Zinc in PDB 8w9d: Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1

The structure of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1 also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1 (pdb code 8w9d). 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 1, PDB code: 8w9d:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1000 b:50.8 occ:1.00 ND1 E:HIS283 2.1 37.0 1.0 SG E:CYS263 2.3 41.6 1.0 SG E:CYS266 2.3 37.1 1.0 SG E:CYS286 2.4 32.5 1.0 CB E:CYS263 2.9 41.6 1.0 CG E:HIS283 3.1 37.0 1.0 CE1 E:HIS283 3.1 37.0 1.0 CB E:CYS286 3.2 32.5 1.0 CB E:HIS283 3.4 37.0 1.0 CB E:CYS266 3.5 37.1 1.0 N E:CYS266 3.8 37.1 1.0 N E:HIS283 3.9 37.0 1.0 NE2 E:HIS283 4.2 37.0 1.0 CD2 E:HIS283 4.2 37.0 1.0 CA E:CYS266 4.2 37.1 1.0 CA E:HIS283 4.3 37.0 1.0 CA E:CYS263 4.4 41.6 1.0 CB E:ALA265 4.6 35.7 1.0 CD C:ARG300 4.6 22.3 1.0 CA E:CYS286 4.6 32.5 1.0 NH1 C:ARG300 4.7 22.3 1.0 NE C:ARG300 4.8 22.3 1.0 CZ C:ARG300 4.9 22.3 1.0 C E:ALA265 4.9 35.7 1.0 C E:CYS266 5.0 37.1 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:109.0 occ:1.00 SG E:CYS303 2.3 77.3 1.0 SG E:CYS306 2.3 87.6 1.0 SG E:CYS278 2.4 80.6 1.0 CB E:CYS306 2.5 87.6 1.0 SG E:CYS275 2.9 75.0 1.0 N E:CYS303 3.6 77.3 1.0 CB E:CYS303 3.7 77.3 1.0 CA E:CYS306 3.7 87.6 1.0 N E:CYS306 3.7 87.6 1.0 CB E:CYS278 3.8 80.6 1.0 CB E:THR277 4.1 86.6 1.0 CA E:CYS303 4.2 77.3 1.0 N E:CYS278 4.2 80.6 1.0 CB E:CYS275 4.4 75.0 1.0 CG2 E:THR277 4.5 86.6 1.0 C E:HIS302 4.6 83.2 1.0 CA E:CYS278 4.6 80.6 1.0 C E:CYS303 4.7 77.3 1.0 CA E:HIS302 4.8 83.2 1.0 C E:CYS306 4.8 87.6 1.0 CB E:HIS302 4.9 83.2 1.0 O E:CYS303 4.9 77.3 1.0 OG1 E:THR277 4.9 86.6 1.0 C E:GLU305 5.0 74.2 1.0 C E:THR277 5.0 86.6 1.0

Zinc binding site 3 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1002 b:60.2 occ:1.00 SG E:CYS443 2.2 42.1 1.0 NE2 E:HIS469 2.3 41.9 1.0 CB E:CYS466 2.3 39.1 1.0 SG E:CYS440 2.3 43.6 1.0 CB E:CYS440 3.0 43.6 1.0 CD2 E:HIS469 3.1 41.9 1.0 CE1 E:HIS469 3.3 41.9 1.0 N E:CYS466 3.3 39.1 1.0 CA E:CYS466 3.4 39.1 1.0 SG E:CYS466 3.6 39.1 1.0 CB E:CYS443 3.6 42.1 1.0 N E:CYS443 3.8 42.1 1.0 CA E:CYS443 4.3 42.1 1.0 C E:CYS466 4.3 39.1 1.0 CG E:HIS469 4.3 41.9 1.0 ND1 E:HIS469 4.3 41.9 1.0 OG1 E:THR445 4.4 33.6 1.0 O E:CYS466 4.5 39.1 1.0 CA E:CYS440 4.5 43.6 1.0 C E:LYS465 4.6 42.1 1.0 CB E:TYR442 4.7 47.2 1.0 C E:CYS443 4.9 42.1 1.0 N E:GLN444 4.9 40.6 1.0 C E:TYR442 4.9 47.2 1.0 N E:TYR442 4.9 47.2 1.0 CB E:THR445 4.9 33.6 1.0 CB E:LEU468 5.0 38.0 1.0

Zinc binding site 4 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1003 b:54.5 occ:1.00 SG E:CYS417 2.3 31.2 1.0 SG E:CYS420 2.3 34.5 1.0 SG E:CYS451 2.4 35.1 1.0 ND1 E:HIS448 2.7 31.3 1.0 CB E:CYS417 3.1 31.2 1.0 CB E:HIS448 3.2 31.3 1.0 CG E:HIS448 3.2 31.3 1.0 CB E:CYS420 3.5 34.5 1.0 CB E:CYS451 3.6 35.1 1.0 CE1 E:HIS448 3.7 31.3 1.0 N E:CYS420 3.9 34.5 1.0 N E:HIS448 4.0 31.3 1.0 CA E:HIS448 4.2 31.3 1.0 CA E:CYS420 4.3 34.5 1.0 CD2 E:HIS448 4.4 31.3 1.0 CA E:CYS417 4.5 31.2 1.0 NE2 E:HIS448 4.6 31.3 1.0 CB E:LYS419 4.7 31.8 1.0 N E:LYS419 4.9 31.8 1.0 C E:LYS419 4.9 31.8 1.0 CA E:CYS451 4.9 35.1 1.0 C E:CYS417 5.0 31.2 1.0

Zinc binding site 5 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1000 b:46.6 occ:1.00 ND1 B:HIS188 2.4 29.6 1.0 OD1 B:ASP186 2.6 28.4 1.0 OD2 B:ASP274 2.8 34.5 1.0 CE1 B:HIS188 3.2 29.6 1.0 CG B:HIS188 3.4 29.6 1.0 NZ H:LYS19 3.4 30.0 1.0 CG B:ASP186 3.5 28.4 1.0 CB B:HIS188 3.7 29.6 1.0 OD2 B:ASP186 3.8 28.4 1.0 OH B:TYR313 3.8 42.7 1.0 CG B:ASP274 3.9 34.5 1.0 NE2 B:HIS151 4.0 29.0 1.0 NE2 B:HIS150 4.0 30.1 1.0 NE2 B:HIS188 4.3 29.6 1.0 OD1 B:ASP274 4.4 34.5 1.0 CD2 B:HIS188 4.4 29.6 1.0 CA B:GLY311 4.5 35.8 1.0 CE H:LYS19 4.5 30.0 1.0 CD2 B:HIS151 4.5 29.0 1.0 CE2 B:TYR313 4.6 42.7 1.0 N B:HIS188 4.6 29.6 1.0 CZ B:TYR313 4.6 42.7 1.0 CB B:ASP186 4.7 28.4 1.0 CE1 B:HIS150 4.8 30.1 1.0 CA B:HIS188 4.8 29.6 1.0 N B:GLY311 4.9 35.8 1.0

Zinc binding site 6 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1000 b:200.1 occ:1.00 ND1 F:HIS283 2.2 191.8 1.0 CE1 F:HIS283 2.8 191.8 1.0 CB F:CYS263 2.9 194.5 1.0 CG F:HIS283 3.3 191.8 1.0 SG F:CYS286 3.4 186.7 1.0 SG F:CYS263 3.5 194.5 1.0 NH1 D:ARG303 3.5 185.7 1.0 CB F:HIS283 3.9 191.8 1.0 NE2 F:HIS283 4.0 191.8 1.0 O F:CYS263 4.0 194.5 1.0 SG F:CYS266 4.0 193.7 1.0 CB F:ALA265 4.0 193.9 1.0 CA F:CYS263 4.2 194.5 1.0 CD2 F:HIS283 4.2 191.8 1.0 N F:CYS266 4.3 193.7 1.0 C F:CYS263 4.4 194.5 1.0 N F:HIS283 4.4 191.8 1.0 CB F:CYS286 4.5 186.7 1.0 NH1 D:ARG300 4.6 187.9 1.0 CZ D:ARG303 4.6 185.7 1.0 CB F:CYS266 4.7 193.7 1.0 N F:ALA265 4.8 193.9 1.0 CA F:ALA265 4.8 193.9 1.0 CA F:HIS283 4.8 191.8 1.0 O F:GLN268 4.9 194.0 1.0 NH2 D:ARG303 4.9 185.7 1.0 C F:ALA265 4.9 193.9 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1001 b:201.8 occ:1.00 N F:CYS303 2.1 186.7 1.0 CB F:CYS275 2.7 189.3 1.0 SG F:CYS303 2.9 186.7 1.0 CB F:CYS303 2.9 186.7 1.0 SG F:CYS275 3.0 189.3 1.0 CA F:CYS303 3.0 186.7 1.0 C F:HIS302 3.1 188.0 1.0 CA F:HIS302 3.3 188.0 1.0 CB F:CYS278 3.4 187.6 1.0 SG F:CYS306 3.5 184.3 1.0 CB F:HIS302 3.6 188.0 1.0 C F:CYS303 3.8 186.7 1.0 O F:CYS303 3.8 186.7 1.0 CA F:CYS275 4.1 189.3 1.0 SG F:CYS278 4.1 187.6 1.0 O F:HIS302 4.3 188.0 1.0 CB F:CYS306 4.4 184.3 1.0 N F:CYS306 4.5 184.3 1.0 CA F:CYS278 4.6 187.6 1.0 N F:CYS278 4.6 187.6 1.0 N F:CYS275 4.7 189.3 1.0 N F:HIS302 4.7 188.0 1.0 CG F:HIS302 4.7 188.0 1.0 N F:ASN304 4.8 182.7 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