Zinc in PDB 8w9e: Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2

The structure of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 (pdb code 8w9e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2, PDB code: 8w9e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1000 b:103.6 occ:1.00 ND1 E:HIS283 2.2 101.4 1.0 SG E:CYS263 2.3 117.8 1.0 SG E:CYS286 2.4 96.5 1.0 SG E:CYS266 2.4 105.0 1.0 CE1 E:HIS283 2.9 101.4 1.0 CB E:CYS263 3.1 117.8 1.0 CG E:HIS283 3.2 101.4 1.0 CB E:CYS266 3.3 105.0 1.0 NH1 C:ARG300 3.3 72.3 1.0 CB E:HIS283 3.7 101.4 1.0 CB E:CYS286 3.8 96.5 1.0 NE2 E:HIS283 3.9 101.4 1.0 CD2 E:HIS283 4.1 101.4 1.0 N E:CYS266 4.1 105.0 1.0 CA E:CYS266 4.3 105.0 1.0 N E:HIS283 4.3 101.4 1.0 CZ C:ARG300 4.6 72.3 1.0 CA E:CYS263 4.6 117.8 1.0 CA E:HIS283 4.6 101.4 1.0 O E:CYS263 4.9 117.8 1.0 CB E:ALA265 5.0 104.1 1.0

Zinc binding site 2 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:202.0 occ:1.00 SG E:CYS275 2.3 161.5 1.0 SG E:CYS303 2.4 145.7 1.0 SG E:CYS278 2.4 166.2 1.0 SG E:CYS306 2.5 146.4 1.0 CB E:CYS303 3.0 145.7 1.0 CB E:CYS278 3.2 166.2 1.0 OG1 E:THR277 3.2 167.2 1.0 N E:CYS278 3.2 166.2 1.0 N E:CYS303 3.4 145.7 1.0 CB E:CYS306 3.4 146.4 1.0 CB E:CYS275 3.7 161.5 1.0 CA E:CYS278 3.7 166.2 1.0 C E:THR277 3.8 167.2 1.0 CA E:CYS303 3.8 145.7 1.0 CB E:THR277 4.1 167.2 1.0 CA E:THR277 4.2 167.2 1.0 N E:CYS306 4.3 146.4 1.0 N E:THR277 4.3 167.2 1.0 O E:CYS278 4.4 166.2 1.0 O E:THR277 4.4 167.2 1.0 CA E:CYS306 4.5 146.4 1.0 C E:CYS278 4.5 166.2 1.0 C E:CYS303 4.6 145.7 1.0 C E:HIS302 4.6 156.4 1.0 O E:CYS303 4.8 145.7 1.0 CA E:HIS302 4.9 156.4 1.0 CA E:CYS275 5.0 161.5 1.0

Zinc binding site 3 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1002 b:117.6 occ:1.00 SG E:CYS443 2.2 83.1 1.0 SG E:CYS440 2.3 80.5 1.0 SG E:CYS466 2.4 85.8 1.0 CB E:CYS466 2.7 85.8 1.0 CB E:CYS440 2.8 80.5 1.0 N E:CYS466 3.1 85.8 1.0 NE2 E:HIS469 3.1 89.5 1.0 CA E:CYS466 3.5 85.8 1.0 CB E:CYS443 3.7 83.1 1.0 N E:CYS443 3.8 83.1 1.0 CD2 E:HIS469 3.8 89.5 1.0 CE1 E:HIS469 4.2 89.5 1.0 C E:LYS465 4.2 78.3 1.0 CA E:CYS440 4.3 80.5 1.0 CA E:CYS443 4.3 83.1 1.0 N E:GLN444 4.4 76.8 1.0 CA E:LYS465 4.6 78.3 1.0 CG2 E:THR445 4.6 76.9 1.0 C E:CYS466 4.7 85.8 1.0 N E:TYR442 4.7 84.6 1.0 CB E:TYR442 4.8 84.6 1.0 C E:CYS443 4.8 83.1 1.0 C E:TYR442 4.9 84.6 1.0 C E:CYS440 5.0 80.5 1.0

Zinc binding site 4 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1003 b:111.9 occ:1.00 ND1 E:HIS448 2.0 72.0 1.0 SG E:CYS420 2.3 89.6 1.0 SG E:CYS417 2.4 90.1 1.0 SG E:CYS451 2.4 70.3 1.0 CG E:HIS448 2.6 72.0 1.0 CB E:HIS448 2.7 72.0 1.0 CE1 E:HIS448 3.2 72.0 1.0 CB E:CYS417 3.5 90.1 1.0 CB E:CYS420 3.6 89.6 1.0 CD2 E:HIS448 3.9 72.0 1.0 CA E:HIS448 4.0 72.0 1.0 CB E:CYS451 4.0 70.3 1.0 NE2 E:HIS448 4.1 72.0 1.0 N E:HIS448 4.1 72.0 1.0 N E:CYS420 4.1 89.6 1.0 CA E:CYS420 4.5 89.6 1.0 CB E:LYS419 4.8 83.2 1.0 N E:CYS451 4.9 70.3 1.0 C E:LYS419 4.9 83.2 1.0 CA E:CYS417 4.9 90.1 1.0 C E:HIS448 4.9 72.0 1.0

Zinc binding site 5 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:56.8 occ:1.00 OD2 B:ASP274 2.3 55.2 1.0 ND1 B:HIS188 2.5 53.9 1.0 CE1 B:HIS188 2.6 53.9 1.0 OD2 B:ASP186 2.7 45.2 1.0 OH B:TYR313 3.3 72.3 1.0 CG B:ASP274 3.5 55.2 1.0 CG B:ASP186 3.5 45.2 1.0 OD1 B:ASP186 3.5 45.2 1.0 CG B:HIS188 3.8 53.9 1.0 NE2 B:HIS188 3.9 53.9 1.0 NE2 B:HIS151 4.1 41.8 1.0 OD1 B:ASP274 4.1 55.2 1.0 CA B:GLY311 4.2 49.2 1.0 CZ B:TYR313 4.2 72.3 1.0 CE2 B:TYR313 4.2 72.3 1.0 CD2 B:HIS188 4.5 53.9 1.0 CB B:ASP274 4.5 55.2 1.0 CB B:HIS188 4.6 53.9 1.0 N B:GLY311 4.7 49.2 1.0 CE1 B:HIS150 4.8 37.8 1.0 CD2 B:HIS151 4.8 41.8 1.0 CB B:ASP186 4.9 45.2 1.0

Zinc binding site 6 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1000 b:269.1 occ:1.00 ND1 F:HIS283 2.2 230.4 1.0 SG F:CYS263 2.4 226.8 1.0 CB F:HIS283 2.4 230.4 1.0 SG F:CYS286 2.4 233.2 1.0 CG F:HIS283 2.5 230.4 1.0 SG F:CYS266 3.1 227.8 1.0 CB F:CYS263 3.4 226.8 1.0 CE1 F:HIS283 3.4 230.4 1.0 N F:HIS283 3.4 230.4 1.0 CA F:HIS283 3.5 230.4 1.0 CD2 F:HIS283 3.7 230.4 1.0 CB F:CYS266 3.7 227.8 1.0 CB F:CYS286 4.0 233.2 1.0 NE2 F:HIS283 4.1 230.4 1.0 N F:CYS266 4.4 227.8 1.0 C F:HIS283 4.5 230.4 1.0 C F:PHE282 4.7 225.9 1.0 CA F:CYS266 4.7 227.8 1.0 CA F:CYS263 4.8 226.8 1.0 OE1 F:GLN350 4.8 219.3 1.0 CB F:ALA265 4.8 226.5 1.0 O F:HIS283 4.9 230.4 1.0 N F:CYS286 4.9 233.2 1.0 NH1 D:ARG300 5.0 216.0 1.0

Zinc binding site 7 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1001 b:229.7 occ:1.00 CB F:CYS275 2.4 219.2 1.0 CB F:CYS303 2.5 224.4 1.0 SG F:CYS303 2.5 224.4 1.0 N F:CYS303 2.8 224.4 1.0 CA F:CYS303 3.2 224.4 1.0 SG F:CYS275 3.2 219.2 1.0 SG F:CYS278 3.2 214.9 1.0 CA F:CYS275 3.7 219.2 1.0 CE2 F:PHE282 3.8 225.9 1.0 C F:HIS302 3.8 223.3 1.0 N F:CYS275 4.0 219.2 1.0 O F:LYS280 4.0 219.1 1.0 CZ F:PHE282 4.1 225.9 1.0 CA F:HIS302 4.2 223.3 1.0 CZ3 F:TRP301 4.3 220.7 1.0 CB F:LYS280 4.4 219.1 1.0 C F:CYS303 4.4 224.4 1.0 CH2 F:TRP301 4.6 220.7 1.0 ND2 F:ASN347 4.6 217.7 1.0 O F:HIS302 4.8 223.3 1.0 C F:CYS275 4.8 219.2 1.0 C F:LYS280 4.9 219.1 1.0 O F:CYS303 4.9 224.4 1.0 CE3 F:TRP301 4.9 220.7 1.0 O F:CYS278 4.9 214.9 1.0 CB F:HIS302 4.9 223.3 1.0 CD2 F:PHE282 5.0 225.9 1.0 CB F:CYS278 5.0 214.9 1.0

C.Wang, C.Chu, Z.Guo, X.Zhan. Structures and Dynamics of RPD3S Complex Bound to Nucleosome. Sci Adv V. 10 K7678 2024.
ISSN: ESSN 2375-2548
PubMed: 38598631
DOI: 10.1126/SCIADV.ADK7678