Zinc in PDB 7td5: Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12

All present enzymatic activity of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12:
2.1.1.356;

The structure of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12, PDB code: 7td5 was solved by L.Gong, L.Jiao, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.52 / 2.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	231.87, 64.428, 254.496, 90, 109.89, 90
R / Rfree (%)	19.6 / 23

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 (pdb code 7td5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12, PDB code: 7td5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:33.8 occ:1.00 ND1 A:HIS310 2.0 31.3 1.0 SG A:CYS302 2.1 34.2 1.0 SG A:CYS307 2.2 31.7 0.9 SG A:CYS299 2.4 25.3 1.0 CE1 A:HIS310 3.0 31.4 1.0 CG A:HIS310 3.1 30.9 1.0 CB A:CYS307 3.2 32.2 1.0 CB A:CYS302 3.2 26.0 1.0 CB A:CYS299 3.3 24.0 1.0 CB A:HIS310 3.5 35.3 1.0 N A:CYS302 3.7 24.8 1.0 N A:HIS310 3.8 37.1 1.0 CA A:CYS302 4.0 25.0 1.0 NE2 A:HIS310 4.1 31.4 1.0 CD2 A:HIS310 4.2 30.6 1.0 CA A:HIS310 4.2 39.4 1.0 CB A:LEU309 4.4 32.0 1.0 CB A:ARG301 4.5 24.4 1.0 CA A:CYS307 4.6 32.9 1.0 CA A:CYS299 4.7 24.1 1.0 C A:LEU309 4.7 35.4 1.0 C A:ARG301 4.8 24.7 1.0 N A:LEU309 4.8 32.0 1.0 CA A:LEU309 4.9 32.8 1.0

Zinc binding site 2 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:48.9 occ:1.00 SG A:CYS465 2.4 56.0 1.0 SG A:CYS337 2.5 63.0 1.0 SG A:CYS333 2.6 73.2 1.0 SG A:CYS454 2.7 53.5 0.9 CB A:CYS337 3.3 63.3 1.0 CB A:CYS465 3.3 53.8 1.0 CA A:CYS337 3.5 64.2 1.0 CB A:CYS454 3.5 49.8 1.0 CA A:CYS454 3.6 48.7 1.0 N A:PHE338 3.8 61.9 1.0 CB A:CYS333 3.9 71.6 1.0 CD1 A:PHE338 3.9 60.0 1.0 N A:CYS454 4.1 48.5 1.0 C A:CYS337 4.2 63.2 1.0 N A:CYS333 4.2 70.6 1.0 CE1 A:PHE338 4.5 60.4 1.0 N A:CYS337 4.7 66.0 1.0 CA A:CYS333 4.7 71.4 1.0 CA A:CYS465 4.7 54.0 1.0 C A:PHE453 4.8 48.9 1.0 C A:CYS454 4.9 48.6 1.0 CA A:PHE338 5.0 60.8 1.0 CG A:PHE338 5.0 59.4 1.0

Zinc binding site 3 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:47.9 occ:1.00 SG A:CYS550 2.3 49.9 1.0 SG A:CYS531 2.3 79.3 1.0 SG A:CYS544 2.4 47.4 1.0 SG A:CYS554 2.5 61.6 1.0 CB A:CYS544 3.2 45.0 1.0 CB A:CYS550 3.2 48.6 1.0 CB A:CYS531 3.5 79.9 1.0 CB A:CYS554 3.7 60.3 1.0 ZN A:ZN1004 3.9 66.0 1.0 SG A:CYS524 4.1 61.0 1.0 ZN A:ZN1005 4.1 55.4 1.0 CB A:ASN556 4.1 54.9 1.0 CG A:ARG557 4.4 51.2 1.0 CA A:CYS544 4.6 43.9 1.0 CA A:CYS550 4.7 48.5 1.0 OD1 A:ASN556 4.8 61.4 1.0 NE A:ARG557 4.9 54.0 1.0 CA A:CYS531 4.9 80.2 1.0 N A:ARG557 4.9 51.4 1.0 CA A:ASN556 4.9 54.2 1.0 CB A:CYS548 4.9 39.9 1.0 CG A:ASN556 5.0 59.1 1.0

Zinc binding site 4 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:66.0 occ:1.00 NE2 A:HIS526 2.0 71.8 1.0 SG A:CYS531 2.2 79.3 1.0 SG A:CYS535 2.3 60.8 1.0 SG A:CYS524 2.5 61.0 1.0 CE1 A:HIS526 2.7 71.8 1.0 CB A:CYS524 3.0 57.0 1.0 CD2 A:HIS526 3.3 70.5 1.0 CB A:CYS535 3.3 65.2 1.0 CB A:CYS531 3.5 79.9 1.0 ZN A:ZN1005 3.8 55.4 1.0 CA A:CYS531 3.8 80.2 1.0 ZN A:ZN1003 3.9 47.9 1.0 SG A:CYS544 3.9 47.4 1.0 ND1 A:HIS526 4.0 71.2 1.0 CG A:HIS526 4.2 69.2 1.0 CA A:CYS535 4.4 66.6 1.0 CB A:CYS550 4.4 48.6 1.0 CA A:CYS524 4.4 55.8 1.0 N A:CYS531 4.5 80.1 1.0 SG A:CYS550 4.7 49.9 1.0 SG A:CYS537 4.8 58.8 0.9 C A:CYS524 4.9 57.7 1.0 CD A:PRO536 5.0 64.4 1.0

Zinc binding site 5 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:55.4 occ:1.00 SG A:CYS537 2.2 58.8 0.9 SG A:CYS544 2.3 47.4 1.0 SG A:CYS548 2.4 43.1 1.0 SG A:CYS524 2.4 61.0 1.0 CB A:CYS524 3.1 57.0 1.0 CB A:CYS537 3.4 60.5 1.0 CB A:CYS544 3.4 45.0 1.0 CB A:CYS548 3.5 39.9 1.0 N A:CYS524 3.6 53.4 1.0 CA A:CYS544 3.6 43.9 1.0 ZN A:ZN1004 3.8 66.0 1.0 CA A:CYS524 4.0 55.8 1.0 ZN A:ZN1003 4.1 47.9 1.0 SG A:CYS535 4.2 60.8 1.0 SG A:CYS531 4.5 79.3 1.0 SG A:CYS550 4.5 49.9 1.0 N A:CYS544 4.6 44.3 1.0 CA A:CYS537 4.7 60.8 1.0 CA A:CYS548 4.7 39.7 1.0 C A:PRO523 4.7 52.1 1.0 CE1 A:TYR521 4.7 49.8 1.0 C A:CYS544 4.8 42.9 1.0 N A:GLU545 4.8 41.3 1.0 N A:CYS537 4.8 61.5 1.0 CA A:PRO523 4.9 51.2 1.0 C A:CYS524 5.0 57.7 1.0 OH A:TYR521 5.0 51.8 1.0

Zinc binding site 6 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:37.6 occ:1.00 SG A:CYS589 2.1 35.1 1.0 SG A:CYS602 2.2 39.4 1.0 SG A:CYS581 2.4 30.3 1.0 SG A:CYS567 2.4 39.4 1.0 CB A:CYS589 3.0 34.4 1.0 CB A:CYS567 3.3 42.6 1.0 CB A:CYS602 3.3 37.8 1.0 CB A:CYS581 3.5 30.1 1.0 ZN A:ZN1008 3.7 37.8 1.0 ZN A:ZN1007 3.9 41.3 1.0 SG A:CYS561 4.0 48.7 1.0 CB A:ALA591 4.2 27.2 1.0 CA A:CYS589 4.4 34.2 1.0 CB A:ASN604 4.5 34.5 1.0 CA A:CYS602 4.5 37.2 1.0 CB A:CYS586 4.6 29.5 1.0 CA A:CYS567 4.7 44.2 1.0 C A:CYS589 4.7 34.0 1.0 O A:CYS589 4.8 34.1 1.0 CA A:CYS581 4.9 30.4 1.0 N A:ALA591 4.9 28.7 1.0 N A:CYS567 5.0 44.2 1.0 O A:GLN566 5.0 44.6 1.0

Zinc binding site 7 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:41.3 occ:1.00 SG A:CYS586 2.2 27.9 1.0 SG A:CYS581 2.2 30.3 1.0 SG A:CYS561 2.3 48.7 1.0 SG A:CYS574 2.3 43.5 1.0 CB A:CYS581 3.2 30.1 1.0 CB A:CYS586 3.2 29.5 1.0 CB A:CYS574 3.4 42.3 1.0 CB A:CYS561 3.5 46.7 1.0 CA A:CYS581 3.5 30.4 1.0 ZN A:ZN1008 3.6 37.8 1.0 N A:CYS561 3.8 46.8 1.0 ZN A:ZN1006 3.9 37.6 1.0 CA A:CYS561 4.2 46.8 1.0 SG A:CYS572 4.3 50.0 1.0 C A:GLY560 4.4 47.5 1.0 N A:ASP582 4.4 29.6 1.0 CA A:CYS586 4.5 31.0 1.0 N A:CYS581 4.5 30.8 1.0 C A:CYS581 4.5 30.4 1.0 SG A:CYS589 4.5 35.1 1.0 CA A:GLY560 4.7 47.3 1.0 CA A:CYS574 4.8 42.5 1.0 ND2 A:ASN604 4.8 38.1 1.0 SG A:CYS567 4.8 39.4 1.0 N A:CYS574 4.9 43.1 1.0 O A:CYS561 5.0 48.8 1.0 C A:CYS561 5.0 47.8 1.0

Zinc binding site 8 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:37.8 occ:1.00 SG A:CYS561 2.3 48.7 1.0 SG A:CYS572 2.3 50.0 1.0 SG A:CYS567 2.4 39.4 1.0 SG A:CYS563 2.4 49.9 1.0 CB A:CYS563 3.1 46.6 1.0 CB A:CYS561 3.2 46.7 1.0 CB A:CYS572 3.3 49.4 1.0 CB A:CYS567 3.4 42.6 1.0 ZN A:ZN1007 3.6 41.3 1.0 ZN A:ZN1006 3.7 37.6 1.0 SG A:CYS581 3.8 30.3 1.0 CA A:CYS572 4.1 49.4 1.0 CA A:CYS567 4.2 44.2 1.0 CD A:PRO573 4.4 44.2 1.0 CA A:CYS563 4.4 46.5 1.0 N A:CYS563 4.5 46.0 1.0 CB A:CYS589 4.6 34.4 1.0 SG A:CYS574 4.6 43.5 1.0 SG A:CYS589 4.6 35.1 1.0 CA A:CYS561 4.7 46.8 1.0 C A:CYS572 4.8 47.5 1.0 N A:PRO573 4.9 45.5 1.0 CB A:CYS574 4.9 42.3 1.0 N A:CYS567 5.0 44.2 1.0

Zinc binding site 9 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1001 b:137.1 occ:1.00 ND1 F:HIS310 1.9 127.2 1.0 SG F:CYS299 2.2 120.6 1.0 SG F:CYS302 2.2 116.2 1.0 SG F:CYS307 2.5 120.5 0.9 CE1 F:HIS310 2.9 127.5 1.0 CG F:HIS310 3.1 125.6 1.0 CB F:CYS302 3.1 113.7 1.0 CB F:CYS299 3.2 119.5 1.0 CB F:CYS307 3.4 118.8 1.0 CB F:HIS310 3.5 124.5 1.0 N F:CYS302 3.5 113.3 1.0 CA F:CYS302 3.9 113.2 1.0 NE2 F:HIS310 4.0 127.4 1.0 N F:HIS310 4.1 123.0 1.0 CD2 F:HIS310 4.1 126.4 1.0 CB F:ARG301 4.2 114.9 1.0 CA F:HIS310 4.4 124.2 1.0 C F:ARG301 4.5 113.9 1.0 CA F:CYS299 4.6 119.5 1.0 CB F:LEU309 4.7 121.8 1.0 CA F:ARG301 4.7 114.3 1.0 N F:ARG301 4.8 115.1 1.0 CA F:CYS307 4.9 118.6 1.0 C F:LEU309 4.9 122.4 1.0 CD F:ARG301 4.9 119.9 1.0

Zinc binding site 10 out of 16 in the Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Human PRC2-EZH1 Containing Phosphorylated SUZ12 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1002 b:189.3 occ:1.00 SG F:CYS465 2.4 189.5 1.0 SG F:CYS454 2.7 192.8 0.9 CB F:CYS465 3.3 187.2 1.0 CB F:CYS454 3.5 189.8 1.0 CA F:CYS454 3.6 189.1 1.0 N F:CYS454 4.1 189.1 1.0 CA F:CYS465 4.8 186.7 1.0 C F:PHE453 4.8 189.5 1.0 C F:CYS454 4.9 188.9 1.0

L.Gong, X.Liu, L.Jiao, X.Yang, A.Lemoff, X.Liu. CK2-Mediated Phosphorylation of SUZ12 Promotes PRC2 Function By Stabilizing Enzyme Active Site. Nat Commun V. 13 6781 2022.
ISSN: ESSN 2041-1723
PubMed: 36351927
DOI: 10.1038/S41467-022-34431-1