Zinc in PDB 7yi0: Cryo-Em Structure of RPD3S Complex

All present enzymatic activity of Cryo-Em Structure of RPD3S Complex:
3.5.1.98;

The binding sites of Zinc atom in the Cryo-Em Structure of RPD3S Complex (pdb code 7yi0). 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 RPD3S Complex, PDB code: 7yi0:
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 RPD3S Complex


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 RPD3S Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:44.0 occ:1.00 OD2 B:ASP186 2.2 29.8 1.0 ND1 B:HIS188 2.3 36.2 1.0 OD2 B:ASP274 2.3 27.5 1.0 OD1 B:ASP186 2.4 41.5 1.0 CG B:ASP186 2.5 26.6 1.0 CG B:HIS188 3.2 31.6 1.0 CE1 B:HIS188 3.3 35.7 1.0 CG B:ASP274 3.5 25.5 1.0 CB B:HIS188 3.5 26.0 1.0 CE1 B:HIS150 3.8 30.7 1.0 CB B:ASP186 3.9 16.0 1.0 CB B:ASP274 4.0 19.3 1.0 NE2 B:HIS150 4.1 24.2 1.0 N B:HIS188 4.1 29.2 1.0 CA B:GLY311 4.3 16.6 1.0 NE2 B:HIS188 4.4 29.4 1.0 CD2 B:HIS188 4.4 30.8 1.0 NE2 B:HIS151 4.4 17.9 1.0 CA B:HIS188 4.4 23.6 1.0 OD1 B:ASP274 4.5 30.4 1.0 OH B:TYR313 4.6 41.7 1.0 CG2 B:VAL187 4.6 24.0 1.0 N B:VAL187 4.8 27.8 1.0 N B:GLY311 4.8 18.1 1.0

Zinc binding site 2 out of 7 in the Cryo-Em Structure of RPD3S Complex


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 RPD3S Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:77.5 occ:1.00 ND1 D:HIS283 2.1 47.4 1.0 SG D:CYS266 2.3 45.5 1.0 SG D:CYS286 2.3 44.5 1.0 SG D:CYS263 2.3 61.3 1.0 CB D:CYS263 3.0 60.9 1.0 CE1 D:HIS283 3.0 45.3 1.0 CG D:HIS283 3.1 41.9 1.0 CB D:CYS286 3.1 39.0 1.0 CB D:HIS283 3.4 41.4 1.0 CB D:CYS266 3.7 43.2 1.0 N D:CYS266 4.0 42.3 1.0 NE2 D:HIS283 4.2 47.4 1.0 CD2 D:HIS283 4.2 47.1 1.0 N D:HIS283 4.3 48.0 1.0 NE C:ARG300 4.4 28.8 1.0 CA D:CYS266 4.4 45.0 1.0 CB D:ALA265 4.4 40.0 1.0 CA D:CYS263 4.4 58.6 1.0 CA D:HIS283 4.5 42.5 1.0 CA D:CYS286 4.6 35.5 1.0 CD C:ARG300 4.7 22.2 1.0 CZ C:ARG300 4.8 30.1 1.0 C D:ALA265 4.9 35.4 1.0 CG C:ARG300 4.9 23.7 1.0 C D:CYS263 5.0 59.7 1.0 N D:ALA265 5.0 46.7 1.0 NH2 C:ARG300 5.0 25.4 1.0 N D:CYS286 5.0 40.1 1.0

Zinc binding site 3 out of 7 in the Cryo-Em Structure of RPD3S Complex


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 RPD3S Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:148.3 occ:1.00 SG D:CYS278 2.3 100.5 1.0 SG D:CYS306 2.3 96.5 1.0 SG D:CYS303 2.3 97.5 1.0 SG D:CYS275 2.3 91.6 1.0 CB D:CYS275 3.3 90.1 1.0 OG1 D:THR277 3.4 101.3 1.0 CB D:CYS306 3.6 94.9 1.0 N D:CYS303 3.7 93.0 1.0 NZ D:LYS280 3.8 84.3 1.0 CB D:CYS278 3.9 95.1 1.0 CB D:CYS303 4.0 92.2 1.0 N D:CYS278 4.0 95.6 1.0 CA D:CYS303 4.4 92.9 1.0 CA D:CYS278 4.5 94.3 1.0 CA D:HIS302 4.7 97.2 1.0 CB D:THR277 4.7 100.4 1.0 C D:THR277 4.7 100.8 1.0 CB D:HIS302 4.7 98.1 1.0 O D:CYS278 4.7 93.5 1.0 C D:HIS302 4.7 95.6 1.0 CA D:CYS306 4.7 95.0 1.0 N D:THR277 4.8 98.8 1.0 CA D:CYS275 4.8 89.8 1.0 N D:CYS306 4.8 96.0 1.0 CA D:THR277 5.0 99.7 1.0 C D:CYS278 5.0 92.5 1.0

Zinc binding site 4 out of 7 in the Cryo-Em Structure of RPD3S Complex


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 RPD3S Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:51.5 occ:1.00 NE2 D:HIS469 2.1 28.4 1.0 SG D:CYS466 2.3 27.8 1.0 SG D:CYS443 2.3 20.6 1.0 SG D:CYS440 2.3 27.4 1.0 CE1 D:HIS469 3.1 22.7 1.0 CD2 D:HIS469 3.1 18.4 1.0 CB D:CYS466 3.4 22.6 1.0 CB D:CYS440 3.6 22.7 1.0 N D:CYS466 3.7 13.4 1.0 N D:CYS443 3.7 27.3 1.0 CB D:CYS443 3.8 27.4 1.0 CG2 D:THR445 3.9 31.7 1.0 CA D:CYS466 4.1 13.3 1.0 ND1 D:HIS469 4.2 15.5 1.0 CG D:HIS469 4.2 9.5 1.0 CB D:TYR442 4.3 25.7 1.0 CA D:CYS443 4.3 23.2 1.0 O D:CYS466 4.5 31.2 1.0 C D:CYS466 4.7 19.2 1.0 N D:TYR442 4.7 38.6 1.0 C D:TYR442 4.7 31.2 1.0 C D:LYS465 4.8 22.0 1.0 CA D:TYR442 4.8 27.8 1.0 C D:CYS443 4.9 29.8 1.0 CA D:CYS440 4.9 25.5 1.0 N D:THR445 5.0 19.0 1.0 CA D:LYS465 5.0 24.6 1.0 N D:GLN444 5.0 26.7 1.0

Zinc binding site 5 out of 7 in the Cryo-Em Structure of RPD3S Complex


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 RPD3S Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn704 b:74.6 occ:1.00 ND1 D:HIS448 2.1 29.9 1.0 SG D:CYS417 2.3 23.7 1.0 SG D:CYS420 2.3 37.2 1.0 SG D:CYS451 2.3 46.3 1.0 CB D:CYS417 2.9 19.2 1.0 CG D:HIS448 2.9 29.3 1.0 CE1 D:HIS448 3.1 22.1 1.0 CB D:HIS448 3.2 25.9 1.0 CB D:CYS420 3.4 18.6 1.0 CB D:CYS451 3.5 29.6 1.0 N D:CYS420 3.9 25.9 1.0 CD2 D:HIS448 4.0 25.5 1.0 NE2 D:HIS448 4.1 18.9 1.0 N D:HIS448 4.1 19.0 1.0 CA D:HIS448 4.3 21.3 1.0 CA D:CYS420 4.3 18.8 1.0 CA D:CYS417 4.4 15.1 1.0 O D:GLN422 4.6 16.2 1.0 CB D:LYS419 4.7 15.3 1.0 CA D:CYS451 4.8 20.2 1.0 C D:CYS417 4.8 21.3 1.0 C D:LYS419 4.9 21.4 1.0 N D:LYS419 4.9 16.1 1.0

Zinc binding site 6 out of 7 in the Cryo-Em Structure of RPD3S Complex


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 RPD3S Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn701 b:133.1 occ:1.00 SG F:CYS278 2.3 108.6 1.0 SG F:CYS275 2.3 118.3 1.0 N F:CYS278 3.4 106.8 1.0 CB F:CYS278 3.6 106.7 1.0 SG F:CYS303 3.6 93.1 1.0 SG F:CYS306 3.7 101.5 1.0 CB F:CYS306 3.8 99.1 1.0 CB F:CYS275 3.9 113.9 1.0 CB F:THR277 4.0 109.4 1.0 CA F:CYS278 4.0 106.2 1.0 N F:THR277 4.2 109.6 1.0 O F:CYS278 4.3 105.2 1.0 C F:THR277 4.3 109.0 1.0 CA F:THR277 4.4 109.6 1.0 OD1 F:ASP276 4.4 113.0 1.0 ND1 F:HIS302 4.6 107.7 1.0 C F:CYS278 4.7 105.6 1.0 O F:GLU305 4.7 96.2 1.0 N F:CYS303 4.8 99.2 1.0 N F:ASP276 4.8 113.3 1.0 CG2 F:THR277 4.8 107.6 1.0 OG1 F:THR277 4.8 108.1 1.0

Zinc binding site 7 out of 7 in the Cryo-Em Structure of RPD3S Complex


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 RPD3S Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn702 b:167.8 occ:1.00 SG F:CYS286 2.3 106.9 1.0 SG F:CYS263 2.3 96.0 1.0 SG F:CYS266 2.3 104.1 1.0 CD2 F:HIS283 3.1 100.8 1.0 CB F:CYS286 3.2 103.8 1.0 CB F:CYS266 3.4 98.7 1.0 CB F:CYS263 3.5 95.7 1.0 N F:CYS266 3.5 100.5 1.0 CG F:HIS283 3.7 101.0 1.0 CB F:ALA265 3.9 89.9 1.0 CB F:HIS283 4.0 100.2 1.0 NE2 F:HIS283 4.0 99.8 1.0 CA F:CYS266 4.1 99.8 1.0 C F:ALA265 4.3 92.0 1.0 CA F:ALA265 4.5 90.8 1.0 NE E:ARG300 4.6 91.3 1.0 CD E:ARG300 4.6 91.0 1.0 N F:ALA265 4.7 90.7 1.0 CA F:CYS286 4.7 103.3 1.0 CG E:ARG300 4.7 92.1 1.0 O F:CYS263 4.7 95.8 1.0 ND1 F:HIS283 4.8 100.8 1.0 CA F:CYS263 4.8 97.1 1.0 CE1 F:HIS283 4.9 100.9 1.0 C F:CYS263 4.9 96.7 1.0 C F:CYS266 5.0 100.7 1.0

H.P.Guan, P.Wang, C.Y.Yan, H.T.Li. Dynamic and Multivalent Engagement Determines Context-Dependent Nucleosomal Deacetylation By the RPD3S Complex To Be Published.