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Potassium in PDB 8i03: Cryo-Em Structure of the SIN3L Complex From S. Pombe

Enzymatic activity of Cryo-Em Structure of the SIN3L Complex From S. Pombe

All present enzymatic activity of Cryo-Em Structure of the SIN3L Complex From S. Pombe:
3.5.1.98;

Other elements in 8i03:

The structure of Cryo-Em Structure of the SIN3L Complex From S. Pombe 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 the SIN3L Complex From S. Pombe (pdb code 8i03). 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 the SIN3L Complex From S. Pombe, PDB code: 8i03:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8i03

Go back to Potassium Binding Sites List in 8i03
Potassium binding site 1 out of 4 in the Cryo-Em Structure of the SIN3L Complex From S. Pombe


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 the SIN3L Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:5.5
occ:1.00
 OD1 C:ASP171 2.5 6.7 1.0
O C:HIS175 2.6 5.1 1.0
O C:ASP173 2.7 6.6 1.0
O C:PHE195 2.8 6.6 1.0
O C:ASP171 3.2 6.7 1.0
N C:PHE195 3.4 6.6 1.0
CG C:ASP171 3.4 6.7 1.0
C C:PHE195 3.5 6.6 1.0
CB C:SER194 3.7 9.3 1.0
C C:ASP171 3.7 6.7 1.0
C C:HIS175 3.8 5.1 1.0
C C:ASP173 3.8 6.6 1.0
CB C:HIS196 4.0 6.5 1.0
CB C:ASP171 4.0 6.7 1.0
C C:SER194 4.0 9.3 1.0
N C:ASP173 4.1 6.6 1.0
OG C:SER194 4.1 9.3 1.0
CA C:SER194 4.1 9.3 1.0
CA C:PHE195 4.1 6.6 1.0
N C:ILE172 4.2 5.9 1.0
N C:HIS196 4.3 6.5 1.0
CA C:ILE172 4.3 5.9 1.0
C C:ILE172 4.3 5.9 1.0
OD2 C:ASP171 4.3 6.7 1.0
CA C:HIS196 4.4 6.5 1.0
ND1 C:HIS196 4.4 6.5 1.0
CA C:ASP173 4.4 6.6 1.0
CA C:ASP171 4.5 6.7 1.0
CA C:HIS176 4.5 5.8 1.0
N C:HIS175 4.5 5.1 1.0
N C:GLY177 4.6 11.9 1.0
N C:HIS176 4.6 5.8 1.0
CG C:HIS196 4.6 6.5 1.0
CB C:ASP173 4.8 6.6 1.0
C C:VAL174 4.8 5.9 1.0
CA C:HIS175 4.8 5.1 1.0
O C:SER194 4.9 9.3 1.0
N C:VAL174 4.9 5.9 1.0
CB C:PHE195 4.9 6.6 1.0
C C:HIS176 5.0 5.8 1.0

Potassium binding site 2 out of 4 in 8i03

Go back to Potassium Binding Sites List in 8i03
Potassium binding site 2 out of 4 in the Cryo-Em Structure of the SIN3L Complex From S. Pombe


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 the SIN3L Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:4.7
occ:1.00
 O C:PHE184 2.6 3.6 1.0
O C:VAL190 2.7 4.7 1.0
O C:THR187 2.7 6.6 1.0
O C:TYR219 2.8 11.5 1.0
CB C:TYR219 3.5 11.5 1.0
C C:TYR219 3.7 11.5 1.0
C C:PHE184 3.8 3.6 1.0
C C:THR187 3.9 6.6 1.0
C C:VAL190 3.9 4.7 1.0
O C:TYR185 4.2 5.6 1.0
CA C:TYR219 4.3 11.5 1.0
N C:THR187 4.3 6.6 1.0
CG2 C:THR187 4.3 6.6 1.0
C C:TYR185 4.4 5.6 1.0
CA C:MET191 4.5 7.5 1.0
CA C:TYR185 4.5 5.6 1.0
CB C:PHE184 4.6 3.6 1.0
N C:TYR185 4.6 5.6 1.0
CA C:THR187 4.6 6.6 1.0
N C:MET191 4.7 7.5 1.0
N C:ALA220 4.7 8.6 1.0
CG C:TYR219 4.7 11.5 1.0
CA C:GLY216 4.7 12.2 1.0
O C:GLY216 4.8 12.2 1.0
CG2 C:THR192 4.8 10.7 1.0
CA C:PHE184 4.8 3.6 1.0
N C:THR192 4.9 10.7 1.0
N C:ASP188 4.9 7.8 1.0
CA C:VAL190 4.9 4.7 1.0
N C:VAL190 5.0 4.7 1.0

Potassium binding site 3 out of 4 in 8i03

Go back to Potassium Binding Sites List in 8i03
Potassium binding site 3 out of 4 in the Cryo-Em Structure of the SIN3L Complex From S. Pombe


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 the SIN3L Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:1.6
occ:1.00
 O D:ASP173 2.6 8.9 1.0
OD2 D:ASP171 2.6 35.7 1.0
O D:HIS175 2.9 4.4 1.0
O D:PHE195 3.3 7.0 1.0
O D:ASP171 3.4 35.7 1.0
N D:PHE195 3.4 7.0 1.0
CG D:ASP171 3.5 35.7 1.0
C D:PHE195 3.6 7.0 1.0
CB D:SER194 3.6 6.9 1.0
C D:ASP173 3.7 8.9 1.0
CB D:HIS196 3.8 5.8 1.0
C D:ASP171 3.9 35.7 1.0
CA D:SER194 3.9 6.9 1.0
N D:ASP173 3.9 8.9 1.0
CB D:ASP171 3.9 35.7 1.0
C D:HIS175 4.0 4.4 1.0
C D:SER194 4.0 6.9 1.0
CA D:PHE195 4.1 7.0 1.0
N D:HIS196 4.1 5.8 1.0
CA D:HIS196 4.2 5.8 1.0
CA D:HIS176 4.3 3.5 1.0
CA D:ASP173 4.3 8.9 1.0
ND1 D:HIS196 4.4 5.8 1.0
N D:ILE172 4.4 12.3 1.0
N D:GLY177 4.5 4.0 1.0
OD1 D:ASP171 4.5 35.7 1.0
CA D:ILE172 4.6 12.3 1.0
C D:ILE172 4.6 12.3 1.0
CA D:ASP171 4.6 35.7 1.0
CG D:HIS196 4.6 5.8 1.0
N D:HIS176 4.6 3.5 1.0
CB D:ASP173 4.6 8.9 1.0
OG D:SER194 4.7 6.9 1.0
C D:HIS176 4.8 3.5 1.0
C D:VAL174 4.8 5.8 1.0
N D:VAL174 4.9 5.8 1.0
O D:VAL174 4.9 5.8 1.0
N D:HIS175 4.9 4.4 1.0
CB D:PHE195 5.0 7.0 1.0

Potassium binding site 4 out of 4 in 8i03

Go back to Potassium Binding Sites List in 8i03
Potassium binding site 4 out of 4 in the Cryo-Em Structure of the SIN3L Complex From S. Pombe


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 the SIN3L Complex From S. Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:29.1
occ:1.00
 O D:PHE184 2.6 4.6 1.0
O D:VAL190 2.7 5.5 1.0
O D:THR187 3.0 9.5 1.0
O D:TYR219 3.6 11.6 1.0
C D:PHE184 3.8 4.6 1.0
C D:VAL190 3.9 5.5 1.0
CB D:TYR219 4.1 11.6 1.0
C D:THR187 4.2 9.5 1.0
C D:TYR219 4.2 11.6 1.0
CG2 D:THR192 4.2 8.5 1.0
CA D:MET191 4.4 8.0 1.0
CB D:PHE184 4.4 4.6 1.0
CG2 D:THR187 4.5 9.5 1.0
CA D:TYR185 4.5 10.3 1.0
N D:THR187 4.5 9.5 1.0
C D:TYR185 4.6 10.3 1.0
O D:TYR185 4.6 10.3 1.0
N D:MET191 4.6 8.0 1.0
N D:TYR185 4.6 10.3 1.0
N D:THR192 4.8 8.5 1.0
CA D:PHE184 4.8 4.6 1.0
CA D:TYR219 4.8 11.6 1.0
CA D:THR187 4.9 9.5 1.0
CA D:VAL190 4.9 5.5 1.0
N D:ALA220 4.9 7.4 1.0
O D:GLY216 4.9 15.9 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: Tue Aug 13 00:01:48 2024

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