Zinc in PDB 8hxx: Cryo-Em Structure of the Histone Deacetylase Complex RPD3S

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

The binding sites of Zinc atom in the Cryo-Em Structure of the Histone Deacetylase Complex RPD3S (pdb code 8hxx). 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 Histone Deacetylase Complex RPD3S, PDB code: 8hxx:
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 Histone Deacetylase Complex RPD3S


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 Histone Deacetylase Complex RPD3S within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn501 b:162.2 occ:1.00 OD1 L:ASP186 2.0 110.9 1.0 OD2 L:ASP274 2.0 123.1 1.0 OD2 L:ASP186 2.0 108.8 1.0 CG L:ASP186 2.2 106.6 1.0 ND1 L:HIS188 2.3 97.2 1.0 CG L:ASP274 3.0 119.7 1.0 CE1 L:HIS188 3.2 100.0 1.0 CG L:HIS188 3.3 92.4 1.0 OD1 L:ASP274 3.5 124.0 1.0 NE2 L:HIS150 3.6 97.1 1.0 CB L:HIS188 3.6 91.3 1.0 CB L:ASP186 3.7 101.6 1.0 OH L:TYR313 3.8 118.5 1.0 N L:HIS188 4.0 101.1 1.0 NE2 L:HIS151 4.1 104.5 1.0 CE1 L:HIS150 4.1 99.5 1.0 CB L:ASP274 4.2 111.5 1.0 CA L:GLY311 4.3 113.8 1.0 NE2 L:HIS188 4.4 96.3 1.0 CA L:HIS188 4.4 92.3 1.0 CD2 L:HIS188 4.4 90.3 1.0 NZ E:LYS23 4.5 27.1 1.0 N L:VAL187 4.6 98.4 1.0 N L:GLY311 4.7 112.8 1.0 CD2 L:HIS150 4.7 98.7 1.0 CA L:ASP186 4.7 95.0 1.0 CD2 L:HIS151 4.7 94.4 1.0 CZ L:TYR313 4.8 122.7 1.0 CG1 L:VAL187 4.8 94.1 1.0 C L:ASP186 5.0 104.5 1.0

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


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 Histone Deacetylase Complex RPD3S within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn701 b:154.1 occ:1.00 ND1 N:HIS283 2.1 96.3 1.0 SG N:CYS266 2.3 111.2 1.0 SG N:CYS263 2.3 123.4 1.0 SG N:CYS286 2.3 106.0 1.0 CG N:HIS283 2.8 91.7 1.0 CB N:HIS283 2.9 92.8 1.0 CB N:CYS263 3.1 111.8 1.0 CE1 N:HIS283 3.2 100.1 1.0 CB N:CYS286 3.4 95.2 1.0 CB N:CYS266 3.4 102.6 1.0 N N:CYS266 3.7 100.1 1.0 N N:HIS283 3.8 93.7 1.0 CA N:HIS283 4.0 89.3 1.0 CD2 N:HIS283 4.0 97.9 1.0 NE2 N:HIS283 4.2 100.2 1.0 CA N:CYS266 4.2 101.2 1.0 CB N:ALA265 4.3 98.2 1.0 NE M:ARG300 4.3 100.8 1.0 CA N:CYS263 4.5 111.4 1.0 CD M:ARG300 4.6 95.4 1.0 CG M:ARG300 4.6 95.8 1.0 C N:ALA265 4.6 99.3 1.0 CA N:CYS286 4.7 92.4 1.0 N N:ALA265 4.8 97.7 1.0 CA N:ALA265 4.8 97.0 1.0 CZ M:ARG300 4.9 104.5 1.0 C N:CYS266 5.0 106.2 1.0

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


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 Histone Deacetylase Complex RPD3S within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn702 b:131.3 occ:1.00 ND1 N:HIS448 2.1 80.1 1.0 SG N:CYS417 2.3 96.8 1.0 SG N:CYS420 2.3 98.0 1.0 SG N:CYS451 2.3 98.5 1.0 CG N:HIS448 2.7 69.4 1.0 CB N:HIS448 2.8 64.3 1.0 CB N:CYS417 3.0 83.8 1.0 CE1 N:HIS448 3.2 81.7 1.0 CB N:CYS420 3.2 85.3 1.0 CB N:CYS451 3.5 85.5 1.0 N N:CYS420 3.7 81.5 1.0 N N:HIS448 3.8 75.2 1.0 CA N:HIS448 3.9 65.1 1.0 CD2 N:HIS448 4.0 69.5 1.0 CA N:CYS420 4.1 83.9 1.0 NE2 N:HIS448 4.2 74.0 1.0 CA N:CYS417 4.4 73.7 1.0 C N:CYS417 4.7 81.2 1.0 CA N:CYS451 4.8 84.1 1.0 O N:GLN422 4.8 96.0 1.0 N N:LYS419 4.8 74.2 1.0 C N:LYS419 4.8 82.5 1.0 N N:CYS451 4.8 79.3 1.0 CB N:LYS419 4.8 82.8 1.0 C N:CYS420 4.9 85.7 1.0

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


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 Histone Deacetylase Complex RPD3S within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn703 b:210.9 occ:1.00 CB N:CYS278 1.9 145.8 1.0 SG N:CYS303 2.3 147.0 1.0 SG N:CYS306 2.3 148.0 1.0 SG N:CYS275 2.3 141.7 1.0 SG N:CYS278 2.3 142.0 1.0 CB N:CYS306 2.9 141.8 1.0 CA N:CYS278 3.4 142.5 1.0 CB N:CYS303 3.5 133.1 1.0 CB N:CYS275 3.6 136.6 1.0 N N:CYS303 3.9 130.4 1.0 N N:CYS278 3.9 140.9 1.0 CA N:CYS306 4.0 139.0 1.0 N N:CYS306 4.0 139.4 1.0 C N:CYS278 4.2 142.2 1.0 CA N:CYS303 4.3 131.0 1.0 C N:THR277 4.4 143.7 1.0 O N:THR277 4.4 144.8 1.0 O N:CYS278 4.5 144.9 1.0 OG1 N:THR277 4.9 148.2 1.0 C N:CYS303 4.9 133.4 1.0 CA N:CYS275 5.0 133.2 1.0

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


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 Histone Deacetylase Complex RPD3S within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn704 b:149.9 occ:1.00 NE2 N:HIS469 1.9 85.2 1.0 SG N:CYS440 2.3 96.9 1.0 SG N:CYS443 2.3 82.7 1.0 SG N:CYS466 2.3 112.1 1.0 CD2 N:HIS469 2.8 84.1 1.0 CE1 N:HIS469 2.8 86.0 1.0 CB N:CYS440 3.1 86.3 1.0 CB N:CYS466 3.4 85.3 1.0 CB N:CYS443 3.4 82.8 1.0 N N:CYS443 3.6 77.5 1.0 ND1 N:HIS469 3.8 81.7 1.0 CG N:HIS469 3.8 71.8 1.0 N N:CYS466 4.0 77.7 1.0 CA N:CYS443 4.0 80.8 1.0 CA N:CYS466 4.3 76.7 1.0 OG1 N:THR445 4.3 71.4 1.0 CB N:THR445 4.5 64.4 1.0 C N:CYS443 4.6 80.9 1.0 CA N:CYS440 4.6 70.5 1.0 CB N:TYR442 4.6 76.8 1.0 N N:GLN444 4.7 70.6 1.0 N N:THR445 4.7 53.1 1.0 C N:TYR442 4.7 83.4 1.0 N N:TYR442 4.8 69.4 1.0 CA N:TYR442 4.9 74.2 1.0 C N:CYS466 5.0 82.5 1.0 O N:CYS466 5.0 94.9 1.0

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


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 Histone Deacetylase Complex RPD3S within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn701 b:219.4 occ:1.00 ND1 P:HIS283 2.1 184.6 1.0 SG P:CYS263 2.3 188.3 1.0 SG P:CYS266 2.3 192.2 1.0 SG P:CYS286 2.3 184.3 1.0 CE1 P:HIS283 2.6 183.9 1.0 CG P:HIS283 2.6 184.6 1.0 CB P:CYS263 3.1 185.5 1.0 CB P:CYS266 3.1 185.7 1.0 NE2 P:HIS283 3.3 184.5 1.0 CB P:HIS283 3.3 183.3 1.0 CD2 P:HIS283 3.3 184.7 1.0 CB P:CYS286 3.5 184.0 1.0 N P:CYS266 3.7 186.6 1.0 N P:HIS283 3.8 181.2 1.0 NH2 O:ARG300 3.8 105.7 1.0 CA P:CYS266 4.0 186.0 1.0 CA P:HIS283 4.2 182.2 1.0 CB P:ALA265 4.6 173.5 1.0 CA P:CYS263 4.6 184.1 1.0 O P:GLN268 4.7 183.1 1.0 CZ O:ARG300 4.7 105.9 1.0 C P:PHE282 4.8 172.7 1.0 C P:ALA265 4.8 177.0 1.0 OE1 P:GLN268 4.8 181.5 1.0 C P:CYS266 4.8 186.7 1.0 CA P:CYS286 4.9 184.1 1.0

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


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 Histone Deacetylase Complex RPD3S within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn702 b:262.1 occ:1.00 SG P:CYS278 2.3 204.8 1.0 SG P:CYS303 2.3 188.2 1.0 SG P:CYS275 2.3 197.6 1.0 SG P:CYS306 2.3 201.8 1.0 CB P:CYS303 3.1 185.2 1.0 CB P:CYS306 3.5 193.4 1.0 CB P:CYS275 3.6 194.1 1.0 N P:CYS303 3.9 187.3 1.0 CB P:CYS278 4.0 198.7 1.0 CA P:CYS303 4.1 185.7 1.0 N P:CYS306 4.1 190.6 1.0 N P:CYS278 4.1 198.5 1.0 OD1 P:ASP276 4.3 202.3 1.0 CA P:CYS306 4.4 192.0 1.0 CA P:CYS278 4.6 197.5 1.0 C P:CYS303 4.8 184.6 1.0 CA P:CYS275 4.9 193.9 1.0 O P:CYS278 4.9 194.6 1.0 N P:THR277 4.9 208.4 1.0

H.Cui, H.Wang. Structure of Histone Deacetylase Complex RPD3S Bound to Nucleosome Nat.Struct.Biol. 2023.
ISSN: ISSN 1072-8368
DOI: 10.1038/S41594-023-01121-5