Zinc in PDB 8fyh: G4 Rna-Mediated PRC2 Dimer

All present enzymatic activity of G4 Rna-Mediated PRC2 Dimer:
2.1.1.356;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the G4 Rna-Mediated PRC2 Dimer (pdb code 8fyh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the G4 Rna-Mediated PRC2 Dimer, PDB code: 8fyh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:62.2 occ:0.47 NE2 A:HIS530 2.1 62.9 1.0 SG A:CYS535 2.3 64.5 1.0 SG A:CYS539 2.3 63.0 1.0 SG A:CYS528 2.3 60.9 1.0 CB A:CYS528 2.5 60.9 1.0 CE1 A:HIS530 3.0 62.9 1.0 CD2 A:HIS530 3.0 62.9 1.0 CB A:CYS539 3.0 63.0 1.0 ZN A:ZN802 3.6 54.5 0.4 ZN A:ZN803 3.6 57.8 0.7 CB A:CYS535 3.7 64.5 1.0 CA A:CYS528 4.0 60.9 1.0 SG A:CYS548 4.0 52.0 1.0 ND1 A:HIS530 4.1 62.9 1.0 CG A:HIS530 4.1 62.9 1.0 CB A:CYS554 4.1 63.1 1.0 CA A:CYS539 4.2 63.0 1.0 CA A:CYS535 4.4 64.5 1.0 SG A:CYS541 4.4 58.4 1.0 C A:CYS528 4.5 60.9 1.0 SG A:CYS554 4.6 63.1 1.0 CD A:PRO540 4.8 61.2 1.0 N A:CYS528 4.8 60.9 1.0 O A:CYS528 4.8 60.9 1.0 C A:CYS539 4.9 63.0 1.0 CB A:CYS541 5.0 58.4 1.0

Zinc binding site 2 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:54.5 occ:0.40 SG A:CYS528 2.3 60.9 1.0 SG A:CYS552 2.3 54.7 1.0 SG A:CYS541 2.3 58.4 1.0 SG A:CYS548 2.3 52.0 1.0 CB A:CYS552 2.9 54.7 1.0 CB A:CYS528 3.3 60.9 1.0 CB A:CYS548 3.3 52.0 1.0 CB A:CYS541 3.4 58.4 1.0 ZN A:ZN801 3.6 62.2 0.5 CA A:CYS548 3.6 52.0 1.0 N A:CYS528 3.7 60.9 1.0 ZN A:ZN803 3.8 57.8 0.7 SG A:CYS539 4.0 63.0 1.0 CA A:CYS528 4.1 60.9 1.0 CA A:CYS552 4.2 54.7 1.0 SG A:CYS554 4.4 63.1 1.0 N A:GLU549 4.6 51.7 1.0 C A:CYS548 4.6 52.0 1.0 CE1 A:TYR525 4.6 52.8 1.0 N A:CYS548 4.6 52.0 1.0 SG A:CYS535 4.7 64.5 1.0 C A:PRO527 4.8 57.3 1.0 CA A:CYS541 4.8 58.4 1.0 CA A:PRO527 4.9 57.3 1.0 OH A:TYR525 5.0 52.8 1.0 N A:CYS541 5.0 58.4 1.0

Zinc binding site 3 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:57.8 occ:0.67 SG A:CYS554 2.3 63.1 1.0 SG A:CYS558 2.3 60.1 1.0 SG A:CYS535 2.3 64.5 1.0 SG A:CYS548 2.3 52.0 1.0 CB A:CYS554 3.1 63.1 1.0 CB A:CYS535 3.1 64.5 1.0 CB A:CYS558 3.2 60.1 1.0 CB A:CYS548 3.4 52.0 1.0 ZN A:ZN801 3.6 62.2 0.5 ZN A:ZN802 3.8 54.5 0.4 SG A:CYS528 3.9 60.9 1.0 CA A:CYS554 4.5 63.1 1.0 CA A:CYS535 4.6 64.5 1.0 CA A:CYS558 4.7 60.1 1.0 CB A:ASN560 4.7 48.5 1.0 CA A:CYS548 4.8 52.0 1.0 CB A:CYS552 4.8 54.7 1.0 SG A:CYS539 4.9 63.0 1.0

Zinc binding site 4 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:44.5 occ:0.49 SG A:CYS567 2.3 42.4 1.0 SG A:CYS571 2.3 43.4 1.0 SG A:CYS565 2.3 41.2 1.0 SG A:CYS576 2.3 41.6 1.0 CB A:CYS567 3.0 42.4 1.0 CB A:CYS576 3.1 41.6 1.0 CB A:CYS571 3.1 43.4 1.0 CB A:CYS565 3.3 41.2 1.0 ZN A:ZN805 3.8 48.4 0.6 ZN A:ZN806 3.8 40.8 0.0 CA A:CYS571 3.8 43.4 1.0 CA A:CYS576 4.0 41.6 1.0 SG A:CYS585 4.1 40.3 1.0 N A:CYS567 4.1 42.4 1.0 CA A:CYS567 4.2 42.4 1.0 CB A:CYS593 4.5 45.2 1.0 CA A:CYS565 4.6 41.2 1.0 CD A:PRO577 4.6 37.4 1.0 C A:CYS576 4.7 41.6 1.0 N A:CYS571 4.8 43.4 1.0 C A:CYS565 4.8 41.2 1.0 SG A:CYS578 4.9 39.2 1.0 C A:CYS571 4.9 43.4 1.0 CB A:CYS578 4.9 39.2 1.0 O A:CYS571 4.9 43.4 1.0 N A:PRO577 4.9 37.4 1.0

Zinc binding site 5 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:48.4 occ:0.62 SG A:CYS606 2.3 45.5 1.0 SG A:CYS585 2.3 40.3 1.0 SG A:CYS593 2.3 45.2 1.0 SG A:CYS571 2.3 43.4 1.0 CB A:CYS593 3.0 45.2 1.0 CB A:CYS606 3.0 45.5 1.0 CB A:CYS571 3.0 43.4 1.0 CB A:CYS585 3.4 40.3 1.0 ZN A:ZN804 3.8 44.5 0.5 ZN A:ZN806 3.9 40.8 0.0 SG A:CYS565 4.1 41.2 1.0 CA A:CYS606 4.2 45.5 1.0 CA A:CYS593 4.4 45.2 1.0 CA A:CYS571 4.5 43.4 1.0 O A:CYS593 4.6 45.2 1.0 C A:CYS593 4.7 45.2 1.0 CB A:ALA595 4.8 46.8 1.0 O A:GLN570 4.8 45.2 1.0 CA A:CYS585 4.8 40.3 1.0 CB A:CYS590 4.8 40.9 1.0 N A:CYS571 4.9 43.4 1.0 CB A:ASN608 4.9 40.3 1.0 N A:ASN608 4.9 40.3 1.0

Zinc binding site 6 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:40.8 occ:0.00 SG A:CYS578 2.3 39.2 1.0 SG A:CYS585 2.3 40.3 1.0 SG A:CYS590 2.3 40.9 1.0 SG A:CYS565 2.3 41.2 1.0 CB A:CYS565 3.2 41.2 1.0 CB A:CYS585 3.3 40.3 1.0 CB A:CYS590 3.3 40.9 1.0 CB A:CYS578 3.4 39.2 1.0 CA A:CYS585 3.7 40.3 1.0 N A:CYS565 3.8 41.2 1.0 ZN A:ZN804 3.8 44.5 0.5 ZN A:ZN805 3.9 48.4 0.6 CA A:CYS565 4.0 41.2 1.0 SG A:CYS576 4.4 41.6 1.0 O A:CYS565 4.5 41.2 1.0 SG A:CYS593 4.6 45.2 1.0 C A:CYS565 4.6 41.2 1.0 CA A:CYS590 4.6 40.9 1.0 C A:CYS585 4.7 40.3 1.0 SG A:CYS571 4.7 43.4 1.0 N A:CYS585 4.7 40.3 1.0 CA A:CYS578 4.7 39.2 1.0 N A:ASP586 4.8 38.5 1.0 N A:CYS578 4.9 39.2 1.0 C A:GLY564 4.9 40.7 1.0

Zinc binding site 7 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:54.4 occ:0.51 ND1 A:HIS297 2.1 50.9 1.0 SG A:CYS294 2.3 52.8 1.0 SG A:CYS286 2.3 47.7 1.0 SG A:CYS289 2.3 48.9 1.0 CE1 A:HIS297 2.6 50.9 1.0 CB A:CYS289 2.8 48.9 1.0 CB A:CYS294 2.8 52.8 1.0 CB A:CYS286 3.2 47.7 1.0 CG A:HIS297 3.4 50.9 1.0 N A:CYS289 3.6 48.9 1.0 CA A:CYS289 3.7 48.9 1.0 NE2 A:HIS297 3.9 50.9 1.0 CB A:HIS297 4.1 50.9 1.0 CD2 A:HIS297 4.3 50.9 1.0 CA A:CYS294 4.3 52.8 1.0 N A:HIS297 4.4 50.9 1.0 C A:CYS289 4.6 48.9 1.0 CA A:CYS286 4.6 47.7 1.0 C A:ARG288 4.6 47.4 1.0 CB A:ARG288 4.7 47.4 1.0 CB A:LEU296 4.7 52.8 1.0 O A:CYS286 4.7 47.7 1.0 CA A:HIS297 4.8 50.9 1.0 C A:CYS286 4.9 47.7 1.0 C A:CYS294 4.9 52.8 1.0 N A:CYS294 5.0 52.8 1.0

Zinc binding site 8 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn801 b:64.9 occ:0.47 NE2 G:HIS530 2.1 72.3 1.0 SG G:CYS528 2.3 66.9 1.0 SG G:CYS539 2.3 72.8 1.0 SG G:CYS535 2.3 75.4 1.0 CB G:CYS528 2.5 66.9 1.0 CD2 G:HIS530 2.9 72.3 1.0 CB G:CYS539 3.0 72.8 1.0 CE1 G:HIS530 3.1 72.3 1.0 ZN G:ZN802 3.6 59.7 0.3 ZN G:ZN803 3.6 66.0 0.7 CB G:CYS535 3.7 75.4 1.0 SG G:CYS548 4.0 59.3 1.0 CA G:CYS528 4.0 66.9 1.0 CG G:HIS530 4.1 72.3 1.0 ND1 G:HIS530 4.2 72.3 1.0 CA G:CYS539 4.2 72.8 1.0 CB G:CYS554 4.2 68.1 1.0 CA G:CYS535 4.3 75.4 1.0 SG G:CYS541 4.5 66.1 1.0 C G:CYS528 4.5 66.9 1.0 SG G:CYS554 4.7 68.1 1.0 CD G:PRO540 4.7 69.2 1.0 N G:CYS528 4.8 66.9 1.0 O G:CYS528 4.8 66.9 1.0 C G:CYS539 4.9 72.8 1.0

Zinc binding site 9 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn802 b:59.7 occ:0.29 SG G:CYS528 2.3 66.9 1.0 SG G:CYS552 2.3 62.9 1.0 SG G:CYS541 2.3 66.1 1.0 SG G:CYS548 2.3 59.3 1.0 CB G:CYS552 3.0 62.9 1.0 CB G:CYS548 3.3 59.3 1.0 CB G:CYS528 3.3 66.9 1.0 CB G:CYS541 3.4 66.1 1.0 CA G:CYS548 3.6 59.3 1.0 ZN G:ZN801 3.6 64.9 0.5 N G:CYS528 3.8 66.9 1.0 ZN G:ZN803 3.8 66.0 0.7 SG G:CYS539 4.0 72.8 1.0 CA G:CYS528 4.2 66.9 1.0 CA G:CYS552 4.3 62.9 1.0 SG G:CYS554 4.4 68.1 1.0 N G:GLU549 4.5 59.7 1.0 C G:CYS548 4.6 59.3 1.0 N G:CYS548 4.6 59.3 1.0 SG G:CYS535 4.7 75.4 1.0 CE1 G:TYR525 4.7 59.0 1.0 C G:PRO527 4.8 62.3 1.0 CA G:CYS541 4.8 66.1 1.0 CA G:PRO527 5.0 62.3 1.0 N G:CYS541 5.0 66.1 1.0

Zinc binding site 10 out of 14 in the G4 Rna-Mediated PRC2 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of G4 Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn803 b:66.0 occ:0.68 SG G:CYS558 2.3 61.0 1.0 SG G:CYS554 2.3 68.1 1.0 SG G:CYS535 2.3 75.4 1.0 SG G:CYS548 2.3 59.3 1.0 CB G:CYS554 3.0 68.1 1.0 CB G:CYS535 3.0 75.4 1.0 CB G:CYS558 3.2 61.0 1.0 CB G:CYS548 3.3 59.3 1.0 ZN G:ZN801 3.6 64.9 0.5 ZN G:ZN802 3.8 59.7 0.3 SG G:CYS528 3.9 66.9 1.0 CA G:CYS554 4.5 68.1 1.0 CA G:CYS535 4.5 75.4 1.0 CA G:CYS558 4.6 61.0 1.0 CA G:CYS548 4.8 59.3 1.0 CB G:ASN560 4.8 56.3 1.0 CB G:CYS552 4.8 62.9 1.0 SG G:CYS539 4.8 72.8 1.0

J.Song, A.R.Gooding, W.O.Hemphill, B.D.Love, A.Robertson, L.Yao, L.I.Zon, T.E.North, V.Kasinath, T.R.Cech. Structural Basis For Inactivation of PRC2 By G-Quadruplex Rna. Science V. 381 1331 2023.
ISSN: ESSN 1095-9203
PubMed: 37733873
DOI: 10.1126/SCIENCE.ADH0059