Zinc in PDB 5vk3: Apo CTPRC2 with E840A and K852D Mutations in EZH2

The structure of Apo CTPRC2 with E840A and K852D Mutations in EZH2, PDB code: 5vk3 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)	44.75 / 2.11
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.594, 138.004, 224.366, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21.4

The binding sites of Zinc atom in the Apo CTPRC2 with E840A and K852D Mutations in EZH2 (pdb code 5vk3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Apo CTPRC2 with E840A and K852D Mutations in EZH2, PDB code: 5vk3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Apo CTPRC2 with E840A and K852D Mutations in EZH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo CTPRC2 with E840A and K852D Mutations in EZH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8001 b:21.1 occ:1.00 SG B:CYS748 2.3 20.2 1.0 SG B:CYS760 2.3 18.6 1.0 SG B:CYS755 2.3 18.6 1.0 SG B:CYS727 2.4 23.2 1.0 CB B:CYS755 3.2 14.0 1.0 CB B:CYS727 3.2 18.5 1.0 CB B:CYS760 3.3 13.0 1.0 CB B:CYS748 3.3 19.4 1.0 CA B:CYS755 3.6 15.8 1.0 N B:CYS727 3.6 18.8 1.0 ZN B:ZN8003 3.8 21.9 1.0 ZN B:ZN8002 3.9 21.6 1.0 CA B:CYS727 4.0 24.3 1.0 SG B:CYS746 4.3 23.0 1.0 O B:HOH8306 4.4 22.6 1.0 N B:CYS755 4.5 19.9 1.0 CA B:CYS760 4.5 21.3 1.0 N B:ASP756 4.5 19.3 1.0 SG B:CYS763 4.6 22.7 1.0 C B:CYS755 4.6 20.7 1.0 C B:GLY726 4.6 26.0 1.0 CA B:CYS748 4.7 23.0 1.0 SG B:CYS736 4.7 20.6 1.0 C B:CYS727 4.8 31.4 1.0 N B:CYS748 4.9 20.2 1.0 CA B:GLY726 4.9 25.8 1.0 O B:CYS727 5.0 25.7 1.0

Zinc binding site 2 out of 8 in the Apo CTPRC2 with E840A and K852D Mutations in EZH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apo CTPRC2 with E840A and K852D Mutations in EZH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8002 b:21.6 occ:1.00 SG B:CYS763 2.3 22.7 1.0 SG B:CYS736 2.3 20.6 1.0 SG B:CYS755 2.4 18.6 1.0 SG B:CYS784 2.4 15.8 1.0 CB B:CYS784 3.1 11.4 1.0 CB B:CYS763 3.2 22.2 1.0 CB B:CYS736 3.2 19.2 1.0 CB B:CYS755 3.3 14.0 1.0 ZN B:ZN8003 3.8 21.9 1.0 ZN B:ZN8001 3.9 21.1 1.0 CA B:CYS784 3.9 17.0 1.0 SG B:CYS727 4.0 23.2 1.0 CB B:ALA765 4.4 18.7 1.0 CB B:ASN786 4.6 17.8 1.0 CB B:CYS760 4.6 13.0 1.0 CA B:CYS763 4.6 23.2 1.0 CA B:CYS736 4.7 22.2 1.0 CA B:CYS755 4.7 15.8 1.0 C B:CYS784 4.9 20.8 1.0 N B:CYS784 4.9 16.1 1.0

Zinc binding site 3 out of 8 in the Apo CTPRC2 with E840A and K852D Mutations in EZH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apo CTPRC2 with E840A and K852D Mutations in EZH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8003 b:21.9 occ:1.00 SG B:CYS746 2.3 23.0 1.0 SG B:CYS729 2.3 25.8 1.0 SG B:CYS727 2.3 23.2 1.0 SG B:CYS736 2.4 20.6 1.0 CB B:CYS727 3.2 18.5 1.0 CB B:CYS729 3.2 25.0 1.0 CB B:CYS746 3.2 18.9 1.0 CB B:CYS736 3.2 19.2 1.0 CA B:CYS736 3.7 22.2 1.0 ZN B:ZN8001 3.8 21.1 1.0 ZN B:ZN8002 3.8 21.6 1.0 CA B:CYS746 4.0 19.3 1.0 SG B:CYS755 4.0 18.6 1.0 N B:CYS729 4.3 21.1 1.0 N B:CYS736 4.3 18.8 1.0 CA B:CYS729 4.4 25.7 1.0 CA B:CYS727 4.6 24.3 1.0 C B:CYS746 4.8 25.8 1.0 SG B:CYS763 4.9 22.7 1.0 CB B:CYS748 4.9 19.4 1.0 CB B:CYS763 4.9 22.2 1.0 C B:CYS727 4.9 31.4 1.0 SG B:CYS748 4.9 20.2 1.0 C B:CYS736 5.0 26.1 1.0

Zinc binding site 4 out of 8 in the Apo CTPRC2 with E840A and K852D Mutations in EZH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Apo CTPRC2 with E840A and K852D Mutations in EZH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8004 b:32.8 occ:1.00 NE2 B:HIS687 2.0 38.9 1.0 SG B:CYS697 2.3 36.2 1.0 SG B:CYS691 2.3 31.7 1.0 SG B:CYS685 2.4 31.5 1.0 CE1 B:HIS687 3.0 43.4 1.0 CD2 B:HIS687 3.0 42.2 1.0 CB B:CYS685 3.1 30.3 1.0 CB B:CYS691 3.1 24.9 1.0 CB B:CYS697 3.1 32.6 1.0 CA B:CYS691 3.6 30.8 1.0 ZN B:ZN8006 3.6 30.2 1.0 ZN B:ZN8005 3.9 32.5 1.0 SG B:CYS709 4.1 29.1 1.0 CA B:CYS697 4.1 39.7 1.0 ND1 B:HIS687 4.1 40.8 1.0 CG B:HIS687 4.2 42.5 1.0 O B:HOH8489 4.4 34.7 1.0 CA B:CYS685 4.5 30.7 1.0 N B:CYS691 4.6 34.7 1.0 SG B:CYS699 4.7 30.5 1.0 C B:CYS691 4.8 36.3 1.0 C B:CYS697 4.9 36.1 1.0 SG B:CYS715 5.0 31.2 1.0 C B:CYS685 5.0 34.0 1.0

Zinc binding site 5 out of 8 in the Apo CTPRC2 with E840A and K852D Mutations in EZH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Apo CTPRC2 with E840A and K852D Mutations in EZH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8005 b:32.5 occ:1.00 SG B:CYS715 2.3 31.2 1.0 SG B:CYS720 2.3 30.4 1.0 SG B:CYS709 2.4 29.1 1.0 SG B:CYS691 2.4 31.7 1.0 CB B:CYS709 3.2 22.8 1.0 CB B:CYS720 3.2 31.9 1.0 CB B:CYS715 3.3 30.6 1.0 CB B:CYS691 3.4 24.9 1.0 ZN B:ZN8006 3.9 30.2 1.0 ZN B:ZN8004 3.9 32.8 1.0 SG B:CYS685 4.1 31.5 1.0 O B:HOH8413 4.3 38.2 1.0 CA B:CYS720 4.6 33.2 1.0 CA B:CYS709 4.7 25.8 1.0 CB B:LEU722 4.7 29.7 1.0 O B:HOH8555 4.7 38.4 1.0 CA B:CYS715 4.7 35.4 1.0 CA B:CYS691 4.8 30.8 1.0 CB B:CYS713 4.9 22.8 1.0

Zinc binding site 6 out of 8 in the Apo CTPRC2 with E840A and K852D Mutations in EZH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Apo CTPRC2 with E840A and K852D Mutations in EZH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8006 b:30.2 occ:1.00 SG B:CYS699 2.3 30.5 1.0 SG B:CYS709 2.3 29.1 1.0 SG B:CYS685 2.3 31.5 1.0 SG B:CYS713 2.4 27.2 1.0 CB B:CYS709 3.2 22.8 1.0 CB B:CYS713 3.2 22.8 1.0 CB B:CYS685 3.3 30.3 1.0 CB B:CYS699 3.4 30.1 1.0 ZN B:ZN8004 3.6 32.8 1.0 CA B:CYS709 3.6 25.8 1.0 ZN B:ZN8005 3.9 32.5 1.0 N B:CYS685 3.9 26.4 1.0 O B:HOH8238 4.2 31.2 1.0 SG B:CYS697 4.2 36.2 1.0 CA B:CYS685 4.2 30.7 1.0 SG B:CYS715 4.4 31.2 1.0 SG B:CYS691 4.6 31.7 1.0 CA B:CYS713 4.6 29.8 1.0 N B:CYS709 4.6 20.4 1.0 N B:GLU710 4.7 30.9 1.0 C B:CYS709 4.7 30.4 1.0 CA B:CYS699 4.8 30.2 1.0 N B:CYS699 4.9 23.5 1.0 O B:CYS685 5.0 35.8 1.0

Zinc binding site 7 out of 8 in the Apo CTPRC2 with E840A and K852D Mutations in EZH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Apo CTPRC2 with E840A and K852D Mutations in EZH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8007 b:18.5 occ:1.00 ND1 B:HIS518 2.0 18.0 1.0 SG B:CYS511 2.3 17.6 1.0 SG B:CYS516 2.3 18.0 1.0 SG B:CYS508 2.4 21.4 1.0 CE1 B:HIS518 2.9 24.5 1.0 CB B:CYS508 3.0 18.1 1.0 CG B:HIS518 3.1 23.8 1.0 CB B:CYS516 3.1 16.1 1.0 CB B:CYS511 3.4 13.7 1.0 CB B:HIS518 3.6 17.0 1.0 O B:HOH8505 3.8 25.5 1.0 N B:CYS511 3.9 18.2 1.0 NE2 B:HIS518 4.0 21.9 1.0 N B:HIS518 4.1 15.1 1.0 CA B:CYS511 4.2 17.9 1.0 CD2 B:HIS518 4.2 16.7 1.0 CA B:HIS518 4.5 16.9 1.0 N B:GLU517 4.5 18.1 1.0 CA B:CYS508 4.5 20.5 1.0 CA B:CYS516 4.5 18.5 1.0 O B:HOH8412 4.6 26.1 1.0 C B:CYS511 4.7 22.3 1.0 CB B:ILE510 4.7 20.5 1.0 C B:CYS516 4.8 21.9 1.0 N B:PHE512 4.8 19.5 1.0 O B:SER513 4.9 22.9 1.0 C B:ILE510 4.9 19.2 1.0 O B:HOH8279 5.0 24.6 1.0

Zinc binding site 8 out of 8 in the Apo CTPRC2 with E840A and K852D Mutations in EZH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Apo CTPRC2 with E840A and K852D Mutations in EZH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8008 b:55.2 occ:1.00 SG B:CYS570 2.2 53.8 1.0 SG B:CYS625 2.2 51.6 1.0 SG B:CYS615 2.5 58.6 1.0 SG B:CYS574 2.6 63.1 1.0 CB B:CYS570 2.8 52.7 1.0 CB B:CYS615 3.1 39.7 1.0 CB B:CYS625 3.2 39.1 1.0 CB B:CYS574 3.4 56.3 1.0 CA B:CYS574 3.5 55.9 1.0 CA B:CYS615 3.6 39.0 1.0 N B:CYS570 3.8 69.2 1.0 CA B:CYS570 3.9 63.6 1.0 N B:TYR575 4.1 65.0 1.0 N B:CYS615 4.1 34.3 1.0 CD1 B:TYR575 4.2 77.9 1.0 C B:CYS574 4.3 62.7 1.0 O B:HOH8172 4.4 40.5 1.0 C B:CYS570 4.6 68.8 1.0 N B:CYS574 4.6 55.6 1.0 CA B:CYS625 4.6 49.1 1.0 O B:CYS570 4.6 68.5 1.0 CE1 B:TYR575 4.7 79.2 1.0 C B:GLU614 4.9 44.8 1.0 C B:CYS615 5.0 45.4 1.0

M.Bratkowski, X.Yang, X.Liu. Polycomb Repressive Complex 2 in An Autoinhibited State. J. Biol. Chem. V. 292 13323 2017.
ISSN: ESSN 1083-351X
PubMed: 28607149
DOI: 10.1074/JBC.M117.787572