Atomistry » Zinc » PDB 8j62-8jp5 » 8jho
Atomistry »
  Zinc »
    PDB 8j62-8jp5 »
      8jho »

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

Go back to Zinc Binding Sites List in 8jho
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

Go back to Zinc Binding Sites List in 8jho
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

Go back to Zinc Binding Sites List in 8jho
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

Go back to Zinc Binding Sites List in 8jho
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

Go back to Zinc Binding Sites List in 8jho
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

Go back to Zinc Binding Sites List in 8jho
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

Go back to Zinc Binding Sites List in 8jho
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: Thu Oct 31 08:19:03 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy