Zinc in PDB 5kkl: Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M

The structure of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M, PDB code: 5kkl 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)	48.74 / 2.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.254, 80.559, 133.220, 90.00, 107.42, 90.00
R / Rfree (%)	18.6 / 23.4

The binding sites of Zinc atom in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M (pdb code 5kkl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M, PDB code: 5kkl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8001 b:80.4 occ:1.00 SG B:CYS760 2.2 89.4 1.0 SG B:CYS727 2.3 83.4 1.0 SG B:CYS748 2.4 76.2 1.0 SG B:CYS755 2.5 81.6 1.0 CB B:CYS727 3.1 81.0 1.0 CB B:CYS755 3.2 75.3 1.0 CB B:CYS760 3.2 86.8 1.0 N B:CYS727 3.6 79.5 1.0 CB B:CYS748 3.7 72.5 1.0 CA B:CYS755 3.8 71.9 1.0 CA B:CYS727 3.9 81.7 1.0 ZN B:ZN8003 3.9 86.5 1.0 ZN B:ZN8002 4.0 75.8 1.0 SG B:CYS763 4.4 96.9 1.0 CA B:CYS760 4.4 88.4 1.0 C B:GLY726 4.6 80.9 1.0 SG B:CYS736 4.6 97.2 1.0 SG B:CYS746 4.6 91.4 1.0 N B:CYS755 4.7 70.1 1.0 O B:CYS727 4.8 87.8 1.0 N B:ASP756 4.8 73.1 1.0 C B:CYS755 4.8 75.3 1.0 C B:CYS727 4.8 88.2 1.0 CA B:GLY726 4.9 73.8 1.0 CA B:CYS748 5.0 72.2 1.0

Zinc binding site 2 out of 8 in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8002 b:75.8 occ:1.00 SG B:CYS736 2.2 97.2 1.0 SG B:CYS784 2.3 85.4 1.0 SG B:CYS755 2.7 81.6 1.0 SG B:CYS763 2.8 96.9 1.0 CB B:CYS736 2.9 91.7 1.0 CB B:CYS784 3.2 86.2 1.0 CB B:CYS763 3.5 97.6 1.0 CA B:CYS784 3.7 88.9 1.0 CB B:CYS755 3.7 75.3 1.0 ZN B:ZN8003 3.8 86.5 1.0 SG B:CYS727 4.0 83.4 1.0 ZN B:ZN8001 4.0 80.4 1.0 O B:CYS763 4.2 0.1 1.0 CA B:CYS736 4.3 94.0 1.0 C B:CYS763 4.4 0.6 1.0 CB B:ASN786 4.5 75.6 1.0 C B:CYS784 4.6 89.1 1.0 CA B:CYS763 4.6 0.4 1.0 N B:CYS784 4.7 93.5 1.0 N B:GLN785 4.8 84.9 1.0 N B:CYS736 4.9 97.8 1.0 N B:ASN786 4.9 77.2 1.0 CB B:ALA765 5.0 86.5 1.0

Zinc binding site 3 out of 8 in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8003 b:86.5 occ:1.00 SG B:CYS746 2.2 91.4 1.0 SG B:CYS736 2.2 97.2 1.0 SG B:CYS729 2.6 93.2 1.0 SG B:CYS727 2.7 83.4 1.0 CB B:CYS729 2.9 91.2 1.0 CB B:CYS746 3.1 91.5 1.0 CB B:CYS736 3.2 91.7 1.0 CB B:CYS727 3.2 81.0 1.0 CA B:CYS736 3.6 94.0 1.0 ZN B:ZN8002 3.8 75.8 1.0 CA B:CYS746 3.9 92.6 1.0 ZN B:ZN8001 3.9 80.4 1.0 N B:CYS736 4.2 97.8 1.0 SG B:CYS755 4.3 81.6 1.0 CA B:CYS729 4.3 94.7 1.0 N B:CYS729 4.6 93.6 1.0 SG B:CYS748 4.6 76.2 1.0 CA B:CYS727 4.7 81.7 1.0 C B:CYS746 4.7 92.7 1.0 CB B:CYS748 4.8 72.5 1.0 C B:CYS736 4.9 97.1 1.0 N B:ILE747 4.9 87.4 1.0 OG1 B:THR735 5.0 0.4 1.0 CB B:CYS763 5.0 97.6 1.0

Zinc binding site 4 out of 8 in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8004 b:72.4 occ:1.00 NE2 B:HIS687 2.1 85.9 1.0 SG B:CYS691 2.2 82.9 1.0 SG B:CYS697 2.2 65.3 1.0 SG B:CYS685 2.3 69.6 1.0 CB B:CYS685 2.9 64.2 1.0 CE1 B:HIS687 2.9 87.9 1.0 CB B:CYS697 3.2 63.2 1.0 CD2 B:HIS687 3.2 84.8 1.0 CB B:CYS691 3.3 81.9 1.0 ZN B:ZN8006 3.6 66.2 1.0 ZN B:ZN8005 3.7 69.4 1.0 CA B:CYS691 3.8 82.9 1.0 ND1 B:HIS687 4.1 88.7 1.0 CA B:CYS697 4.1 61.5 1.0 CG B:HIS687 4.2 84.7 1.0 SG B:CYS709 4.3 60.9 1.0 CA B:CYS685 4.3 62.1 1.0 SG B:CYS699 4.7 60.1 1.0 N B:CYS691 4.7 85.9 1.0 C B:CYS691 4.8 87.4 1.0 C B:CYS685 4.8 68.1 1.0 CD B:PRO698 4.8 56.2 1.0 C B:CYS697 4.9 63.2 1.0 SG B:CYS715 4.9 74.6 1.0 O B:PRO690 5.0 88.7 1.0

Zinc binding site 5 out of 8 in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8005 b:69.4 occ:1.00 SG B:CYS715 2.2 74.6 1.0 SG B:CYS691 2.2 82.9 1.0 SG B:CYS720 2.4 74.2 1.0 SG B:CYS709 2.5 60.9 1.0 CB B:CYS715 3.1 72.7 1.0 CB B:CYS691 3.2 81.9 1.0 CB B:CYS720 3.3 72.7 1.0 CB B:CYS709 3.4 58.4 1.0 ZN B:ZN8004 3.7 72.4 1.0 ZN B:ZN8006 3.7 66.2 1.0 SG B:CYS685 3.9 69.6 1.0 CA B:CYS715 4.5 72.2 1.0 CA B:CYS691 4.6 82.9 1.0 CB B:LEU722 4.7 67.7 1.0 CA B:CYS720 4.8 76.1 1.0 SG B:CYS697 4.8 65.3 1.0 CA B:CYS709 4.9 57.0 1.0 CB B:CYS713 4.9 53.7 1.0 N B:LYS723 4.9 70.6 1.0

Zinc binding site 6 out of 8 in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8006 b:66.2 occ:1.00 SG B:CYS699 2.2 60.1 1.0 SG B:CYS685 2.2 69.6 1.0 SG B:CYS709 2.3 60.9 1.0 SG B:CYS713 2.4 55.3 1.0 CB B:CYS699 3.4 58.5 1.0 CB B:CYS709 3.4 58.4 1.0 CB B:CYS713 3.4 53.7 1.0 CB B:CYS685 3.5 64.2 1.0 ZN B:ZN8004 3.6 72.4 1.0 ZN B:ZN8005 3.7 69.4 1.0 CA B:CYS709 3.9 57.0 1.0 N B:CYS685 3.9 60.6 1.0 SG B:CYS697 4.0 65.3 1.0 CA B:CYS685 4.3 62.1 1.0 SG B:CYS715 4.4 74.6 1.0 SG B:CYS691 4.4 82.9 1.0 CA B:CYS713 4.7 51.9 1.0 CA B:CYS699 4.7 57.6 1.0 C B:CYS709 4.9 60.7 1.0 N B:CYS699 4.9 57.2 1.0 O B:CYS685 4.9 67.6 1.0 N B:CYS709 4.9 58.4 1.0 N B:GLU710 4.9 55.4 1.0

Zinc binding site 7 out of 8 in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8007 b:40.5 occ:1.00 ND1 B:HIS518 1.9 47.3 1.0 SG B:CYS511 2.2 39.7 1.0 SG B:CYS516 2.3 40.9 1.0 SG B:CYS508 2.3 37.6 1.0 CE1 B:HIS518 2.9 47.8 1.0 CG B:HIS518 3.0 45.3 1.0 CB B:CYS516 3.0 37.7 1.0 CB B:CYS508 3.1 35.0 1.0 CB B:HIS518 3.3 41.3 1.0 CB B:CYS511 3.4 39.7 1.0 N B:CYS511 3.9 41.5 1.0 NE2 B:HIS518 4.1 48.4 1.0 CD2 B:HIS518 4.1 47.7 1.0 N B:HIS518 4.2 37.7 1.0 CA B:CYS511 4.2 41.7 1.0 CA B:HIS518 4.3 39.5 1.0 CA B:CYS516 4.4 35.8 1.0 CA B:CYS508 4.5 35.9 1.0 N B:GLU517 4.6 34.9 1.0 C B:CYS511 4.8 46.5 1.0 CB B:ILE510 4.8 40.2 1.0 C B:CYS516 4.8 35.8 1.0 N B:PHE512 4.9 43.8 1.0 O B:SER513 4.9 41.8 1.0 N B:SER513 4.9 41.3 1.0 C B:ILE510 5.0 45.0 1.0 CB B:SER513 5.0 40.9 1.0

Zinc binding site 8 out of 8 in the Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of CTPRC2 in Complex with H3K27ME3 and H3K27M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8008 b:0.4 occ:1.00 SG B:CYS625 2.2 0.2 1.0 SG B:CYS615 2.5 0.5 1.0 SG B:CYS574 2.8 0.4 1.0 CA B:CYS574 2.9 0.5 1.0 CB B:CYS625 3.1 0.7 1.0 SG B:CYS570 3.2 0.6 1.0 CB B:CYS574 3.3 0.2 1.0 N B:CYS574 3.6 0.3 1.0 O B:GLU573 3.7 0.4 1.0 C B:CYS574 3.8 0.9 1.0 CB B:CYS615 3.9 0.4 1.0 C B:GLU573 3.9 0.7 1.0 CA B:CYS615 4.0 0.2 1.0 CZ B:TYR575 4.0 0.2 1.0 CE1 B:TYR575 4.1 0.8 1.0 O B:ASN572 4.1 0.8 1.0 OH B:TYR575 4.2 0.3 1.0 O B:CYS574 4.3 0.7 1.0 CE2 B:TYR575 4.5 0.6 1.0 N B:CYS615 4.6 0.2 1.0 CB B:CYS570 4.6 0.2 1.0 CA B:CYS625 4.6 0.1 1.0 CD1 B:TYR575 4.6 0.4 1.0 N B:TYR575 4.6 0.2 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