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 Basal State, PDB code: 5kji:
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 Basal 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 Basal State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8001 b:41.1 occ:1.00 SG B:CYS748 2.3 36.6 1.0 SG B:CYS760 2.3 42.6 1.0 SG B:CYS755 2.4 41.0 1.0 SG B:CYS727 2.5 59.9 1.0 CB B:CYS755 3.0 35.8 1.0 CB B:CYS727 3.1 55.7 1.0 CB B:CYS760 3.3 39.5 1.0 CB B:CYS748 3.5 33.1 1.0 CA B:CYS755 3.6 34.9 1.0 N B:CYS727 3.9 55.9 1.0 CA B:CYS727 4.0 55.6 1.0 ZN B:ZN8003 4.1 51.4 1.0 ZN B:ZN8002 4.1 45.1 1.0 SG B:CYS763 4.3 60.5 1.0 N B:ASP756 4.5 36.7 1.0 N B:CYS755 4.5 35.0 1.0 SG B:CYS746 4.6 55.2 1.0 CA B:CYS760 4.6 40.1 1.0 C B:CYS755 4.6 39.1 1.0 C B:GLY726 4.6 58.5 1.0 SG B:CYS736 4.6 44.5 1.0 CA B:CYS748 4.8 34.6 1.0 CA B:GLY726 5.0 49.8 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal 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 Basal State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8002 b:45.1 occ:1.00 SG B:CYS763 2.2 60.5 1.0 SG B:CYS784 2.4 52.0 1.0 SG B:CYS736 2.5 44.5 1.0 SG B:CYS755 2.6 41.0 1.0 CB B:CYS784 2.8 49.7 1.0 CB B:CYS736 3.4 41.5 1.0 CB B:CYS755 3.4 35.8 1.0 CB B:CYS763 3.6 55.7 1.0 ZN B:ZN8001 4.1 41.1 1.0 CA B:CYS784 4.1 50.2 1.0 ZN B:ZN8003 4.2 51.4 1.0 CB B:ASN786 4.4 33.3 1.0 SG B:CYS727 4.4 59.9 1.0 CB B:ALA765 4.5 44.0 1.0 CA B:CYS763 4.6 55.4 1.0 CB B:CYS760 4.8 39.5 1.0 CA B:CYS736 4.8 44.4 1.0 CA B:CYS755 4.8 34.9 1.0 C B:CYS763 4.9 56.5 1.0 O B:CYS763 4.9 58.6 1.0 N B:ASN786 4.9 35.4 1.0 N B:ALA765 5.0 45.6 1.0 N B:CYS784 5.0 53.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal 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 Basal State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8003 b:51.4 occ:1.00 SG B:CYS727 2.1 59.9 1.0 SG B:CYS736 2.3 44.5 1.0 SG B:CYS746 2.4 55.2 1.0 SG B:CYS729 2.4 60.0 1.0 CB B:CYS746 3.1 53.3 1.0 CB B:CYS729 3.1 55.7 1.0 CB B:CYS736 3.4 41.5 1.0 CB B:CYS727 3.6 55.7 1.0 CA B:CYS736 3.8 44.4 1.0 CA B:CYS746 3.9 54.0 1.0 ZN B:ZN8001 4.1 41.1 1.0 ZN B:ZN8002 4.2 45.1 1.0 SG B:CYS755 4.2 41.0 1.0 N B:CYS736 4.3 47.5 1.0 SG B:CYS763 4.4 60.5 1.0 CA B:CYS729 4.5 56.7 1.0 OE1 B:GLN740 4.5 0.1 1.0 CA B:CYS727 4.6 55.6 1.0 N B:CYS729 4.7 56.0 1.0 C B:CYS746 4.7 53.7 1.0 SG B:CYS748 4.9 36.6 1.0 N B:ILE747 5.0 48.2 1.0 CB B:CYS748 5.0 33.1 1.0 OG1 B:THR735 5.0 66.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal 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 Basal State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8004 b:48.5 occ:1.00 NE2 B:HIS687 2.1 47.7 1.0 SG B:CYS697 2.2 43.0 1.0 SG B:CYS685 2.2 49.5 1.0 SG B:CYS691 2.3 44.4 1.0 CE1 B:HIS687 3.0 48.2 1.0 CD2 B:HIS687 3.1 47.2 1.0 CB B:CYS697 3.2 41.6 1.0 CB B:CYS691 3.3 42.6 1.0 CB B:CYS685 3.3 44.3 1.0 CA B:CYS691 3.7 44.2 1.0 ZN B:ZN8006 3.9 41.3 1.0 ZN B:ZN8005 4.1 46.3 1.0 ND1 B:HIS687 4.1 49.1 1.0 CG B:HIS687 4.2 46.8 1.0 CA B:CYS697 4.2 42.1 1.0 SG B:CYS709 4.4 39.9 1.0 CA B:CYS685 4.4 43.1 1.0 N B:CYS691 4.6 46.6 1.0 C B:CYS691 4.8 49.0 1.0 O B:PRO690 4.8 54.0 1.0 SG B:CYS699 4.8 40.4 1.0 CD B:PRO698 4.8 40.6 1.0 C B:CYS697 4.9 43.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal 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 Basal State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8005 b:46.3 occ:1.00 SG B:CYS715 2.2 45.7 1.0 SG B:CYS720 2.3 52.0 1.0 SG B:CYS691 2.3 44.4 1.0 SG B:CYS709 2.4 39.9 1.0 CB B:CYS715 3.2 42.5 1.0 CB B:CYS720 3.2 48.9 1.0 CB B:CYS709 3.2 35.5 1.0 CB B:CYS691 3.2 42.6 1.0 ZN B:ZN8006 4.0 41.3 1.0 ZN B:ZN8004 4.1 48.5 1.0 SG B:CYS685 4.2 49.5 1.0 CA B:CYS715 4.6 41.9 1.0 CA B:CYS720 4.6 51.0 1.0 CB B:LEU722 4.6 39.1 1.0 CA B:CYS691 4.7 44.2 1.0 CG B:LYS723 4.7 44.4 1.0 CA B:CYS709 4.7 35.1 1.0 N B:LYS723 4.8 38.9 1.0 CB B:CYS713 4.9 26.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal 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 Basal State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8006 b:41.3 occ:1.00 SG B:CYS685 2.2 49.5 1.0 SG B:CYS699 2.2 40.4 1.0 SG B:CYS713 2.2 30.0 1.0 SG B:CYS709 2.3 39.9 1.0 CB B:CYS713 3.1 26.6 1.0 CB B:CYS685 3.2 44.3 1.0 CB B:CYS709 3.3 35.5 1.0 CB B:CYS699 3.4 37.9 1.0 N B:CYS685 3.7 43.3 1.0 CA B:CYS709 3.7 35.1 1.0 ZN B:ZN8004 3.9 48.5 1.0 ZN B:ZN8005 4.0 46.3 1.0 CA B:CYS685 4.0 43.1 1.0 O B:HOH8144 4.1 30.3 1.0 CA B:CYS713 4.3 26.7 1.0 SG B:CYS715 4.3 45.7 1.0 SG B:CYS697 4.4 43.0 1.0 SG B:CYS691 4.5 44.4 1.0 CA B:CYS699 4.7 37.8 1.0 C B:CYS709 4.7 38.3 1.0 N B:CYS709 4.8 36.5 1.0 N B:GLU710 4.8 32.2 1.0 C B:PRO684 4.9 44.9 1.0 N B:CYS699 4.9 38.0 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal 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 Basal State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8007 b:32.0 occ:1.00 ND1 B:HIS518 2.0 31.8 1.0 SG B:CYS511 2.1 25.0 1.0 SG B:CYS516 2.3 29.3 1.0 SG B:CYS508 2.4 26.4 1.0 CE1 B:HIS518 2.9 30.8 1.0 CG B:HIS518 3.1 31.2 1.0 CB B:CYS508 3.1 22.4 1.0 CB B:CYS516 3.3 24.8 1.0 CB B:CYS511 3.3 22.4 1.0 CB B:HIS518 3.5 28.3 1.0 N B:CYS511 3.7 24.5 1.0 CA B:CYS511 4.0 23.3 1.0 NE2 B:HIS518 4.1 31.5 1.0 CD2 B:HIS518 4.2 32.0 1.0 N B:HIS518 4.2 26.8 1.0 CA B:HIS518 4.5 27.6 1.0 C B:CYS511 4.6 29.0 1.0 CA B:CYS508 4.6 22.5 1.0 CA B:CYS516 4.7 24.6 1.0 N B:PHE512 4.7 22.2 1.0 N B:GLU517 4.7 25.9 1.0 CB B:ILE510 4.7 31.4 1.0 O B:SER513 4.8 27.7 1.0 O B:HOH8132 4.8 41.6 1.0 C B:ILE510 4.9 31.8 1.0 N B:SER513 4.9 25.1 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of An Active Polycomb Repressive Complex 2 in the Basal 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 Basal State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8008 b:52.7 occ:1.00 SG B:CYS570 2.4 45.6 1.0 SG B:CYS625 2.4 55.8 1.0 SG B:CYS574 2.5 64.9 1.0 SG B:CYS615 2.6 53.4 1.0 CB B:CYS570 3.0 41.8 1.0 CB B:CYS574 3.2 61.5 1.0 CA B:CYS574 3.3 60.9 1.0 CB B:CYS625 3.4 52.6 1.0 CB B:CYS615 3.5 47.0 1.0 N B:CYS570 3.7 45.9 1.0 N B:TYR575 3.8 60.1 1.0 CA B:CYS615 3.8 45.7 1.0 CA B:CYS570 3.9 43.8 1.0 C B:CYS574 4.1 65.2 1.0 N B:CYS615 4.2 46.2 1.0 CD1 B:TYR575 4.3 61.9 1.0 N B:CYS574 4.4 61.0 1.0 C B:CYS570 4.6 52.7 1.0 O B:CYS570 4.7 54.0 1.0 CA B:CYS625 4.8 52.8 1.0 C B:PRO569 4.9 52.9 1.0 CE1 B:TYR575 4.9 62.9 1.0 C B:GLU614 5.0 50.0 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