Zinc in PDB 8tof: RPD3S Bound to An H3K36CME3 Modified Nucleosome

All present enzymatic activity of RPD3S Bound to An H3K36CME3 Modified Nucleosome:
3.5.1.98;

The binding sites of Zinc atom in the RPD3S Bound to An H3K36CME3 Modified Nucleosome (pdb code 8tof). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the RPD3S Bound to An H3K36CME3 Modified Nucleosome, PDB code: 8tof:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the RPD3S Bound to An H3K36CME3 Modified Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RPD3S Bound to An H3K36CME3 Modified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:131.8 occ:1.00 OD2 B:ASP186 1.8 90.2 1.0 OD2 B:ASP274 2.3 95.7 1.0 ND1 B:HIS188 2.3 83.0 1.0 CG B:ASP186 2.6 89.4 1.0 OD1 B:ASP186 2.7 94.1 1.0 CE1 B:HIS188 3.2 87.4 1.0 CG B:HIS188 3.3 81.2 1.0 CG B:ASP274 3.4 93.1 1.0 NZ x:LYS1 3.5 105.8 1.0 CB B:HIS188 3.6 80.9 1.0 OH B:TYR313 3.9 93.0 1.0 CA B:GLY311 3.9 84.7 1.0 NE2 B:HIS151 4.0 85.4 1.0 NE2 B:HIS150 4.0 81.3 1.0 CB B:ASP186 4.0 81.9 1.0 CB B:ASP274 4.0 87.0 1.0 N B:HIS188 4.2 90.8 1.0 OD1 B:ASP274 4.3 94.4 1.0 NE2 B:HIS188 4.4 88.6 1.0 CD2 B:HIS188 4.4 86.3 1.0 CE x:LYS1 4.5 104.4 1.0 N B:GLY311 4.5 81.8 1.0 CA B:HIS188 4.5 82.3 1.0 CE2 B:TYR313 4.6 88.8 1.0 CZ B:TYR313 4.7 90.3 1.0 CG1 B:VAL187 4.7 86.4 1.0 CD2 B:HIS151 4.7 79.3 1.0 C B:GLY311 4.8 87.2 1.0 CE1 B:HIS150 4.8 82.0 1.0 N B:VAL187 4.9 88.8 1.0 CD2 B:HIS150 5.0 79.4 1.0 CE1 B:HIS151 5.0 86.0 1.0

Zinc binding site 2 out of 5 in the RPD3S Bound to An H3K36CME3 Modified Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RPD3S Bound to An H3K36CME3 Modified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn701 b:156.0 occ:1.00 ND1 G:HIS283 2.0 121.7 1.0 SG G:CYS263 2.3 130.0 1.0 SG G:CYS266 2.3 119.6 1.0 SG G:CYS286 2.3 121.5 1.0 CE1 G:HIS283 2.9 122.9 1.0 CB G:CYS263 3.1 128.2 1.0 CG G:HIS283 3.1 120.5 1.0 CB G:CYS266 3.2 113.4 1.0 CB G:CYS286 3.3 114.8 1.0 CB G:HIS283 3.6 118.7 1.0 N G:CYS266 3.6 114.2 1.0 CA G:CYS266 4.0 112.3 1.0 NE2 G:HIS283 4.0 123.6 1.0 CD2 G:HIS283 4.1 121.4 1.0 N G:HIS283 4.2 120.5 1.0 NE D:ARG300 4.3 89.2 1.0 CA G:CYS263 4.5 128.5 1.0 CA G:HIS283 4.5 120.0 1.0 CB G:ALA265 4.6 119.6 1.0 C G:CYS266 4.7 115.2 1.0 C G:ALA265 4.7 116.4 1.0 CA G:CYS286 4.8 111.5 1.0 CZ D:ARG300 4.8 91.2 1.0 NH2 D:ARG300 4.8 92.0 1.0 CD D:ARG300 4.8 88.5 1.0 N G:ASN267 4.9 119.3 1.0 C G:CYS263 4.9 126.4 1.0 O G:CYS263 5.0 125.5 1.0

Zinc binding site 3 out of 5 in the RPD3S Bound to An H3K36CME3 Modified Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RPD3S Bound to An H3K36CME3 Modified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn702 b:129.7 occ:1.00 ND1 G:HIS448 2.1 78.3 1.0 SG G:CYS420 2.3 91.6 1.0 SG G:CYS417 2.3 108.8 1.0 SG G:CYS451 2.3 104.0 1.0 CG G:HIS448 2.7 77.7 1.0 CB G:HIS448 2.7 78.7 1.0 CB G:CYS417 3.0 92.0 1.0 CB G:CYS451 3.2 90.5 1.0 CE1 G:HIS448 3.2 83.5 1.0 CB G:CYS420 3.5 93.7 1.0 N G:HIS448 3.6 75.6 1.0 N G:CYS420 3.7 92.6 1.0 CA G:HIS448 3.8 77.1 1.0 CD2 G:HIS448 4.0 78.6 1.0 NE2 G:HIS448 4.2 82.0 1.0 CA G:CYS420 4.2 87.0 1.0 CA G:CYS417 4.4 91.4 1.0 CA G:CYS451 4.6 88.3 1.0 CB G:LYS419 4.6 92.4 1.0 N G:LYS419 4.7 86.8 1.0 C G:LYS419 4.7 94.1 1.0 N G:CYS451 4.7 87.9 1.0 C G:HIS448 4.8 84.1 1.0 C G:CYS417 4.8 90.9 1.0 C G:TRP447 4.8 82.5 1.0 O G:HIS448 4.9 89.6 1.0 CA G:LYS419 4.9 88.8 1.0

Zinc binding site 4 out of 5 in the RPD3S Bound to An H3K36CME3 Modified Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RPD3S Bound to An H3K36CME3 Modified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn703 b:132.7 occ:1.00 NE2 G:HIS469 2.1 107.7 1.0 SG G:CYS466 2.3 116.5 1.0 SG G:CYS440 2.3 106.3 1.0 SG G:CYS443 2.3 102.2 1.0 CE1 G:HIS469 2.8 105.1 1.0 CD2 G:HIS469 3.0 100.5 1.0 CB G:CYS440 3.0 90.1 1.0 O G:CYS443 3.2 98.9 1.0 CB G:CYS466 3.3 100.9 1.0 N G:CYS443 3.5 91.9 1.0 N G:CYS466 3.5 101.2 1.0 CB G:CYS443 3.6 88.3 1.0 ND1 G:HIS469 3.8 100.7 1.0 CA G:CYS443 3.9 88.3 1.0 CG G:HIS469 3.9 96.2 1.0 C G:CYS443 3.9 92.0 1.0 CA G:CYS466 4.0 98.9 1.0 CB G:TYR442 4.4 94.6 1.0 CA G:CYS440 4.5 90.0 1.0 C G:TYR442 4.6 97.5 1.0 C G:LYS465 4.7 92.7 1.0 N G:TYR442 4.8 98.5 1.0 CA G:TYR442 4.9 96.2 1.0 CB G:THR445 4.9 78.6 1.0 CA G:LYS465 4.9 88.4 1.0 C G:CYS440 5.0 92.4 1.0 OG1 G:THR445 5.0 83.1 1.0

Zinc binding site 5 out of 5 in the RPD3S Bound to An H3K36CME3 Modified Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of RPD3S Bound to An H3K36CME3 Modified Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn704 b:213.1 occ:1.00 CB G:CYS278 2.2 167.4 1.0 SG G:CYS278 2.3 166.3 1.0 SG G:CYS275 2.3 165.7 1.0 SG G:CYS303 2.7 168.5 1.0 N G:CYS278 2.8 168.3 1.0 CA G:CYS278 3.0 167.0 1.0 CB G:CYS275 3.2 164.4 1.0 SG G:CYS306 3.2 174.7 1.0 CB G:CYS303 3.2 165.6 1.0 OG1 G:THR277 3.3 171.3 1.0 N G:CYS303 3.3 165.5 1.0 CB G:CYS306 3.7 177.5 1.0 CA G:CYS303 3.8 165.5 1.0 C G:THR277 4.0 173.1 1.0 C G:CYS278 4.0 165.4 1.0 O G:CYS278 4.3 165.4 1.0 CB G:THR277 4.3 172.8 1.0 C G:HIS302 4.4 165.3 1.0 CA G:HIS302 4.5 165.8 1.0 CA G:THR277 4.5 173.3 1.0 CA G:CYS275 4.6 164.7 1.0 N G:THR277 4.7 172.5 1.0 CZ3 G:TRP301 4.7 154.2 1.0 N G:CYS306 4.7 179.5 1.0 C G:CYS303 4.7 164.9 1.0 O G:CYS303 4.8 165.1 1.0 CA G:CYS306 4.8 179.2 1.0 O G:THR277 5.0 171.8 1.0

J.W.Markert, S.M.Vos, L.Farnung. Structure of the Complete Saccharomyces Cerevisiae RPD3S-Nucleosome Complex. Nat Commun V. 14 8128 2023.
ISSN: ESSN 2041-1723
PubMed: 38065958
DOI: 10.1038/S41467-023-43968-8