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Potassium in PDB 6hsh: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat, PDB code: 6hsh was solved by T.B.Shaik, M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.47 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.750, 70.800, 97.820, 78.03, 75.67, 85.74
R / Rfree (%) 16.8 / 20.2

Other elements in 6hsh:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat (pdb code 6hsh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat, PDB code: 6hsh:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6hsh

Go back to Potassium Binding Sites List in 6hsh
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:22.0
occ:1.00
 O A:VAL203 2.6 19.3 1.0
O A:PHE197 2.6 20.2 1.0
OG A:SER243 2.6 20.4 1.0
O A:HOH750 2.8 19.9 1.0
O A:SER200 2.8 24.1 1.0
CB A:SER243 3.4 22.2 1.0
O A:SER243 3.5 20.9 1.0
C A:PHE197 3.6 20.1 1.0
C A:VAL203 3.8 16.7 1.0
C A:SER243 3.9 21.4 1.0
C A:SER200 3.9 26.3 1.0
CB A:PHE197 4.0 18.4 1.0
CA A:SER243 4.3 20.0 1.0
CA A:PHE197 4.4 18.3 1.0
N A:SER200 4.4 21.2 1.0
N A:TRP198 4.5 19.6 1.0
CA A:VAL204 4.5 19.1 1.0
CA A:TRP198 4.6 16.7 1.0
C A:TRP198 4.6 20.5 1.0
O A:TRP198 4.6 20.8 1.0
N A:VAL204 4.6 17.1 1.0
N A:ALA244 4.6 18.3 1.0
N A:THR205 4.6 17.8 1.0
CA A:SER200 4.6 25.3 0.5
CA A:SER200 4.6 25.2 0.5
OG1 A:THR205 4.7 20.2 1.0
CG2 A:THR205 4.8 19.2 1.0
CA A:VAL203 4.8 15.9 1.0
CB A:SER200 4.8 24.2 0.5
O A:GLY240 4.9 22.4 1.0
CB A:SER200 4.9 25.2 0.5
N A:PRO201 4.9 21.3 1.0
CB A:VAL203 4.9 20.6 1.0
N A:VAL203 5.0 17.6 1.0
CA A:ALA244 5.0 23.5 1.0

Potassium binding site 2 out of 8 in 6hsh

Go back to Potassium Binding Sites List in 6hsh
Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:18.4
occ:1.00
 O A:VAL208 2.6 18.4 1.0
O A:ASP186 2.6 18.9 1.0
O A:HIS188 2.8 17.5 1.0
OD1 A:ASP184 2.8 18.2 1.0
O A:ASP184 2.8 16.4 1.0
OG A:SER207 2.9 18.4 1.0
N A:ASP186 3.3 15.1 1.0
C A:ASP184 3.4 16.9 1.0
C A:ASP186 3.5 20.1 1.0
CG A:ASP184 3.5 20.3 1.0
C A:VAL208 3.6 18.1 1.0
CA A:ASP186 3.7 16.8 1.0
CB A:ASP186 3.8 15.4 1.0
C A:HIS188 3.8 15.3 1.0
CB A:HIS209 3.8 15.3 1.0
CB A:ASP184 3.8 18.7 1.0
C A:LEU185 3.9 19.1 1.0
N A:VAL208 3.9 16.4 1.0
N A:LEU185 4.1 15.7 1.0
CB A:SER207 4.1 20.5 1.0
CA A:ASP184 4.2 19.5 1.0
ND1 A:HIS209 4.2 20.0 1.0
CA A:LEU185 4.3 17.7 1.0
CA A:HIS209 4.4 17.0 1.0
CA A:SER207 4.4 16.0 1.0
N A:GLY190 4.4 15.2 1.0
OD2 A:ASP184 4.4 19.1 1.0
N A:HIS188 4.5 18.1 1.0
N A:HIS209 4.5 17.9 1.0
CA A:VAL208 4.5 18.0 1.0
C A:SER207 4.5 19.5 1.0
CA A:HIS189 4.5 16.1 1.0
CG A:HIS209 4.5 20.0 1.0
N A:HIS189 4.5 16.7 1.0
O A:LEU185 4.5 16.9 1.0
N A:LEU187 4.7 15.7 1.0
C A:LEU187 4.7 16.8 1.0
O A:HOH749 4.7 23.2 1.0
CA A:HIS188 4.8 15.7 1.0
C A:HIS189 4.8 18.2 1.0
CE1 A:HIS141 4.9 22.8 1.0

Potassium binding site 3 out of 8 in 6hsh

Go back to Potassium Binding Sites List in 6hsh
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:20.9
occ:1.00
 O B:PHE197 2.6 19.7 1.0
O B:VAL203 2.6 25.8 1.0
OG B:SER243 2.6 21.6 1.0
O B:SER200 2.8 27.0 1.0
O B:HOH728 2.9 18.6 1.0
CB B:SER243 3.5 22.6 1.0
C B:PHE197 3.6 25.1 1.0
O B:SER243 3.6 21.1 1.0
C B:VAL203 3.8 20.4 1.0
CB B:PHE197 3.9 19.3 1.0
C B:SER200 4.0 26.9 1.0
C B:SER243 4.0 22.8 1.0
CA B:PHE197 4.3 22.1 1.0
CA B:SER243 4.4 17.4 1.0
N B:TRP198 4.4 22.7 1.0
N B:SER200 4.5 25.4 1.0
CA B:TRP198 4.5 21.9 1.0
CA B:VAL204 4.6 16.6 1.0
C B:TRP198 4.6 18.8 1.0
N B:ALA244 4.6 18.1 1.0
O B:TRP198 4.6 19.9 1.0
N B:VAL204 4.6 19.4 1.0
N B:THR205 4.7 17.9 1.0
CA B:SER200 4.7 26.0 0.6
CA B:SER200 4.7 26.8 0.4
CA B:VAL203 4.8 18.2 1.0
OG1 B:THR205 4.8 21.9 1.0
CG2 B:THR205 4.8 18.4 1.0
CB B:VAL203 4.9 19.5 1.0
O B:GLY240 4.9 20.7 1.0
N B:VAL203 4.9 20.2 1.0
CB B:SER200 4.9 30.9 0.6
N B:PRO201 5.0 23.8 1.0

Potassium binding site 4 out of 8 in 6hsh

Go back to Potassium Binding Sites List in 6hsh
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:17.3
occ:1.00
 OD1 B:ASP184 2.6 16.4 1.0
O B:ASP186 2.6 16.3 1.0
O B:VAL208 2.7 16.0 1.0
O B:ASP184 2.7 16.1 1.0
O B:HIS188 2.7 17.0 1.0
OG B:SER207 2.9 16.6 1.0
N B:ASP186 3.3 18.9 1.0
CG B:ASP184 3.4 19.3 1.0
C B:ASP184 3.4 15.8 1.0
C B:ASP186 3.5 15.6 1.0
C B:VAL208 3.7 17.3 1.0
CA B:ASP186 3.7 17.8 1.0
C B:HIS188 3.7 16.6 1.0
CB B:ASP186 3.8 14.6 1.0
CB B:ASP184 3.8 17.6 1.0
C B:LEU185 3.8 18.9 1.0
CB B:HIS209 3.8 20.2 1.0
N B:VAL208 3.9 18.4 1.0
N B:LEU185 4.0 15.7 1.0
CB B:SER207 4.1 19.6 1.0
CA B:ASP184 4.2 16.1 1.0
CA B:LEU185 4.2 16.7 1.0
ND1 B:HIS209 4.3 17.4 1.0
OD2 B:ASP184 4.3 17.5 1.0
CA B:SER207 4.4 17.8 1.0
CA B:HIS209 4.4 13.5 1.0
N B:GLY190 4.4 18.4 1.0
N B:HIS188 4.4 15.3 1.0
CA B:HIS189 4.5 18.0 1.0
N B:HIS189 4.5 17.6 1.0
CA B:VAL208 4.5 16.9 1.0
C B:SER207 4.5 17.7 1.0
N B:HIS209 4.5 14.2 1.0
O B:LEU185 4.5 18.2 1.0
CG B:HIS209 4.6 16.7 1.0
N B:LEU187 4.7 17.1 1.0
O B:HOH756 4.7 20.8 1.0
CA B:HIS188 4.7 15.8 1.0
C B:LEU187 4.7 16.8 1.0
C B:HIS189 4.7 16.6 1.0
CE1 B:HIS141 5.0 19.4 1.0
CG1 B:VAL208 5.0 19.0 1.0

Potassium binding site 5 out of 8 in 6hsh

Go back to Potassium Binding Sites List in 6hsh
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:23.1
occ:1.00
 O C:VAL203 2.5 25.3 1.0
O C:PHE197 2.6 22.3 1.0
OG C:SER243 2.6 22.2 1.0
O C:HOH742 2.8 19.9 1.0
O C:SER200 2.8 32.1 1.0
O C:SER243 3.4 24.0 1.0
CB C:SER243 3.4 23.8 1.0
C C:PHE197 3.6 21.3 1.0
C C:VAL203 3.7 25.7 1.0
C C:SER243 3.9 20.5 1.0
CB C:PHE197 3.9 19.9 1.0
C C:SER200 4.0 29.2 1.0
CA C:SER243 4.3 17.3 1.0
CA C:PHE197 4.4 20.4 1.0
N C:SER200 4.4 26.8 1.0
CA C:VAL204 4.4 20.7 1.0
N C:TRP198 4.4 21.2 1.0
N C:ALA244 4.5 18.1 1.0
N C:VAL204 4.5 19.3 1.0
CA C:TRP198 4.6 23.0 1.0
N C:THR205 4.6 19.4 1.0
CA C:SER200 4.6 30.6 0.5
CA C:SER200 4.6 30.6 0.5
C C:TRP198 4.6 26.1 1.0
OG1 C:THR205 4.6 20.6 1.0
O C:TRP198 4.7 24.0 1.0
CB C:SER200 4.7 31.2 0.5
CG2 C:THR205 4.7 19.6 1.0
CA C:VAL203 4.8 18.8 1.0
CB C:SER200 4.8 31.4 0.5
CB C:VAL203 4.9 21.3 1.0
O C:GLY240 4.9 22.6 1.0
N C:VAL203 4.9 21.2 1.0
CA C:ALA244 4.9 19.2 1.0
C C:VAL204 5.0 20.2 1.0
N C:PRO201 5.0 27.5 1.0

Potassium binding site 6 out of 8 in 6hsh

Go back to Potassium Binding Sites List in 6hsh
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:17.8
occ:1.00
 O C:VAL208 2.6 16.8 1.0
O C:ASP186 2.6 20.4 1.0
OD1 C:ASP184 2.7 19.9 1.0
O C:HIS188 2.8 17.2 1.0
O C:ASP184 2.8 17.9 1.0
OG C:SER207 2.9 16.1 1.0
N C:ASP186 3.3 18.0 1.0
C C:ASP184 3.4 14.8 1.0
CG C:ASP184 3.4 19.9 1.0
C C:ASP186 3.4 14.9 1.0
C C:VAL208 3.7 15.3 1.0
CA C:ASP186 3.7 18.3 1.0
CB C:ASP186 3.8 17.8 1.0
CB C:ASP184 3.8 17.0 1.0
C C:HIS188 3.8 18.5 1.0
C C:LEU185 3.8 17.7 1.0
CB C:HIS209 3.9 18.0 1.0
N C:VAL208 3.9 17.3 1.0
N C:LEU185 4.0 14.6 1.0
CB C:SER207 4.1 20.0 1.0
CA C:ASP184 4.2 13.9 1.0
CA C:LEU185 4.2 13.6 1.0
OD2 C:ASP184 4.3 18.7 1.0
ND1 C:HIS209 4.3 18.7 1.0
N C:HIS188 4.4 15.0 1.0
CA C:SER207 4.4 17.0 1.0
CA C:HIS209 4.4 15.2 1.0
N C:GLY190 4.4 20.2 1.0
CA C:VAL208 4.5 18.0 1.0
N C:HIS209 4.5 16.8 1.0
C C:SER207 4.5 16.1 1.0
O C:LEU185 4.5 16.5 1.0
CA C:HIS189 4.5 16.5 1.0
N C:HIS189 4.6 17.6 1.0
CG C:HIS209 4.6 17.6 1.0
N C:LEU187 4.6 14.7 1.0
O C:HOH796 4.7 19.8 1.0
C C:LEU187 4.7 17.8 1.0
CA C:HIS188 4.7 20.3 1.0
C C:HIS189 4.8 16.9 1.0
CG1 C:VAL208 5.0 15.6 1.0

Potassium binding site 7 out of 8 in 6hsh

Go back to Potassium Binding Sites List in 6hsh
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:22.9
occ:1.00
 O D:PHE197 2.6 20.5 1.0
O D:VAL203 2.6 23.6 1.0
OG D:SER243 2.6 24.5 1.0
O D:HOH736 2.8 20.6 1.0
O D:SER200 2.9 29.5 1.0
O D:SER243 3.4 24.6 1.0
CB D:SER243 3.5 21.9 1.0
C D:PHE197 3.6 22.3 1.0
C D:VAL203 3.8 25.5 1.0
C D:SER243 3.9 21.1 1.0
CB D:PHE197 4.0 20.4 1.0
C D:SER200 4.0 28.2 1.0
CA D:SER243 4.3 19.2 1.0
CA D:PHE197 4.4 21.0 1.0
N D:SER200 4.4 21.4 1.0
N D:TRP198 4.4 21.6 1.0
CA D:VAL204 4.5 17.5 1.0
N D:ALA244 4.5 20.2 1.0
CA D:TRP198 4.5 20.6 1.0
C D:TRP198 4.6 23.6 1.0
N D:THR205 4.6 20.7 1.0
N D:VAL204 4.6 20.4 1.0
CA D:SER200 4.7 26.4 0.5
O D:TRP198 4.7 21.0 1.0
CA D:SER200 4.7 26.4 0.5
OG1 D:THR205 4.7 19.8 1.0
CG2 D:THR205 4.8 17.7 1.0
CA D:VAL203 4.8 17.9 1.0
O D:GLY240 4.8 23.5 1.0
CB D:SER200 4.9 27.6 0.5
CB D:SER200 4.9 27.8 0.5
CB D:VAL203 5.0 25.2 1.0
N D:PRO201 5.0 26.5 1.0
CA D:ALA244 5.0 19.7 1.0
N D:VAL203 5.0 22.1 1.0
C D:VAL204 5.0 23.5 1.0

Potassium binding site 8 out of 8 in 6hsh

Go back to Potassium Binding Sites List in 6hsh
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:18.4
occ:1.00
 O D:ASP186 2.6 19.0 1.0
O D:VAL208 2.7 18.5 1.0
OD1 D:ASP184 2.7 19.1 1.0
O D:HIS188 2.8 18.2 1.0
O D:ASP184 2.8 18.3 1.0
OG D:SER207 2.9 18.1 1.0
N D:ASP186 3.3 16.7 1.0
C D:ASP184 3.4 18.2 1.0
CG D:ASP184 3.4 21.4 1.0
C D:ASP186 3.4 18.1 1.0
C D:VAL208 3.6 18.3 1.0
CA D:ASP186 3.7 18.9 1.0
CB D:ASP186 3.8 14.7 1.0
C D:HIS188 3.8 19.1 1.0
CB D:ASP184 3.8 19.9 1.0
C D:LEU185 3.9 17.4 1.0
CB D:HIS209 3.9 21.1 1.0
N D:VAL208 3.9 17.2 1.0
N D:LEU185 4.0 18.6 1.0
CB D:SER207 4.1 18.4 1.0
CA D:ASP184 4.2 18.4 1.0
CA D:LEU185 4.3 18.3 1.0
OD2 D:ASP184 4.3 19.9 1.0
ND1 D:HIS209 4.3 21.1 1.0
CA D:SER207 4.4 17.2 1.0
CA D:HIS209 4.4 18.2 1.0
N D:GLY190 4.4 19.2 1.0
N D:HIS209 4.5 18.2 1.0
N D:HIS188 4.5 18.3 1.0
CA D:VAL208 4.5 18.4 1.0
C D:SER207 4.5 18.4 1.0
CA D:HIS189 4.5 18.3 1.0
N D:HIS189 4.6 19.6 1.0
O D:LEU185 4.6 19.5 1.0
CG D:HIS209 4.6 24.8 1.0
N D:LEU187 4.6 17.3 1.0
O D:HOH721 4.7 21.7 1.0
C D:LEU187 4.7 16.1 1.0
C D:HIS189 4.8 21.1 1.0
CA D:HIS188 4.8 18.7 1.0
CE1 D:HIS141 4.9 18.8 1.0

Reference:

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087
Page generated: Mon Aug 12 16:23:55 2024

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