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Zinc in PDB 8jho: Cryo-Em Structure of the Histone Deacetylase Complex RPD3S in Complex with Di-Nucleosome

Enzymatic activity of Cryo-Em Structure of the Histone Deacetylase Complex RPD3S in Complex with Di-Nucleosome

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the Histone Deacetylase Complex RPD3S in Complex with Di-Nucleosome (pdb code 8jho). 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 in Complex with Di-Nucleosome, PDB code: 8jho:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8jho

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of the Histone Deacetylase Complex RPD3S in Complex with Di-Nucleosome


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 in Complex with Di-Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn501

b:74.4
occ:1.00
 OD1 L:ASP186 2.1 54.6 1.0
OD2 L:ASP274 2.2 68.5 1.0
ND1 L:HIS188 2.3 43.1 1.0
OD2 L:ASP186 2.5 56.4 1.0
CG L:ASP186 2.6 52.3 1.0
CG L:ASP274 3.2 62.2 1.0
CG L:HIS188 3.3 39.5 1.0
CE1 L:HIS188 3.3 46.8 1.0
CB L:HIS188 3.5 35.6 1.0
OD1 L:ASP274 3.6 64.8 1.0
OH L:TYR313 3.6 68.9 1.0
NE2 L:HIS150 3.6 46.9 1.0
N L:HIS188 3.9 45.5 1.0
NZ E:LYS18 4.0 30.0 1.0
NE2 L:HIS151 4.0 54.1 1.0
CB L:ASP186 4.1 45.1 1.0
CE1 L:HIS150 4.1 47.0 1.0
CA L:HIS188 4.3 34.0 1.0
NE2 L:HIS188 4.4 44.4 1.0
CD2 L:HIS188 4.4 41.4 1.0
CA L:GLY311 4.5 61.1 1.0
CB L:ASP274 4.5 58.0 1.0
CZ L:TYR313 4.5 71.9 1.0
CE2 L:TYR313 4.6 68.5 1.0
CG1 L:VAL187 4.7 39.5 1.0
CD2 L:HIS151 4.7 44.7 1.0
N L:VAL187 4.7 47.2 1.0
CD2 L:HIS150 4.9 43.3 1.0
CD E:LYS18 4.9 30.0 1.0
N L:GLY311 4.9 65.3 1.0
CE E:LYS18 4.9 30.0 1.0
CA L:ASP186 5.0 43.8 1.0

Zinc binding site 2 out of 7 in 8jho

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


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 in Complex with Di-Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn701

b:89.4
occ:1.00
 ND1 N:HIS283 2.1 43.8 1.0
SG N:CYS266 2.3 62.1 1.0
SG N:CYS263 2.3 58.9 1.0
SG N:CYS286 2.3 45.2 1.0
CG N:HIS283 2.9 38.4 1.0
CB N:HIS283 3.0 39.8 1.0
CB N:CYS263 3.1 56.9 1.0
CE1 N:HIS283 3.1 45.7 1.0
CB N:CYS286 3.4 39.4 1.0
CB N:CYS266 3.5 48.6 1.0
N N:CYS266 3.8 45.2 1.0
N N:HIS283 3.9 44.1 1.0
CD2 N:HIS283 4.0 48.7 1.0
CA N:HIS283 4.1 36.3 1.0
NE2 N:HIS283 4.1 49.5 1.0
CA N:CYS266 4.2 43.2 1.0
NE M:ARG300 4.2 55.1 1.0
CB N:ALA265 4.4 42.2 1.0
CA N:CYS263 4.5 59.2 1.0
CD M:ARG300 4.6 51.2 1.0
CG M:ARG300 4.6 49.4 1.0
C N:ALA265 4.7 43.8 1.0
CA N:CYS286 4.7 37.0 1.0
N N:ALA265 4.8 47.2 1.0
CA N:ALA265 4.9 39.9 1.0
CZ M:ARG300 4.9 57.1 1.0

Zinc binding site 3 out of 7 in 8jho

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


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 in Complex with Di-Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn702

b:62.5
occ:1.00
 ND1 N:HIS448 2.1 26.5 1.0
SG N:CYS417 2.3 30.7 1.0
SG N:CYS420 2.3 35.5 1.0
SG N:CYS451 2.3 46.3 1.0
CG N:HIS448 2.8 14.1 1.0
CB N:HIS448 2.8 10.9 1.0
CB N:CYS417 3.0 17.2 1.0
CE1 N:HIS448 3.2 25.2 1.0
CB N:CYS420 3.3 30.5 1.0
CB N:CYS451 3.5 42.7 1.0
N N:CYS420 3.7 28.8 1.0
N N:HIS448 3.8 24.6 1.0
CA N:HIS448 3.9 11.2 1.0
CD2 N:HIS448 4.0 9.4 1.0
CA N:CYS420 4.1 29.1 1.0
NE2 N:HIS448 4.2 22.3 1.0
CA N:CYS417 4.4 11.7 1.0
CA N:CYS451 4.8 38.3 1.0
C N:CYS417 4.8 30.5 1.0
O N:GLN422 4.8 38.7 1.0
N N:CYS451 4.8 31.9 1.0
N N:LYS419 4.9 11.1 1.0
C N:LYS419 4.9 30.7 1.0
CB N:LYS419 4.9 26.4 1.0
C N:CYS420 5.0 31.1 1.0
C N:HIS448 5.0 26.0 1.0

Zinc binding site 4 out of 7 in 8jho

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


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 in Complex with Di-Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn703

b:144.0
occ:1.00
 CB N:CYS278 1.9 92.0 1.0
SG N:CYS306 2.3 98.4 1.0
SG N:CYS303 2.3 88.5 1.0
SG N:CYS278 2.3 90.9 1.0
SG N:CYS275 2.3 85.6 1.0
CB N:CYS306 3.0 93.9 1.0
CA N:CYS278 3.4 85.6 1.0
CB N:CYS303 3.5 81.7 1.0
CB N:CYS275 3.6 81.3 1.0
N N:CYS303 3.9 80.9 1.0
N N:CYS278 4.0 84.2 1.0
CA N:CYS306 4.1 93.0 1.0
N N:CYS306 4.1 91.3 1.0
C N:CYS278 4.3 85.9 1.0
CA N:CYS303 4.3 79.2 1.0
C N:THR277 4.4 86.5 1.0
O N:THR277 4.4 87.4 1.0
O N:CYS278 4.6 89.6 1.0
OG1 N:THR277 4.9 90.7 1.0
CA N:CYS275 5.0 79.7 1.0
C N:CYS303 5.0 82.8 1.0

Zinc binding site 5 out of 7 in 8jho

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


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 in Complex with Di-Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn704

b:68.9
occ:1.00
 NE2 N:HIS469 2.1 40.0 1.0
SG N:CYS443 2.3 20.4 1.0
SG N:CYS466 2.3 59.5 1.0
SG N:CYS440 2.3 42.6 1.0
CB N:CYS440 2.5 26.5 1.0
CB N:CYS466 2.8 23.6 1.0
CE1 N:HIS469 3.1 43.2 1.0
CD2 N:HIS469 3.1 39.7 1.0
CB N:THR445 3.9 14.1 1.0
N N:CYS466 3.9 20.1 1.0
CA N:CYS466 3.9 17.3 1.0
CB N:CYS443 4.0 36.3 1.0
OG1 N:THR445 4.0 26.3 1.0
CA N:CYS440 4.0 13.5 1.0
N N:CYS443 4.1 25.7 1.0
N N:THR445 4.1 16.3 1.0
ND1 N:HIS469 4.2 33.5 1.0
CG N:HIS469 4.2 22.9 1.0
CA N:CYS443 4.4 28.0 1.0
CA N:THR445 4.6 1.6 1.0
N N:GLN444 4.6 30.7 1.0
O N:THR445 4.6 42.3 1.0
C N:CYS443 4.7 29.5 1.0
C N:CYS466 4.7 27.5 1.0
N N:CYS440 4.7 35.6 1.0
C N:CYS440 4.8 21.2 1.0
O N:CYS466 4.9 46.5 1.0
NE1 N:TRP447 5.0 15.1 1.0
CG2 N:THR445 5.0 17.8 1.0

Zinc binding site 6 out of 7 in 8jho

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


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 in Complex with Di-Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn701

b:190.0
occ:1.00
 ND1 P:HIS283 2.1 99.6 1.0
SG P:CYS266 2.3 108.7 1.0
SG P:CYS263 2.3 101.7 1.0
SG P:CYS286 2.3 95.8 1.0
CG P:HIS283 2.6 98.2 1.0
CE1 P:HIS283 2.7 94.1 1.0
CB P:CYS266 3.0 103.1 1.0
CB P:HIS283 3.2 90.4 1.0
CB P:CYS263 3.2 102.9 1.0
CD2 P:HIS283 3.3 100.8 1.0
NE2 P:HIS283 3.3 99.0 1.0
CB P:CYS286 3.4 93.0 1.0
N P:CYS266 3.7 97.9 1.0
N P:HIS283 3.8 88.3 1.0
NH1 O:ARG300 3.8 94.8 1.0
CA P:CYS266 4.0 100.3 1.0
CA P:HIS283 4.1 89.1 1.0
CA P:CYS263 4.6 103.5 1.0
CB P:ALA265 4.6 88.7 1.0
CA P:CYS286 4.7 90.3 1.0
O P:GLN268 4.7 104.9 1.0
CZ O:ARG300 4.8 95.4 1.0
C P:CYS266 4.8 104.4 1.0
C P:ALA265 4.8 92.9 1.0
C P:PHE282 4.8 93.0 1.0
N P:ASN267 5.0 107.9 1.0

Zinc binding site 7 out of 7 in 8jho

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


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 in Complex with Di-Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn702

b:181.3
occ:1.00
 SG P:CYS275 2.2 141.7 1.0
SG P:CYS303 2.3 120.0 1.0
SG P:CYS278 2.3 142.2 1.0
SG P:CYS306 2.3 139.1 1.0
CB P:CYS303 3.2 121.3 1.0
CB P:CYS275 3.5 140.6 1.0
CB P:CYS306 3.5 134.1 1.0
N P:CYS303 3.8 128.4 1.0
CB P:CYS278 4.0 136.3 1.0
N P:CYS306 4.0 130.7 1.0
CA P:CYS303 4.1 123.9 1.0
OG1 P:THR277 4.2 133.7 1.0
N P:CYS278 4.2 137.8 1.0
OD1 P:ASP276 4.3 140.4 1.0
CA P:CYS306 4.4 133.3 1.0
CA P:CYS278 4.7 136.9 1.0
C P:CYS303 4.7 125.9 1.0
O P:CYS278 4.8 133.0 1.0
CA P:CYS275 4.8 140.5 1.0
CB P:GLU305 4.8 103.9 1.0

Reference:

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
Page generated: Fri Aug 22 11:29:56 2025

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