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Zinc in PDB 8i02: Cryo-Em Structure of the SIN3S Complex From S. Pombe

Enzymatic activity of Cryo-Em Structure of the SIN3S Complex From S. Pombe

All present enzymatic activity of Cryo-Em Structure of the SIN3S Complex From S. Pombe:
3.5.1.98;

Other elements in 8i02:

The structure of Cryo-Em Structure of the SIN3S Complex From S. Pombe also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the SIN3S Complex From S. Pombe (pdb code 8i02). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of the SIN3S Complex From S. Pombe, PDB code: 8i02:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8i02

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of the SIN3S Complex From S. Pombe


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 SIN3S Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:103.6
occ:1.00
 SG F:CYS160 2.5 79.7 1.0
CB F:CYS135 2.9 78.4 1.0
SG F:CYS137 2.9 77.5 1.0
CB F:CYS137 3.3 77.5 1.0
SG F:CYS135 3.4 78.4 1.0
CG2 F:THR162 3.5 76.4 1.0
SG F:CYS163 3.9 79.2 1.0
CB F:CYS160 4.1 79.7 1.0
CA F:CYS135 4.1 78.4 1.0
SG F:CYS132 4.3 81.0 1.0
O F:CYS135 4.4 78.4 1.0
CZ F:PHE139 4.4 76.6 1.0
N F:CYS135 4.5 78.4 1.0
C F:CYS135 4.5 78.4 1.0
CA F:CYS137 4.6 77.5 1.0
N F:CYS137 4.6 77.5 1.0
CB F:THR162 4.9 76.4 1.0
NZ F:LYS166 4.9 77.6 1.0
N F:CYS163 5.0 79.2 1.0

Zinc binding site 2 out of 6 in 8i02

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of the SIN3S Complex From S. Pombe


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 SIN3S Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:82.7
occ:1.00
 ND1 F:HIS140 2.1 76.6 1.0
SG F:CYS120 2.4 75.1 1.0
CB F:HIS140 2.5 76.6 1.0
CG F:HIS140 2.6 76.6 1.0
SG F:CYS143 2.6 76.7 1.0
CB F:CYS143 3.0 76.7 1.0
N F:HIS140 3.1 76.6 1.0
SG F:CYS123 3.3 68.8 1.0
CA F:HIS140 3.3 76.6 1.0
CE1 F:HIS140 3.4 76.6 1.0
CB F:CYS120 3.7 75.1 1.0
CD2 F:HIS140 3.9 76.6 1.0
CB F:ALA122 4.0 68.2 1.0
N F:CYS123 4.1 68.8 1.0
NE2 F:HIS140 4.2 76.6 1.0
CB F:CYS123 4.3 68.8 1.0
C F:PHE139 4.3 76.6 1.0
CA F:CYS143 4.4 76.7 1.0
C F:HIS140 4.5 76.6 1.0
NE E:ARG250 4.5 66.2 1.0
N F:ALA122 4.5 68.2 1.0
CA F:ALA122 4.6 68.2 1.0
NH2 E:ARG250 4.6 66.2 1.0
N F:CYS143 4.7 76.7 1.0
C F:ALA122 4.7 68.2 1.0
O F:HIS140 4.7 76.6 1.0
CA F:PHE139 4.7 76.6 1.0
CA F:CYS123 4.9 68.8 1.0
CZ E:ARG250 4.9 66.2 1.0
CA F:CYS120 4.9 75.1 1.0

Zinc binding site 3 out of 6 in 8i02

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of the SIN3S Complex From S. Pombe


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 SIN3S Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:27.3
occ:1.00
 OD1 B:ASP173 1.8 12.6 1.0
ND1 B:HIS175 2.1 11.0 1.0
OD2 B:ASP261 2.7 9.8 1.0
CG B:ASP173 3.0 12.6 1.0
CG B:HIS175 3.1 11.0 1.0
CE1 B:HIS175 3.1 11.0 1.0
CB B:HIS175 3.4 11.0 1.0
OD2 B:ASP173 3.5 12.6 1.0
CG B:ASP261 3.6 9.8 1.0
OD1 B:ASP261 3.8 9.8 1.0
N B:HIS175 3.9 11.0 1.0
NE2 B:HIS175 4.1 11.0 1.0
CD2 B:HIS175 4.2 11.0 1.0
CB B:ASP173 4.2 12.6 1.0
NE2 B:HIS137 4.3 8.8 1.0
CA B:HIS175 4.3 11.0 1.0
CG1 B:VAL174 4.4 10.3 1.0
CE2 A:PHE381 4.5 23.2 1.0
N B:VAL174 4.5 10.3 1.0
OH B:TYR300 4.6 10.6 1.0
CA B:GLY298 4.6 10.2 1.0
CE1 B:HIS137 4.8 8.8 1.0
CE2 B:TYR300 4.9 10.6 1.0
C B:VAL174 4.9 10.3 1.0

Zinc binding site 4 out of 6 in 8i02

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of the SIN3S Complex From S. Pombe


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 SIN3S Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn701

b:61.8
occ:1.00
 SG G:CYS266 2.2 58.1 1.0
SG G:CYS269 2.5 51.9 1.0
SG G:CYS289 2.5 51.1 1.0
ND1 G:HIS286 2.5 55.8 1.0
CB G:CYS289 2.7 51.1 1.0
CB G:CYS266 2.9 58.1 1.0
CG G:HIS286 3.2 55.8 1.0
CE1 G:HIS286 3.3 55.8 1.0
CB G:HIS286 3.4 55.8 1.0
CB G:CYS269 3.8 51.9 1.0
N G:HIS286 3.8 55.8 1.0
CD2 G:HIS286 4.1 55.8 1.0
N G:CYS269 4.1 51.9 1.0
NE2 G:HIS286 4.2 55.8 1.0
CA G:CYS289 4.2 51.1 1.0
CA G:HIS286 4.3 55.8 1.0
CA G:CYS266 4.4 58.1 1.0
CA G:CYS269 4.5 51.9 1.0
NE D:ARG250 4.6 41.9 1.0
CZ D:ARG250 4.7 41.9 1.0
N G:CYS289 4.7 51.1 1.0
CB G:ALA268 4.8 53.5 1.0
NH2 D:ARG250 4.9 41.9 1.0
C G:PHE285 4.9 58.7 1.0
C G:CYS289 5.0 51.1 1.0
CD D:ARG250 5.0 41.9 1.0

Zinc binding site 5 out of 6 in 8i02

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of the SIN3S Complex From S. Pombe


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 SIN3S Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn702

b:37.0
occ:1.00
 SG G:CYS436 2.2 17.3 1.0
SG G:CYS412 2.3 14.7 1.0
SG G:CYS409 2.5 15.9 1.0
CB G:CYS436 3.3 17.3 1.0
ND1 G:HIS433 3.3 15.8 1.0
CB G:CYS409 3.4 15.9 1.0
CB G:CYS412 3.6 14.7 1.0
CB G:HIS433 3.7 15.8 1.0
N G:CYS412 3.7 14.7 1.0
CG G:HIS433 3.8 15.8 1.0
CE1 G:HIS433 4.2 15.8 1.0
CA G:CYS412 4.3 14.7 1.0
CB G:ARG411 4.3 15.7 1.0
CE2 A:PHE230 4.4 16.1 1.0
N G:HIS433 4.5 15.8 1.0
CD2 A:PHE230 4.6 16.1 1.0
C G:ARG411 4.7 15.7 1.0
CA G:CYS436 4.7 17.3 1.0
CA G:HIS433 4.7 15.8 1.0
N G:ARG411 4.8 15.7 1.0
CA G:ARG411 4.8 15.7 1.0
CD2 G:HIS433 4.8 15.8 1.0
CG G:ARG411 4.8 15.7 1.0
CA G:CYS409 4.9 15.9 1.0

Zinc binding site 6 out of 6 in 8i02

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of the SIN3S Complex From S. Pombe


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 SIN3S Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn703

b:43.7
occ:1.00
 SG G:CYS453 2.1 18.1 1.0
SG G:CYS425 2.4 17.0 1.0
CB G:CYS428 2.5 22.9 1.0
CB G:CYS453 2.9 18.1 1.0
NE2 G:HIS456 2.9 17.6 1.0
CB G:CYS425 3.0 17.0 1.0
SG G:CYS428 3.3 22.9 1.0
CD2 G:HIS456 3.6 17.6 1.0
N G:CYS453 3.8 18.1 1.0
CA G:CYS428 3.8 22.9 1.0
OG G:SER430 3.9 17.2 1.0
CA G:CYS453 3.9 18.1 1.0
N G:CYS428 3.9 22.9 1.0
CE1 G:HIS456 4.0 17.6 1.0
C G:TYR427 4.2 22.6 1.0
O G:TYR427 4.4 22.6 1.0
CA G:CYS425 4.5 17.0 1.0
CB G:SER430 4.6 17.2 1.0
C G:CYS453 4.7 18.1 1.0
C G:CYS428 4.7 22.9 1.0
O G:CYS453 4.9 18.1 1.0
CG G:HIS456 4.9 17.6 1.0
N G:TYR427 4.9 22.6 1.0
CA G:TYR427 5.0 22.6 1.0
C G:LYS452 5.0 19.2 1.0

Reference:

C.Wang, Z.Guo, C.Chu, Y.Lu, X.Zhang, X.Zhan. Two Assembly Modes For SIN3 Histone Deacetylase Complexes. Cell Discov V. 9 42 2023.
ISSN: ESSN 2056-5968
PubMed: 37076472
DOI: 10.1038/S41421-023-00539-X
Page generated: Thu Oct 31 07:35:47 2024

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