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Potassium in PDB 6hsz: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2, PDB code: 6hsz was solved by M.Marek, T.B.Shaik, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.97 / 2.37
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.774, 70.802, 98.343, 77.85, 75.48, 85.28
R / Rfree (%) 15.9 / 22

Other elements in 6hsz:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2 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 A Benzohydroxamate Inhibitor 2 (pdb code 6hsz). 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 A Benzohydroxamate Inhibitor 2, PDB code: 6hsz:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6hsz

Go back to Potassium Binding Sites List in 6hsz
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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 A Benzohydroxamate Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:25.0
occ:1.00
 O A:HIS188 2.7 21.6 1.0
O A:ASP186 2.7 23.8 1.0
OD1 A:ASP184 2.7 30.5 1.0
OG A:SER207 2.8 21.1 1.0
O A:VAL208 2.8 24.2 1.0
O A:ASP184 3.0 25.5 1.0
CG A:ASP184 3.2 32.4 1.0
N A:ASP186 3.4 22.4 1.0
C A:ASP184 3.5 26.3 1.0
C A:ASP186 3.5 24.9 1.0
CB A:ASP184 3.7 28.7 1.0
C A:HIS188 3.7 21.5 1.0
CA A:ASP186 3.8 19.9 1.0
C A:VAL208 3.8 27.0 1.0
CB A:ASP186 3.8 22.3 1.0
CB A:SER207 3.9 24.9 1.0
CB A:HIS209 3.9 23.8 1.0
C A:LEU185 4.0 24.0 1.0
OD2 A:ASP184 4.0 29.9 1.0
N A:VAL208 4.0 22.2 1.0
N A:LEU185 4.1 18.3 1.0
ND1 A:HIS209 4.1 25.2 1.0
CA A:ASP184 4.2 26.7 1.0
N A:GLY190 4.3 23.6 1.0
CA A:SER207 4.3 28.0 1.0
CA A:HIS189 4.3 25.2 1.0
CA A:LEU185 4.4 26.5 1.0
N A:HIS189 4.4 18.8 1.0
C A:SER207 4.5 29.8 1.0
N A:HIS188 4.5 27.6 1.0
CG A:HIS209 4.5 29.4 1.0
CA A:HIS209 4.5 24.1 1.0
O A:LEU185 4.6 28.0 1.0
CA A:VAL208 4.6 23.6 1.0
N A:HIS209 4.6 23.8 1.0
C A:HIS189 4.6 25.9 1.0
N A:LEU187 4.7 23.6 1.0
CE1 A:HIS141 4.7 27.5 1.0
CA A:HIS188 4.8 26.2 1.0
C A:LEU187 4.8 27.1 1.0
O A:HOH653 5.0 18.7 1.0

Potassium binding site 2 out of 8 in 6hsz

Go back to Potassium Binding Sites List in 6hsz
Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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 A Benzohydroxamate Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:31.6
occ:1.00
 O A:PHE197 2.5 24.3 1.0
O A:VAL203 2.6 31.6 1.0
OG A:SER243 2.7 29.8 1.0
O A:SER200 2.9 25.7 1.0
O A:HOH659 2.9 21.8 1.0
O A:SER243 3.3 24.8 1.0
CB A:SER243 3.5 29.2 1.0
C A:PHE197 3.6 25.4 1.0
C A:SER243 3.8 22.9 1.0
C A:VAL203 3.8 31.9 1.0
C A:SER200 4.0 28.3 1.0
CB A:PHE197 4.0 24.8 1.0
CA A:SER243 4.3 27.5 1.0
CA A:PHE197 4.4 22.2 1.0
N A:TRP198 4.5 31.7 1.0
N A:ALA244 4.5 17.1 1.0
CA A:VAL204 4.5 28.6 1.0
N A:SER200 4.5 27.2 1.0
CA A:TRP198 4.6 30.2 1.0
N A:VAL204 4.6 27.3 1.0
C A:TRP198 4.7 27.4 1.0
OG1 A:THR205 4.7 30.1 1.0
N A:THR205 4.7 27.3 1.0
O A:TRP198 4.7 19.3 1.0
CA A:SER200 4.7 31.4 1.0
CG2 A:THR205 4.7 20.7 1.0
O A:GLY240 4.8 31.3 1.0
CA A:VAL203 4.8 30.2 1.0
CA A:ALA244 4.9 25.9 1.0
N A:PRO201 4.9 26.1 1.0
CB A:VAL203 5.0 32.5 1.0
CB A:SER200 5.0 36.5 1.0
N A:VAL203 5.0 22.4 1.0

Potassium binding site 3 out of 8 in 6hsz

Go back to Potassium Binding Sites List in 6hsz
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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 A Benzohydroxamate Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:22.0
occ:1.00
 O B:VAL208 2.6 17.1 1.0
O B:ASP186 2.6 20.4 1.0
OD1 B:ASP184 2.6 26.1 1.0
O B:HIS188 2.7 15.4 1.0
O B:ASP184 2.8 24.2 1.0
OG B:SER207 3.0 19.3 1.0
N B:ASP186 3.3 15.1 1.0
CG B:ASP184 3.4 26.3 1.0
C B:ASP184 3.4 26.0 1.0
C B:ASP186 3.5 22.1 1.0
C B:VAL208 3.7 18.9 1.0
CA B:ASP186 3.8 14.8 1.0
C B:HIS188 3.8 19.3 1.0
C B:LEU185 3.8 25.1 1.0
CB B:ASP184 3.8 22.6 1.0
CB B:HIS209 3.9 14.2 1.0
CB B:ASP186 3.9 16.0 1.0
N B:VAL208 4.0 18.8 1.0
N B:LEU185 4.0 17.7 1.0
CB B:SER207 4.1 20.4 1.0
CA B:ASP184 4.2 20.1 1.0
CA B:LEU185 4.2 23.5 1.0
OD2 B:ASP184 4.3 23.1 1.0
ND1 B:HIS209 4.3 17.6 1.0
N B:HIS188 4.3 23.5 1.0
O B:LEU185 4.4 24.4 1.0
N B:GLY190 4.4 20.2 1.0
CA B:SER207 4.4 26.8 1.0
CA B:HIS209 4.4 25.1 1.0
CA B:VAL208 4.5 20.6 1.0
N B:HIS189 4.5 12.7 1.0
N B:HIS209 4.5 21.8 1.0
CA B:HIS189 4.5 20.2 1.0
C B:SER207 4.6 27.7 1.0
CG B:HIS209 4.6 24.2 1.0
N B:LEU187 4.7 26.2 1.0
C B:LEU187 4.7 24.6 1.0
O B:HOH669 4.7 21.4 1.0
CA B:HIS188 4.7 24.9 1.0
C B:HIS189 4.8 20.1 1.0
CE1 B:HIS141 5.0 25.6 1.0
CG1 B:VAL208 5.0 19.0 1.0

Potassium binding site 4 out of 8 in 6hsz

Go back to Potassium Binding Sites List in 6hsz
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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 A Benzohydroxamate Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:24.6
occ:1.00
 O B:VAL203 2.6 22.9 1.0
O B:PHE197 2.6 22.1 1.0
OG B:SER243 2.7 32.5 1.0
O B:SER200 2.8 38.2 1.0
O B:HOH666 2.8 27.5 1.0
C B:PHE197 3.5 26.3 1.0
CB B:SER243 3.5 21.7 1.0
O B:SER243 3.7 22.9 1.0
CB B:PHE197 3.7 29.6 1.0
C B:VAL203 3.8 28.8 1.0
C B:SER200 4.0 38.4 1.0
C B:SER243 4.0 27.1 1.0
CA B:PHE197 4.2 33.1 1.0
N B:TRP198 4.3 20.4 1.0
CA B:SER243 4.4 23.5 1.0
N B:SER200 4.4 32.3 1.0
CA B:TRP198 4.5 21.2 1.0
CA B:VAL204 4.5 20.4 1.0
N B:VAL204 4.6 15.5 1.0
N B:ALA244 4.7 24.2 1.0
C B:TRP198 4.7 26.7 1.0
CA B:SER200 4.7 39.2 1.0
N B:THR205 4.7 20.4 1.0
O B:TRP198 4.7 25.2 1.0
CG2 B:THR205 4.7 15.4 1.0
CA B:VAL203 4.8 25.4 1.0
OG1 B:THR205 4.8 21.2 1.0
CB B:VAL203 4.9 17.0 1.0
O B:GLY240 4.9 38.8 1.0
CB B:SER200 4.9 44.3 1.0
N B:VAL203 4.9 23.0 1.0
N B:PRO201 4.9 23.9 1.0

Potassium binding site 5 out of 8 in 6hsz

Go back to Potassium Binding Sites List in 6hsz
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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 A Benzohydroxamate Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:27.0
occ:1.00
 O C:ASP186 2.6 22.0 1.0
O C:VAL208 2.6 17.3 1.0
OD1 C:ASP184 2.6 21.2 1.0
O C:ASP184 2.7 23.0 1.0
O C:HIS188 2.8 21.1 1.0
OG C:SER207 3.0 23.7 1.0
N C:ASP186 3.3 18.9 1.0
C C:ASP184 3.4 22.2 1.0
CG C:ASP184 3.4 24.9 1.0
C C:ASP186 3.4 27.0 1.0
C C:VAL208 3.6 20.4 1.0
CA C:ASP186 3.7 21.9 1.0
CB C:ASP186 3.8 22.1 1.0
C C:HIS188 3.8 22.3 1.0
CB C:ASP184 3.8 16.9 1.0
C C:LEU185 3.8 23.5 1.0
CB C:HIS209 3.8 16.6 1.0
N C:VAL208 3.9 24.9 1.0
CB C:SER207 4.0 22.1 1.0
N C:LEU185 4.0 16.9 1.0
CA C:ASP184 4.2 18.3 1.0
CA C:LEU185 4.2 17.4 1.0
CA C:SER207 4.3 30.3 1.0
ND1 C:HIS209 4.3 18.7 1.0
OD2 C:ASP184 4.4 24.1 1.0
N C:HIS188 4.4 29.4 1.0
CA C:HIS209 4.4 22.3 1.0
N C:GLY190 4.4 16.8 1.0
C C:SER207 4.4 22.6 1.0
O C:LEU185 4.5 20.9 1.0
CA C:VAL208 4.5 23.2 1.0
N C:HIS209 4.5 25.0 1.0
CA C:HIS189 4.5 21.2 1.0
N C:HIS189 4.5 14.8 1.0
CG C:HIS209 4.6 19.8 1.0
N C:LEU187 4.7 26.3 1.0
CA C:HIS188 4.7 25.0 1.0
C C:LEU187 4.8 30.5 1.0
C C:HIS189 4.8 22.8 1.0
O C:HOH673 4.9 25.7 1.0

Potassium binding site 6 out of 8 in 6hsz

Go back to Potassium Binding Sites List in 6hsz
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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 A Benzohydroxamate Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:26.7
occ:1.00
 O C:VAL203 2.5 33.1 1.0
OG C:SER243 2.6 21.4 1.0
O C:PHE197 2.7 29.2 1.0
O C:HOH675 2.7 15.0 1.0
O C:SER200 3.0 28.7 1.0
O C:SER243 3.3 30.6 1.0
CB C:SER243 3.4 26.0 1.0
C C:PHE197 3.6 32.3 1.0
C C:VAL203 3.7 32.2 1.0
C C:SER243 3.8 25.7 1.0
CB C:PHE197 3.8 26.3 1.0
C C:SER200 4.1 35.2 1.0
CA C:SER243 4.3 24.4 1.0
CA C:PHE197 4.3 31.0 1.0
CA C:VAL204 4.4 23.7 1.0
N C:TRP198 4.4 34.2 1.0
N C:THR205 4.4 26.7 1.0
N C:SER200 4.5 31.9 1.0
N C:VAL204 4.5 26.4 1.0
N C:ALA244 4.5 23.1 1.0
O C:TRP198 4.5 26.1 1.0
CA C:TRP198 4.6 30.4 1.0
C C:TRP198 4.6 29.8 1.0
CG2 C:THR205 4.7 29.3 1.0
OG1 C:THR205 4.7 26.0 1.0
CA C:SER200 4.8 36.1 1.0
CA C:VAL203 4.8 28.3 1.0
C C:VAL204 4.9 28.4 1.0
O C:GLY240 4.9 33.7 1.0
CA C:ALA244 4.9 23.5 1.0
CB C:VAL203 4.9 24.1 1.0
N C:VAL203 5.0 26.9 1.0

Potassium binding site 7 out of 8 in 6hsz

Go back to Potassium Binding Sites List in 6hsz
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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 A Benzohydroxamate Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:27.6
occ:1.00
 O D:ASP186 2.6 26.0 1.0
O D:VAL208 2.6 26.6 1.0
OD1 D:ASP184 2.6 24.9 1.0
O D:HIS188 2.8 25.0 1.0
OG D:SER207 2.8 27.6 1.0
O D:ASP184 2.9 24.5 1.0
CG D:ASP184 3.3 31.3 1.0
C D:ASP184 3.5 25.4 1.0
N D:ASP186 3.5 20.7 1.0
C D:ASP186 3.5 28.0 1.0
C D:VAL208 3.7 27.6 1.0
CB D:ASP184 3.8 18.1 1.0
CA D:ASP186 3.8 16.3 1.0
C D:HIS188 3.8 26.6 1.0
CB D:ASP186 3.8 23.3 1.0
CB D:HIS209 3.9 27.7 1.0
C D:LEU185 3.9 25.1 1.0
CB D:SER207 4.0 28.5 1.0
N D:VAL208 4.0 24.9 1.0
N D:LEU185 4.1 21.2 1.0
CA D:ASP184 4.2 25.3 1.0
OD2 D:ASP184 4.2 35.4 1.0
N D:GLY190 4.3 28.5 1.0
CA D:SER207 4.3 27.1 1.0
ND1 D:HIS209 4.3 26.2 1.0
CA D:LEU185 4.4 31.6 1.0
CA D:HIS189 4.4 29.9 1.0
CA D:HIS209 4.4 26.6 1.0
N D:HIS188 4.5 31.1 1.0
N D:HIS189 4.5 25.0 1.0
N D:HIS209 4.5 28.5 1.0
C D:SER207 4.5 25.6 1.0
O D:LEU185 4.5 25.8 1.0
CA D:VAL208 4.5 25.3 1.0
CG D:HIS209 4.6 26.2 1.0
CE1 D:HIS141 4.6 28.7 1.0
N D:LEU187 4.7 28.9 1.0
C D:HIS189 4.7 28.1 1.0
C D:LEU187 4.7 26.9 1.0
CA D:HIS188 4.8 28.3 1.0
O D:HOH649 5.0 25.4 1.0

Potassium binding site 8 out of 8 in 6hsz

Go back to Potassium Binding Sites List in 6hsz
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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 A Benzohydroxamate Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:30.1
occ:1.00
 O D:VAL203 2.6 26.5 1.0
O D:PHE197 2.6 22.8 1.0
OG D:SER243 2.6 37.0 1.0
O D:HOH648 2.8 21.8 1.0
O D:SER200 2.9 34.5 1.0
CB D:SER243 3.3 30.4 1.0
O D:SER243 3.5 36.7 1.0
C D:PHE197 3.6 25.1 1.0
C D:SER243 3.8 29.8 1.0
C D:VAL203 3.8 28.4 1.0
CB D:PHE197 3.9 24.9 1.0
C D:SER200 4.0 31.4 1.0
CA D:SER243 4.2 31.6 1.0
CA D:PHE197 4.4 22.1 1.0
N D:ALA244 4.4 22.0 1.0
N D:SER200 4.4 35.7 1.0
N D:TRP198 4.4 23.8 1.0
CA D:VAL204 4.5 26.3 1.0
N D:VAL204 4.6 28.9 1.0
N D:THR205 4.6 31.0 1.0
CA D:TRP198 4.6 24.2 1.0
CA D:SER200 4.6 33.5 1.0
C D:TRP198 4.7 25.2 1.0
O D:GLY240 4.7 34.2 1.0
OG1 D:THR205 4.8 24.1 1.0
O D:TRP198 4.8 28.2 1.0
CB D:SER200 4.8 30.1 1.0
CA D:VAL203 4.8 26.4 1.0
CB D:VAL203 4.9 32.7 1.0
CA D:ALA244 4.9 26.1 1.0
N D:VAL203 4.9 29.1 1.0
C D:VAL204 5.0 28.3 1.0
N D:PRO201 5.0 33.2 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 16:26:55 2024

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