Potassium in PDB 8hpo: Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast

Enzymatic activity of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast

All present enzymatic activity of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast:
3.5.1.98;

Other elements in 8hpo:

The structure of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast (pdb code 8hpo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast, PDB code: 8hpo:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8hpo

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Potassium binding site 1 out of 4 in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K503

b:30.0
occ:1.00
 OD1 F:ASP184 1.8 20.9 1.0
O F:ASP184 2.7 20.9 1.0
O F:HIS188 2.8 19.0 1.0
CG F:ASP184 3.0 20.9 1.0
O F:ASP186 3.3 19.2 1.0
N F:ASP186 3.3 19.2 1.0
C F:ASP184 3.4 20.9 1.0
O F:PHE208 3.4 23.8 1.0
C F:ASP186 3.7 19.2 1.0
CB F:ASP186 3.7 19.2 1.0
CA F:ASP186 3.8 19.2 1.0
CB F:ASP184 3.8 20.9 1.0
N F:PHE208 3.9 23.8 1.0
C F:PHE208 3.9 23.8 1.0
OD2 F:ASP184 3.9 20.9 1.0
C F:HIS188 3.9 19.0 1.0
N F:ILE185 3.9 18.9 1.0
C F:ILE185 4.0 18.9 1.0
OG F:SER207 4.1 42.2 1.0
CA F:ILE185 4.1 18.9 1.0
CB F:HIS209 4.1 21.5 1.0
CA F:ASP184 4.2 20.9 1.0
CB F:SER207 4.2 42.2 1.0
N F:GLY190 4.3 21.3 1.0
CA F:HIS209 4.4 21.5 1.0
CA F:SER207 4.5 42.2 1.0
N F:HIS209 4.5 21.5 1.0
CA F:HIS189 4.5 21.8 1.0
CA F:PHE208 4.6 23.8 1.0
C F:SER207 4.6 42.2 1.0
N F:HIS189 4.7 21.8 1.0
N F:VAL187 4.7 18.1 1.0
C F:HIS189 4.7 21.8 1.0
N F:HIS188 4.8 19.0 1.0
C F:VAL187 5.0 18.1 1.0

Potassium binding site 2 out of 4 in 8hpo

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Potassium binding site 2 out of 4 in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K504

b:30.0
occ:1.00
 O F:PHE197 2.3 17.2 1.0
O F:VAL203 2.6 20.5 1.0
O F:TYR232 2.9 26.3 1.0
O F:THR200 3.1 19.5 1.0
C F:PHE197 3.5 17.2 1.0
C F:VAL203 3.8 20.5 1.0
CB F:TYR232 3.8 26.3 1.0
C F:TYR232 4.0 26.3 1.0
C F:THR200 4.1 19.5 1.0
O F:TYR198 4.1 20.8 1.0
CB F:PHE197 4.3 17.2 1.0
CA F:TYR198 4.3 20.8 1.0
CG2 F:THR200 4.3 19.5 1.0
C F:TYR198 4.3 20.8 1.0
N F:TYR198 4.4 20.8 1.0
CA F:PHE197 4.5 17.2 1.0
N F:THR200 4.5 19.5 1.0
CA F:TYR232 4.5 26.3 1.0
CA F:MET204 4.6 23.9 1.0
N F:MET204 4.6 23.9 1.0
CA F:VAL203 4.7 20.5 1.0
N F:THR205 4.8 24.8 1.0
CB F:VAL203 4.8 20.5 1.0
CA F:THR200 4.8 19.5 1.0
O F:GLY229 4.9 22.2 1.0
N F:VAL203 4.9 20.5 1.0
CG2 F:THR205 4.9 24.8 1.0
CG F:TYR232 5.0 26.3 1.0
N F:ASP201 5.0 25.2 1.0

Potassium binding site 3 out of 4 in 8hpo

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Potassium binding site 3 out of 4 in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K502

b:30.0
occ:1.00
 OD1 G:ASP184 2.5 35.5 1.0
O G:ASP186 2.5 32.5 1.0
OG G:SER207 2.9 39.7 1.0
O G:HIS188 3.0 31.8 1.0
O G:ASP184 3.1 35.5 1.0
CG G:ASP184 3.2 35.5 1.0
N G:ASP186 3.2 32.5 1.0
C G:ASP186 3.4 32.5 1.0
C G:ASP184 3.4 35.5 1.0
CB G:ASP184 3.5 35.5 1.0
O G:PHE208 3.5 37.3 1.0
N G:PHE208 3.7 37.3 1.0
CA G:ASP186 3.7 32.5 1.0
C G:PHE208 3.8 37.3 1.0
CB G:ASP186 3.9 32.5 1.0
N G:ILE185 3.9 32.8 1.0
C G:ILE185 4.0 32.8 1.0
CB G:SER207 4.0 39.7 1.0
C G:HIS188 4.1 31.8 1.0
CA G:ASP184 4.1 35.5 1.0
CA G:ILE185 4.1 32.8 1.0
CB G:HIS209 4.2 37.2 1.0
OD2 G:ASP184 4.2 35.5 1.0
N G:HIS209 4.3 37.2 1.0
CA G:SER207 4.3 39.7 1.0
CA G:PHE208 4.4 37.3 1.0
CA G:HIS209 4.4 37.2 1.0
C G:SER207 4.4 39.7 1.0
N G:GLY190 4.5 43.1 1.0
N G:VAL187 4.6 31.3 1.0
CA G:HIS189 4.7 39.4 1.0
N G:HIS188 4.7 31.8 1.0
N G:HIS189 4.8 39.4 1.0
C G:HIS189 4.9 39.4 1.0
O G:ILE185 4.9 32.8 1.0
C G:VAL187 5.0 31.3 1.0

Potassium binding site 4 out of 4 in 8hpo

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Potassium binding site 4 out of 4 in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K503

b:30.0
occ:1.00
 O G:VAL203 2.8 51.7 1.0
OG1 G:THR205 2.9 51.1 1.0
O G:TYR232 3.0 69.1 1.0
O G:PHE197 3.1 49.4 1.0
C G:VAL203 3.8 51.7 1.0
N G:THR205 3.9 51.1 1.0
O G:THR200 3.9 62.9 1.0
C G:TYR232 3.9 69.1 1.0
CA G:MET204 3.9 56.1 1.0
C G:PHE197 4.2 49.4 1.0
CB G:THR205 4.2 51.1 1.0
C G:MET204 4.3 56.1 1.0
CB G:TYR232 4.3 69.1 1.0
N G:MET204 4.3 56.1 1.0
O G:TYR198 4.4 63.2 1.0
CB G:PHE197 4.6 49.4 1.0
N G:ALA233 4.6 61.9 1.0
CA G:THR205 4.7 51.1 1.0
CA G:ALA233 4.7 61.9 1.0
CA G:TYR232 4.8 69.1 1.0
CB G:ALA233 4.8 61.9 1.0
CA G:TYR198 4.9 63.2 1.0
C G:TYR198 4.9 63.2 1.0
CA G:VAL203 4.9 51.7 1.0
CB G:VAL203 5.0 51.7 1.0
C G:THR200 5.0 62.9 1.0

Reference:

Z.Guo, C.Chu, Y.Lu, X.Zhang, Y.Xiao, M.Wu, S.Gao, C.C.L.Wong, X.Zhan, C.Wang. Structure of A SIN3-Hdac Complex From Budding Yeast. Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
PubMed: 37081318
DOI: 10.1038/S41594-023-00975-Z
Page generated: Thu Jul 27 18:43:54 2023

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