Zinc in PDB 5wf7: Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126

Protein crystallography data

The structure of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126, PDB code: 5wf7 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) 44.14 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 115.875, 136.303, 223.209, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 (pdb code 5wf7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126, PDB code: 5wf7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5wf7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8001

b:44.9
occ:1.00
 SG B:CYS760 2.2 45.0 1.0
SG B:CYS755 2.3 42.8 1.0
SG B:CYS727 2.4 47.7 1.0
SG B:CYS748 2.4 46.6 1.0
CB B:CYS727 3.1 48.8 1.0
CB B:CYS755 3.1 41.4 1.0
CB B:CYS760 3.2 45.7 1.0
CB B:CYS748 3.4 47.3 1.0
N B:CYS727 3.5 52.8 1.0
CA B:CYS755 3.6 40.4 1.0
ZN B:ZN8002 3.8 44.3 1.0
ZN B:ZN8003 3.8 47.6 1.0
CA B:CYS727 3.9 50.0 1.0
O B:HOH8150 4.1 41.7 1.0
N B:ASP756 4.5 42.3 1.0
SG B:CYS746 4.5 46.1 1.0
CA B:CYS760 4.5 47.2 1.0
C B:GLY726 4.5 54.8 1.0
SG B:CYS763 4.5 46.1 1.0
N B:CYS755 4.6 39.0 1.0
C B:CYS755 4.6 39.9 1.0
CA B:CYS748 4.7 51.6 1.0
SG B:CYS736 4.8 46.1 1.0
C B:CYS727 4.8 59.9 1.0
CA B:GLY726 4.8 55.6 1.0
N B:CYS748 4.8 54.7 1.0

Zinc binding site 2 out of 8 in 5wf7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8002

b:44.3
occ:1.00
 SG B:CYS763 2.3 46.1 1.0
SG B:CYS736 2.3 46.1 1.0
SG B:CYS755 2.3 42.8 1.0
SG B:CYS784 2.4 41.9 1.0
CB B:CYS763 3.0 47.6 1.0
CB B:CYS784 3.2 45.4 1.0
CB B:CYS755 3.3 41.4 1.0
CB B:CYS736 3.4 44.9 1.0
SG B:CYS727 3.8 47.7 1.0
ZN B:ZN8001 3.8 44.9 1.0
ZN B:ZN8003 3.8 47.6 1.0
CA B:CYS784 4.0 50.6 1.0
CB B:ALA765 4.4 42.4 1.0
CA B:CYS763 4.5 49.0 1.0
CB B:CYS760 4.6 45.7 1.0
CA B:CYS755 4.8 40.4 1.0
CA B:CYS736 4.8 46.1 1.0
C B:CYS784 4.9 50.9 1.0
C B:CYS763 5.0 54.4 1.0
SG B:CYS760 5.0 45.0 1.0

Zinc binding site 3 out of 8 in 5wf7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8003

b:47.6
occ:1.00
 SG B:CYS727 2.2 47.7 1.0
SG B:CYS729 2.3 53.2 1.0
SG B:CYS746 2.3 46.1 1.0
SG B:CYS736 2.5 46.1 1.0
CB B:CYS727 3.1 48.8 1.0
CB B:CYS729 3.2 51.4 1.0
CB B:CYS746 3.2 47.7 1.0
CB B:CYS736 3.2 44.9 1.0
CA B:CYS736 3.8 46.1 1.0
ZN B:ZN8002 3.8 44.3 1.0
ZN B:ZN8001 3.8 44.9 1.0
CA B:CYS746 4.0 49.2 1.0
SG B:CYS755 4.1 42.8 1.0
N B:CYS729 4.2 53.3 1.0
N B:CYS736 4.3 47.6 1.0
CA B:CYS729 4.3 53.4 1.0
CA B:CYS727 4.5 50.0 1.0
C B:CYS746 4.7 49.3 1.0
CB B:CYS763 4.9 47.6 1.0
C B:CYS727 4.9 59.9 1.0
N B:ILE747 4.9 49.1 1.0
SG B:CYS763 4.9 46.1 1.0
N B:ALA728 5.0 60.8 1.0
CB B:CYS748 5.0 47.3 1.0

Zinc binding site 4 out of 8 in 5wf7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8004

b:52.5
occ:1.00
 NE2 B:HIS687 1.8 54.0 1.0
SG B:CYS691 2.1 59.5 1.0
SG B:CYS697 2.4 57.9 1.0
SG B:CYS685 2.4 55.5 1.0
CB B:CYS691 2.7 55.1 1.0
CE1 B:HIS687 2.7 55.9 1.0
CD2 B:HIS687 2.9 53.4 1.0
CB B:CYS685 3.0 51.0 1.0
CB B:CYS697 3.1 53.3 1.0
CA B:CYS691 3.4 66.1 1.0
ZN B:ZN8006 3.6 48.3 1.0
ZN B:ZN8005 3.8 53.2 1.0
ND1 B:HIS687 3.9 56.6 1.0
CG B:HIS687 3.9 55.0 1.0
SG B:CYS709 4.0 50.3 1.0
CA B:CYS697 4.0 53.2 1.0
N B:CYS691 4.2 67.9 1.0
CA B:CYS685 4.5 48.8 1.0
SG B:CYS699 4.6 51.5 1.0
C B:CYS691 4.7 57.9 1.0
SG B:CYS715 4.8 63.0 1.0
C B:CYS697 4.8 50.7 1.0
CB B:CYS699 5.0 52.0 1.0
C B:CYS685 5.0 50.9 1.0

Zinc binding site 5 out of 8 in 5wf7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8005

b:53.2
occ:1.00
 SG B:CYS715 2.2 63.0 1.0
SG B:CYS720 2.2 55.3 1.0
SG B:CYS709 2.2 50.3 1.0
SG B:CYS691 2.4 59.5 1.0
CB B:CYS720 3.1 57.7 1.0
CB B:CYS715 3.1 58.9 1.0
CB B:CYS709 3.3 55.9 1.0
CB B:CYS691 3.5 55.1 1.0
ZN B:ZN8004 3.8 52.5 1.0
ZN B:ZN8006 3.8 48.3 1.0
SG B:CYS685 3.9 55.5 1.0
O B:HOH8235 4.4 59.1 1.0
CA B:CYS720 4.6 64.3 1.0
CA B:CYS715 4.6 59.6 1.0
CA B:CYS709 4.7 57.0 1.0
CA B:CYS691 4.7 66.1 1.0
CB B:LEU722 4.8 53.3 1.0
N B:CYS691 4.8 67.9 1.0
N B:CYS715 4.9 56.8 1.0
CB B:CYS713 5.0 51.9 1.0

Zinc binding site 6 out of 8 in 5wf7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8006

b:48.3
occ:1.00
 SG B:CYS685 2.1 55.5 1.0
SG B:CYS699 2.2 51.5 1.0
SG B:CYS709 2.2 50.3 1.0
SG B:CYS713 2.4 52.9 1.0
CB B:CYS709 3.1 55.9 1.0
CB B:CYS685 3.2 51.0 1.0
CB B:CYS699 3.3 52.0 1.0
CB B:CYS713 3.3 51.9 1.0
CA B:CYS709 3.6 57.0 1.0
ZN B:ZN8004 3.6 52.5 1.0
ZN B:ZN8005 3.8 53.2 1.0
N B:CYS685 3.9 47.6 1.0
SG B:CYS697 4.0 57.9 1.0
CA B:CYS685 4.1 48.8 1.0
SG B:CYS715 4.2 63.0 1.0
O B:HOH8108 4.2 47.6 1.0
SG B:CYS691 4.5 59.5 1.0
N B:CYS709 4.5 48.0 1.0
CA B:CYS699 4.6 47.2 1.0
CA B:CYS713 4.7 53.4 1.0
C B:CYS709 4.7 56.8 1.0
N B:CYS699 4.8 47.5 1.0
N B:GLU710 4.8 53.0 1.0
O B:CYS685 5.0 53.2 1.0

Zinc binding site 7 out of 8 in 5wf7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8007

b:30.5
occ:1.00
 ND1 B:HIS518 1.9 36.5 1.0
SG B:CYS516 2.1 28.8 1.0
SG B:CYS508 2.2 34.4 1.0
SG B:CYS511 2.4 33.1 1.0
CE1 B:HIS518 2.7 35.1 1.0
CG B:HIS518 3.0 34.4 1.0
CB B:CYS508 3.0 31.9 1.0
CB B:CYS516 3.1 37.8 1.0
CB B:CYS511 3.3 30.2 1.0
CB B:HIS518 3.5 31.4 1.0
NE2 B:HIS518 3.9 33.5 1.0
N B:CYS511 3.9 34.3 1.0
CD2 B:HIS518 4.1 31.1 1.0
N B:HIS518 4.1 38.9 1.0
CA B:CYS511 4.1 36.5 1.0
N B:GLU517 4.3 34.4 1.0
CA B:CYS516 4.4 32.2 1.0
CA B:HIS518 4.5 28.5 1.0
O B:HOH8243 4.5 30.7 1.0
CA B:CYS508 4.5 33.3 1.0
CB B:ILE510 4.7 41.8 1.0
C B:CYS511 4.7 34.9 1.0
C B:CYS516 4.7 33.8 1.0
O B:SER513 4.8 41.4 1.0
N B:PHE512 4.8 34.4 1.0
N B:SER513 5.0 37.8 1.0
C B:ILE510 5.0 33.4 1.0

Zinc binding site 8 out of 8 in 5wf7

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to GSK126 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8008

b:64.4
occ:1.00
 SG B:CYS570 2.2 62.8 1.0
SG B:CYS574 2.4 67.4 1.0
SG B:CYS615 2.4 67.1 1.0
SG B:CYS625 2.6 61.7 1.0
CB B:CYS625 3.0 64.1 1.0
CB B:CYS615 3.1 60.8 1.0
CB B:CYS570 3.2 65.4 1.0
CB B:CYS574 3.2 68.4 1.0
CA B:CYS574 3.3 71.3 1.0
CA B:CYS615 3.6 56.5 1.0
N B:CYS570 3.8 72.9 1.0
CA B:CYS570 4.1 71.8 1.0
N B:CYS615 4.1 57.8 1.0
N B:TYR575 4.1 72.6 1.0
C B:CYS574 4.2 73.0 1.0
N B:CYS574 4.3 71.8 1.0
CD1 B:TYR575 4.4 79.5 1.0
CA B:CYS625 4.5 68.6 1.0
CE1 B:TYR575 4.7 81.1 1.0
C B:CYS570 4.9 72.8 1.0
C B:CYS615 4.9 59.7 1.0
C B:GLU614 5.0 58.9 1.0

Reference:

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
Page generated: Wed Dec 16 11:16:14 2020

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