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Zinc in PDB 8w9f: Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 3

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 3 (pdb code 8w9f). 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 3, PDB code: 8w9f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8w9f

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


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1000

b:64.2
occ:1.00
 NH1 C:ARG300 2.3 34.4 1.0
ND1 E:HIS283 2.3 51.2 1.0
SG E:CYS266 2.4 53.0 1.0
SG E:CYS263 2.4 63.5 1.0
SG E:CYS286 2.7 38.1 1.0
CG E:HIS283 2.9 51.2 1.0
CB E:HIS283 3.1 51.2 1.0
CB E:CYS263 3.2 63.5 1.0
CE1 E:HIS283 3.3 51.2 1.0
CZ C:ARG300 3.5 34.4 1.0
CB E:CYS286 3.8 38.1 1.0
NH2 C:ARG300 4.0 34.4 1.0
CD2 E:HIS283 4.0 51.2 1.0
CB E:CYS266 4.1 53.0 1.0
N E:HIS283 4.1 51.2 1.0
NE2 E:HIS283 4.2 51.2 1.0
CA E:HIS283 4.2 51.2 1.0
NE C:ARG300 4.5 34.4 1.0
N E:CYS266 4.6 53.0 1.0
CA E:CYS263 4.7 63.5 1.0
CD C:ARG300 4.8 34.4 1.0
CA E:CYS266 4.9 53.0 1.0

Zinc binding site 2 out of 7 in 8w9f

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:134.4
occ:1.00
 SG E:CYS303 2.4 84.6 1.0
SG E:CYS275 2.4 87.5 1.0
SG E:CYS306 2.4 85.0 1.0
SG E:CYS278 2.5 89.2 1.0
N E:CYS303 3.0 84.6 1.0
CB E:CYS303 3.0 84.6 1.0
CB E:CYS306 3.1 85.0 1.0
CB E:CYS275 3.1 87.5 1.0
CA E:CYS303 3.6 84.6 1.0
CB E:CYS278 3.6 89.2 1.0
OG1 E:THR277 3.7 88.3 1.0
N E:CYS306 4.0 85.0 1.0
C E:HIS302 4.1 85.6 1.0
N E:CYS278 4.2 89.2 1.0
CA E:CYS306 4.2 85.0 1.0
C E:CYS303 4.3 84.6 1.0
CA E:HIS302 4.3 85.6 1.0
O E:CYS303 4.4 84.6 1.0
CA E:CYS278 4.5 89.2 1.0
CA E:CYS275 4.6 87.5 1.0
CB E:HIS302 4.7 85.6 1.0
C E:THR277 4.8 88.3 1.0
O E:CYS278 4.8 89.2 1.0
N E:THR277 5.0 88.3 1.0

Zinc binding site 3 out of 7 in 8w9f

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


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:39.1
occ:1.00
 SG E:CYS440 2.3 28.0 1.0
SG E:CYS443 2.3 23.4 1.0
CB E:CYS466 2.3 25.3 1.0
SG E:CYS466 2.4 25.3 1.0
CB E:CYS440 2.5 28.0 1.0
N E:CYS466 2.8 25.3 1.0
CA E:CYS466 3.1 25.3 1.0
CB E:CYS443 3.9 23.4 1.0
CA E:CYS440 4.0 28.0 1.0
C E:LYS465 4.0 29.4 1.0
N E:CYS443 4.1 23.4 1.0
CG2 E:THR445 4.1 26.1 1.0
CD2 E:HIS469 4.2 24.4 1.0
NE2 E:HIS469 4.2 24.4 1.0
C E:CYS466 4.3 25.3 1.0
CA E:LYS465 4.4 29.4 1.0
CA E:CYS443 4.6 23.4 1.0
O E:THR445 4.6 26.1 1.0
N E:GLN444 4.7 24.9 1.0
C E:CYS440 4.7 28.0 1.0
N E:CYS440 4.8 28.0 1.0
O E:CYS466 4.8 25.3 1.0
O E:TRP464 4.8 45.0 1.0
CZ3 E:TRP464 4.9 45.0 1.0
N E:ASP441 4.9 25.6 1.0
N E:TYR442 4.9 28.8 1.0
N E:THR445 5.0 26.1 1.0

Zinc binding site 4 out of 7 in 8w9f

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1003

b:82.5
occ:1.00
 ND1 E:HIS448 2.3 34.4 1.0
SG E:CYS420 2.4 30.6 1.0
SG E:CYS451 2.4 26.1 1.0
CG E:HIS448 3.1 34.4 1.0
CB E:HIS448 3.2 34.4 1.0
CE1 E:HIS448 3.3 34.4 1.0
CB E:CYS420 3.7 30.6 1.0
SG E:CYS417 4.0 32.4 1.0
CB E:CYS451 4.1 26.1 1.0
CD2 E:HIS448 4.3 34.4 1.0
NE2 E:HIS448 4.4 34.4 1.0
CB E:CYS417 4.5 32.4 1.0
N E:CYS451 4.6 26.1 1.0
CA E:HIS448 4.6 34.4 1.0
N E:CYS420 4.9 30.6 1.0
N E:HIS448 4.9 34.4 1.0
CD E:ARG424 4.9 29.5 1.0
CA E:CYS451 4.9 26.1 1.0
CA E:CYS420 4.9 30.6 1.0

Zinc binding site 5 out of 7 in 8w9f

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1000

b:26.7
occ:1.00
 OD2 B:ASP274 2.6 25.2 1.0
ND1 B:HIS188 2.6 45.0 1.0
OD2 B:ASP186 2.9 23.9 1.0
OH B:TYR313 3.0 36.7 1.0
OD1 B:ASP186 3.3 23.9 1.0
CG B:HIS188 3.4 45.0 1.0
CG B:ASP186 3.4 23.9 1.0
CB B:HIS188 3.4 45.0 1.0
CE1 B:HIS188 3.7 45.0 1.0
CG B:ASP274 3.7 25.2 1.0
NE2 B:HIS151 4.0 21.4 1.0
NE2 B:HIS150 4.2 23.9 1.0
OD1 B:ASP274 4.2 25.2 1.0
CZ B:TYR313 4.3 36.7 1.0
CD2 B:HIS151 4.4 21.4 1.0
CA B:GLY311 4.5 24.8 1.0
N B:HIS188 4.5 45.0 1.0
CD2 B:HIS188 4.6 45.0 1.0
CA B:HIS188 4.6 45.0 1.0
NE2 B:HIS188 4.7 45.0 1.0
CB B:ASP186 4.8 23.9 1.0
N B:GLY311 4.8 24.8 1.0
CB B:ASP274 4.9 25.2 1.0

Zinc binding site 6 out of 7 in 8w9f

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:133.6
occ:1.00
 ND1 F:HIS283 2.2 95.8 1.0
SG F:CYS286 2.4 90.9 1.0
SG F:CYS266 2.4 88.3 1.0
SG F:CYS263 2.5 95.2 1.0
CB F:HIS283 2.5 95.8 1.0
CG F:HIS283 2.7 95.8 1.0
CB F:CYS263 3.3 95.2 1.0
CE1 F:HIS283 3.4 95.8 1.0
CB F:CYS266 3.5 88.3 1.0
N F:HIS283 3.7 95.8 1.0
CB F:CYS286 3.7 90.9 1.0
CA F:HIS283 3.7 95.8 1.0
CD2 F:HIS283 4.0 95.8 1.0
N F:CYS266 4.2 88.3 1.0
NE2 F:HIS283 4.3 95.8 1.0
CA F:CYS266 4.5 88.3 1.0
C F:HIS283 4.7 95.8 1.0
CA F:CYS263 4.7 95.2 1.0
CA F:CYS286 4.8 90.9 1.0
N F:CYS286 4.9 90.9 1.0
O F:CYS263 4.9 95.2 1.0
CB F:ALA265 4.9 90.0 1.0
C F:PHE282 4.9 97.7 1.0
O F:HIS283 5.0 95.8 1.0

Zinc binding site 7 out of 7 in 8w9f

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


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:121.1
occ:1.00
 SG F:CYS306 2.4 88.1 1.0
SG F:CYS303 2.5 96.3 1.0
SG F:CYS278 2.5 89.7 1.0
SG F:CYS275 2.6 96.4 1.0
N F:CYS303 2.9 96.3 1.0
CB F:CYS303 3.0 96.3 1.0
CB F:CYS306 3.1 88.1 1.0
CB F:CYS275 3.2 96.4 1.0
CA F:CYS303 3.5 96.3 1.0
CB F:CYS278 3.8 89.7 1.0
C F:HIS302 3.9 99.2 1.0
N F:CYS306 4.0 88.1 1.0
OG1 F:THR277 4.1 90.0 1.0
CA F:HIS302 4.1 99.2 1.0
C F:CYS303 4.2 96.3 1.0
CA F:CYS306 4.2 88.1 1.0
O F:CYS303 4.2 96.3 1.0
CB F:HIS302 4.3 99.2 1.0
N F:CYS278 4.4 89.7 1.0
CA F:CYS275 4.7 96.4 1.0
CA F:CYS278 4.7 89.7 1.0
C F:THR277 4.9 90.0 1.0

Reference:

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
Page generated: Fri Aug 22 15:02:57 2025

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