Zinc in PDB 9dch: Single-Stranded Rna-Mediated PRC2 Dimer

All present enzymatic activity of Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer (pdb code 9dch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Single-Stranded Rna-Mediated PRC2 Dimer, PDB code: 9dch:
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 Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:59.9 occ:0.00 NE2 A:HIS530 2.1 65.9 1.0 SG A:CYS539 2.3 59.7 1.0 SG A:CYS535 2.3 62.6 1.0 SG A:CYS528 2.3 55.1 1.0 CB A:CYS528 2.9 55.1 1.0 CE1 A:HIS530 3.0 65.9 1.0 CD2 A:HIS530 3.0 65.9 1.0 CB A:CYS535 3.4 62.6 1.0 CB A:CYS539 3.6 59.7 1.0 ZN A:ZN802 3.7 48.8 0.6 ZN A:ZN803 3.7 52.7 0.1 ND1 A:HIS530 4.0 65.9 1.0 CG A:HIS530 4.1 65.9 1.0 SG A:CYS548 4.1 49.7 1.0 CA A:CYS535 4.1 62.6 1.0 CB A:CYS554 4.2 53.8 1.0 CA A:CYS528 4.3 55.1 1.0 SG A:CYS541 4.4 55.8 1.0 N A:CYS535 4.6 62.6 1.0 C A:CYS528 4.6 55.1 1.0 CA A:CYS539 4.6 59.7 1.0 SG A:CYS554 4.8 53.8 1.0 O A:CYS528 4.9 55.1 1.0

Zinc binding site 2 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:48.8 occ:0.58 SG A:CYS528 2.3 55.1 1.0 SG A:CYS541 2.3 55.8 1.0 SG A:CYS548 2.3 49.7 1.0 SG A:CYS552 2.3 46.3 1.0 CB A:CYS552 3.1 46.3 1.0 CB A:CYS528 3.3 55.1 1.0 CB A:CYS548 3.3 49.7 1.0 CB A:CYS541 3.5 55.8 1.0 ZN A:ZN801 3.7 59.9 0.0 CA A:CYS548 3.7 49.7 1.0 ZN A:ZN803 3.9 52.7 0.1 N A:CYS528 3.9 55.1 1.0 CA A:CYS528 4.2 55.1 1.0 SG A:CYS539 4.2 59.7 1.0 CA A:CYS552 4.3 46.3 1.0 SG A:CYS554 4.6 53.8 1.0 SG A:CYS535 4.6 62.6 1.0 N A:CYS548 4.6 49.7 1.0 C A:CYS548 4.7 49.7 1.0 O A:GLN526 4.9 55.3 1.0 C A:PRO527 4.9 52.7 1.0 CA A:CYS541 4.9 55.8 1.0 O A:CYS528 4.9 55.1 1.0 N A:GLU549 5.0 42.2 1.0

Zinc binding site 3 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:52.7 occ:0.10 SG A:CYS535 2.3 62.6 1.0 SG A:CYS558 2.3 51.1 1.0 SG A:CYS554 2.3 53.8 1.0 SG A:CYS548 2.3 49.7 1.0 CB A:CYS554 3.1 53.8 1.0 CB A:CYS548 3.2 49.7 1.0 CB A:CYS558 3.2 51.1 1.0 CB A:CYS535 3.3 62.6 1.0 ZN A:ZN801 3.7 59.9 0.0 ZN A:ZN802 3.9 48.8 0.6 SG A:CYS528 4.0 55.1 1.0 CA A:CYS554 4.6 53.8 1.0 CB A:ASN560 4.6 43.4 1.0 CA A:CYS558 4.6 51.1 1.0 CA A:CYS548 4.7 49.7 1.0 CA A:CYS535 4.7 62.6 1.0 CB A:CYS552 5.0 46.3 1.0 N A:CYS535 5.0 62.6 1.0

Zinc binding site 4 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:30.2 occ:0.14 SG A:CYS571 2.3 26.5 1.0 SG A:CYS565 2.3 30.9 1.0 SG A:CYS567 2.3 27.7 1.0 SG A:CYS576 2.3 27.9 1.0 CB A:CYS565 2.9 30.9 1.0 CB A:CYS576 3.5 27.9 1.0 ZN A:ZN805 3.8 22.7 0.7 CB A:CYS567 3.8 27.7 1.0 CB A:CYS571 3.8 26.5 1.0 ZN A:ZN806 4.1 27.5 0.0 SG A:CYS593 4.1 25.8 1.0 CA A:CYS565 4.2 30.9 1.0 CA A:CYS571 4.3 26.5 1.0 SG A:CYS585 4.5 26.7 1.0 CA A:CYS576 4.5 27.9 1.0 CB A:CYS578 4.5 24.4 1.0 NH1 H:ARG566 4.6 53.6 1.0 SG A:CYS578 4.8 24.4 1.0 O A:CYS571 4.9 26.5 1.0

Zinc binding site 5 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:22.7 occ:0.71 SG A:CYS593 2.3 25.8 1.0 SG A:CYS571 2.3 26.5 1.0 SG A:CYS585 2.3 26.7 1.0 SG A:CYS606 2.3 26.7 1.0 CB A:CYS571 2.7 26.5 1.0 CB A:CYS606 3.5 26.7 1.0 CB A:CYS585 3.7 26.7 1.0 ZN A:ZN804 3.8 30.2 0.1 CB A:CYS593 3.8 25.8 1.0 ZN A:ZN806 4.0 27.5 0.0 CA A:CYS571 4.2 26.5 1.0 SG A:CYS565 4.2 30.9 1.0 CB A:ASN608 4.3 25.4 1.0 CA A:CYS606 4.7 26.7 1.0 CB A:CYS565 4.7 30.9 1.0 N A:CYS571 4.8 26.5 1.0 O A:CYS571 4.9 26.5 1.0 O A:CYS593 4.9 25.8 1.0 CA A:CYS593 5.0 25.8 1.0 CA A:CYS585 5.0 26.7 1.0

Zinc binding site 6 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:27.5 occ:0.00 SG A:CYS565 2.3 30.9 1.0 SG A:CYS585 2.3 26.7 1.0 SG A:CYS590 2.3 25.9 1.0 SG A:CYS578 2.3 24.4 1.0 CB A:CYS585 3.4 26.7 1.0 CB A:CYS590 3.5 25.9 1.0 CA A:CYS585 3.6 26.7 1.0 CB A:CYS578 3.7 24.4 1.0 CB A:CYS565 3.7 30.9 1.0 ZN A:ZN805 4.0 22.7 0.7 ZN A:ZN804 4.1 30.2 0.1 N A:CYS565 4.1 30.9 1.0 O A:GLU584 4.1 27.1 1.0 CE2 A:PHE562 4.4 31.5 1.0 SG A:CYS571 4.5 26.5 1.0 N A:CYS585 4.5 26.7 1.0 CA A:CYS565 4.5 30.9 1.0 C A:GLU584 4.7 27.1 1.0 C A:CYS585 4.7 26.7 1.0 SG A:CYS576 4.8 27.9 1.0 N A:ASP586 4.8 27.5 1.0 CA A:CYS590 4.8 25.9 1.0 SG A:CYS593 4.9 25.8 1.0 C A:GLY564 4.9 31.5 1.0 CA A:CYS578 5.0 24.4 1.0

Zinc binding site 7 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:44.8 occ:0.11 ND1 A:HIS297 2.1 43.5 1.0 CE1 A:HIS297 2.1 43.5 1.0 SG A:CYS289 2.3 43.2 1.0 SG A:CYS294 2.3 45.0 1.0 SG A:CYS286 2.3 46.8 1.0 CB A:CYS294 2.9 45.0 1.0 NE2 A:HIS297 3.4 43.5 1.0 CG A:HIS297 3.4 43.5 1.0 CB A:CYS286 3.7 46.8 1.0 CB A:LEU296 4.0 46.8 1.0 CD2 A:HIS297 4.1 43.5 1.0 CB A:CYS289 4.1 43.2 1.0 CD1 A:LEU296 4.1 46.8 1.0 N A:HIS297 4.3 43.5 1.0 CB A:HIS297 4.4 43.5 1.0 CA A:CYS294 4.4 45.0 1.0 N A:CYS289 4.5 43.2 1.0 CB A:LYS291 4.6 43.9 1.0 N A:LEU296 4.7 46.8 1.0 CG A:LEU296 4.7 46.8 1.0 CA A:CYS289 4.8 43.2 1.0 CA A:LEU296 4.8 46.8 1.0 O A:CYS286 4.9 46.8 1.0 C A:LEU296 4.9 46.8 1.0 CA A:CYS286 4.9 46.8 1.0 CA A:HIS297 5.0 43.5 1.0

Zinc binding site 8 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn801 b:88.9 occ:0.00 NE2 H:HIS530 2.1 99.3 1.0 SG H:CYS539 2.3 84.2 1.0 SG H:CYS535 2.3 92.9 1.0 SG H:CYS528 2.3 82.7 1.0 CE1 H:HIS530 2.8 99.3 1.0 CB H:CYS539 3.2 84.2 1.0 CB H:CYS528 3.2 82.7 1.0 CD2 H:HIS530 3.2 99.3 1.0 CB H:CYS535 3.3 92.9 1.0 ZN H:ZN802 3.7 76.0 0.2 ZN H:ZN803 3.7 72.2 0.3 ND1 H:HIS530 4.0 99.3 1.0 SG H:CYS548 4.1 66.7 1.0 CG H:HIS530 4.3 99.3 1.0 CA H:CYS535 4.3 92.9 1.0 CA H:CYS539 4.3 84.2 1.0 SG H:CYS541 4.5 78.7 1.0 CB H:CYS554 4.6 88.4 1.0 CA H:CYS528 4.6 82.7 1.0 CD H:PRO540 4.7 82.1 1.0 SG H:CYS554 4.8 88.4 1.0 CB H:CYS541 5.0 78.7 1.0 C H:CYS528 5.0 82.7 1.0

Zinc binding site 9 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn802 b:76.0 occ:0.17 SG H:CYS528 2.3 82.7 1.0 SG H:CYS548 2.3 66.7 1.0 SG H:CYS552 2.3 72.3 1.0 SG H:CYS541 2.3 78.7 1.0 CB H:CYS548 3.2 66.7 1.0 CB H:CYS552 3.4 72.3 1.0 CB H:CYS528 3.5 82.7 1.0 CB H:CYS541 3.6 78.7 1.0 CA H:CYS548 3.6 66.7 1.0 ZN H:ZN801 3.7 88.9 0.0 N H:CYS528 3.8 82.7 1.0 ZN H:ZN803 3.9 72.2 0.3 SG H:CYS539 4.2 84.2 1.0 CA H:CYS528 4.2 82.7 1.0 O H:GLN526 4.4 81.3 1.0 N H:CYS548 4.5 66.7 1.0 O H:CYS528 4.6 82.7 1.0 CA H:CYS552 4.6 72.3 1.0 SG H:CYS554 4.6 88.4 1.0 C H:PRO527 4.6 73.0 1.0 SG H:CYS535 4.7 92.9 1.0 C H:CYS548 4.8 66.7 1.0 CA H:PRO527 4.9 73.0 1.0 C H:CYS528 4.9 82.7 1.0 N H:GLU549 4.9 63.5 1.0 CA H:CYS541 4.9 78.7 1.0

Zinc binding site 10 out of 14 in the Single-Stranded 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 Single-Stranded Rna-Mediated PRC2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn803 b:72.2 occ:0.32 SG H:CYS535 2.3 92.9 1.0 SG H:CYS558 2.3 77.4 1.0 SG H:CYS554 2.3 88.4 1.0 SG H:CYS548 2.3 66.7 1.0 CB H:CYS558 3.3 77.4 1.0 CB H:CYS535 3.3 92.9 1.0 CB H:CYS554 3.4 88.4 1.0 CB H:CYS548 3.4 66.7 1.0 ZN H:ZN801 3.7 88.9 0.0 ZN H:ZN802 3.9 76.0 0.2 SG H:CYS528 4.0 82.7 1.0 CE1 H:HIS530 4.4 99.3 1.0 CA H:CYS535 4.6 92.9 1.0 NE2 H:HIS530 4.6 99.3 1.0 CA H:CYS558 4.7 77.4 1.0 N H:CYS535 4.7 92.9 1.0 CA H:CYS554 4.8 88.4 1.0 CA H:CYS548 4.8 66.7 1.0 CB H:ASN560 4.8 66.4 1.0

J.Song, L.Yao, A.R.Gooding, V.Thron, V.Kasinath, T.R.Cech. Diverse Rna Structures Induce PRC2 Dimerization and Inhibit Histone Methyltransferase Activity. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39257770
DOI: 10.1101/2024.08.29.610323