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Potassium in PDB 6hth: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5, PDB code: 6hth 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) 46.76 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.520, 70.555, 98.232, 78.36, 75.84, 85.74
R / Rfree (%) 21 / 25.7

Other elements in 6hth:

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

Potassium binding site 1 out of 8 in 6hth

Go back to Potassium Binding Sites List in 6hth
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:13.0
occ:1.00
 OD1 A:ASP184 2.5 13.2 1.0
O A:ASP186 2.6 10.0 1.0
O A:VAL208 2.7 11.3 1.0
O A:HIS188 2.8 10.9 1.0
OG A:SER207 2.8 9.5 1.0
O A:ASP184 2.9 17.1 1.0
CG A:ASP184 3.3 17.3 1.0
N A:ASP186 3.3 15.1 1.0
C A:ASP186 3.4 23.0 1.0
C A:ASP184 3.5 12.1 1.0
CA A:ASP186 3.7 14.2 1.0
C A:VAL208 3.7 13.5 1.0
C A:HIS188 3.8 10.9 1.0
CB A:ASP184 3.8 7.7 1.0
CB A:ASP186 3.8 9.7 1.0
CB A:HIS209 3.8 6.3 1.0
C A:LEU185 3.9 11.2 1.0
CB A:SER207 4.0 7.7 1.0
N A:VAL208 4.0 12.8 1.0
N A:LEU185 4.1 9.9 1.0
OD2 A:ASP184 4.2 14.9 1.0
ND1 A:HIS209 4.2 17.0 1.0
CA A:ASP184 4.3 12.2 1.0
N A:GLY190 4.3 8.0 1.0
CA A:LEU185 4.3 9.6 1.0
N A:HIS188 4.3 12.3 1.0
CA A:HIS189 4.4 15.3 1.0
CA A:SER207 4.4 14.0 1.0
CA A:HIS209 4.4 13.1 1.0
N A:HIS189 4.4 10.1 1.0
CG A:HIS209 4.5 17.0 1.0
C A:SER207 4.5 13.6 1.0
N A:HIS209 4.5 11.4 1.0
O A:LEU185 4.6 13.1 1.0
CA A:VAL208 4.6 18.8 1.0
C A:HIS189 4.6 13.8 1.0
N A:LEU187 4.6 14.9 1.0
C A:LEU187 4.7 10.6 1.0
CA A:HIS188 4.8 9.5 1.0
O A:HOH680 4.8 13.5 1.0
CE1 A:HIS141 4.8 14.7 1.0
CG A:ASP186 5.0 16.2 1.0

Potassium binding site 2 out of 8 in 6hth

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:16.5
occ:1.00
 OG A:SER243 2.4 17.8 1.0
O A:PHE197 2.5 10.5 1.0
O A:VAL203 2.7 23.5 1.0
O A:SER200 2.8 30.5 1.0
O A:HOH677 2.9 12.4 1.0
CB A:SER243 3.4 20.7 1.0
C A:PHE197 3.5 5.4 1.0
O A:SER243 3.5 14.2 1.0
C A:SER200 3.9 17.2 1.0
C A:SER243 3.9 14.2 1.0
CB A:PHE197 3.9 7.0 1.0
C A:VAL203 3.9 14.8 1.0
N A:SER200 4.2 15.8 1.0
CA A:SER243 4.3 18.5 1.0
CA A:PHE197 4.3 8.6 1.0
N A:TRP198 4.3 5.9 1.0
CA A:SER200 4.4 19.0 0.5
CA A:SER200 4.4 19.1 0.5
N A:ALA244 4.5 9.1 1.0
CB A:SER200 4.5 17.4 0.5
C A:TRP198 4.5 12.7 1.0
CA A:TRP198 4.6 10.8 1.0
CA A:VAL204 4.6 11.2 1.0
CB A:SER200 4.6 17.6 0.5
O A:TRP198 4.6 17.6 1.0
N A:VAL204 4.7 18.4 1.0
N A:THR205 4.8 20.2 1.0
OG1 A:THR205 4.8 15.2 1.0
O A:GLY240 4.8 14.9 1.0
OG A:SER200 4.8 16.7 0.5
N A:PRO201 4.9 16.2 1.0
CA A:VAL203 4.9 16.7 1.0
CA A:ALA244 4.9 17.8 1.0
CG2 A:THR205 4.9 3.1 1.0
CB A:VAL203 5.0 16.1 1.0
CB A:ALA244 5.0 14.9 1.0

Potassium binding site 3 out of 8 in 6hth

Go back to Potassium Binding Sites List in 6hth
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:11.5
occ:1.00
 O B:VAL208 2.6 10.0 1.0
O B:ASP186 2.6 10.0 1.0
OD1 B:ASP184 2.6 12.2 1.0
O B:ASP184 2.8 15.3 1.0
O B:HIS188 2.9 8.2 1.0
OG B:SER207 2.9 10.5 1.0
N B:ASP186 3.3 4.8 1.0
CG B:ASP184 3.4 7.6 1.0
C B:ASP184 3.4 11.3 1.0
C B:ASP186 3.5 7.7 1.0
C B:VAL208 3.7 4.7 1.0
CB B:HIS209 3.8 1.9 1.0
CA B:ASP186 3.8 5.2 1.0
C B:HIS188 3.8 6.2 1.0
CB B:ASP184 3.8 3.7 1.0
C B:LEU185 3.9 9.6 1.0
CB B:ASP186 3.9 5.6 1.0
N B:VAL208 3.9 7.8 1.0
CB B:SER207 4.0 12.4 1.0
N B:LEU185 4.0 4.4 1.0
CA B:ASP184 4.2 10.1 1.0
ND1 B:HIS209 4.2 8.6 1.0
CA B:LEU185 4.3 4.1 1.0
OD2 B:ASP184 4.3 16.4 1.0
N B:GLY190 4.3 8.1 1.0
CA B:HIS209 4.4 6.1 1.0
N B:HIS188 4.4 13.0 1.0
CA B:SER207 4.4 12.1 1.0
N B:HIS189 4.5 5.2 1.0
C B:SER207 4.5 11.2 1.0
CA B:HIS189 4.5 10.5 1.0
CG B:HIS209 4.5 5.6 1.0
CA B:VAL208 4.5 11.9 1.0
N B:HIS209 4.5 9.0 1.0
O B:LEU185 4.6 10.8 1.0
N B:LEU187 4.6 9.8 1.0
CA B:HIS188 4.7 11.0 1.0
C B:LEU187 4.7 11.5 1.0
C B:HIS189 4.8 13.5 1.0
O B:HOH694 4.8 14.8 1.0

Potassium binding site 4 out of 8 in 6hth

Go back to Potassium Binding Sites List in 6hth
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:18.6
occ:1.00
 O B:PHE197 2.5 15.8 1.0
OG B:SER243 2.6 16.3 1.0
O B:VAL203 2.6 20.8 1.0
O B:SER200 2.8 20.5 1.0
O B:HOH680 2.9 10.8 1.0
CB B:SER243 3.4 17.1 1.0
C B:PHE197 3.5 13.9 1.0
O B:SER243 3.6 18.6 1.0
CB B:PHE197 3.8 8.8 1.0
C B:VAL203 3.9 17.6 1.0
C B:SER200 3.9 24.3 1.0
C B:SER243 4.0 20.3 1.0
CA B:PHE197 4.3 16.0 1.0
CA B:SER243 4.3 18.6 1.0
N B:SER200 4.3 23.2 1.0
N B:TRP198 4.4 9.6 1.0
O B:TRP198 4.5 17.1 1.0
CA B:TRP198 4.5 5.3 1.0
C B:TRP198 4.5 15.8 1.0
CA B:SER200 4.6 22.4 1.0
N B:ALA244 4.6 17.7 1.0
CA B:VAL204 4.6 18.1 1.0
N B:VAL204 4.7 19.5 1.0
N B:THR205 4.7 21.9 1.0
CG2 B:THR205 4.8 7.1 1.0
OG1 B:THR205 4.8 14.5 1.0
O B:GLY240 4.8 13.8 1.0
CA B:VAL203 4.8 11.7 1.0
CB B:SER200 4.9 24.8 1.0
CB B:VAL203 4.9 13.7 1.0
N B:PRO201 5.0 23.2 1.0

Potassium binding site 5 out of 8 in 6hth

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:10.7
occ:1.00
 OD1 C:ASP184 2.5 9.6 1.0
O C:ASP186 2.5 8.0 1.0
O C:VAL208 2.6 11.3 1.0
O C:HIS188 2.8 5.3 1.0
O C:ASP184 2.8 7.3 1.0
OG C:SER207 3.0 15.1 1.0
N C:ASP186 3.2 10.4 1.0
CG C:ASP184 3.3 14.5 1.0
C C:ASP186 3.4 15.0 1.0
C C:ASP184 3.5 9.6 1.0
C C:VAL208 3.7 9.5 1.0
CA C:ASP186 3.7 11.7 1.0
CB C:ASP184 3.7 5.7 1.0
CB C:HIS209 3.8 5.3 1.0
C C:HIS188 3.8 5.6 1.0
C C:LEU185 3.8 10.0 1.0
CB C:ASP186 3.9 11.3 1.0
N C:VAL208 4.0 13.4 1.0
N C:LEU185 4.1 7.5 1.0
CB C:SER207 4.1 9.7 1.0
CA C:ASP184 4.2 7.7 1.0
CA C:LEU185 4.2 7.0 1.0
ND1 C:HIS209 4.3 8.1 1.0
OD2 C:ASP184 4.3 15.2 1.0
CA C:HIS209 4.3 7.1 1.0
N C:GLY190 4.4 5.6 1.0
CA C:SER207 4.4 13.9 1.0
N C:HIS188 4.4 13.5 1.0
CA C:HIS189 4.4 12.3 1.0
N C:HIS189 4.5 8.7 1.0
CG C:HIS209 4.5 5.4 1.0
C C:SER207 4.5 5.7 1.0
O C:LEU185 4.5 13.6 1.0
N C:HIS209 4.5 8.9 1.0
CA C:VAL208 4.5 8.8 1.0
N C:LEU187 4.6 13.6 1.0
C C:HIS189 4.7 11.1 1.0
C C:LEU187 4.7 10.9 1.0
CA C:HIS188 4.7 8.4 1.0

Potassium binding site 6 out of 8 in 6hth

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:18.0
occ:1.00
 O C:PHE197 2.5 15.5 1.0
O C:VAL203 2.6 20.3 1.0
OG C:SER243 2.7 18.2 1.0
O C:HOH687 2.7 14.9 1.0
O C:SER200 2.9 17.5 1.0
C C:PHE197 3.4 12.3 1.0
CB C:SER243 3.4 12.8 1.0
O C:SER243 3.6 18.7 1.0
CB C:PHE197 3.8 16.9 1.0
C C:VAL203 3.8 17.1 1.0
C C:SER243 3.9 17.1 1.0
C C:SER200 4.0 23.6 1.0
CA C:PHE197 4.2 15.3 1.0
N C:TRP198 4.3 18.6 1.0
N C:SER200 4.3 15.8 1.0
CA C:SER243 4.4 6.9 1.0
CA C:TRP198 4.4 12.2 1.0
C C:TRP198 4.5 16.9 1.0
N C:ALA244 4.5 10.5 1.0
O C:TRP198 4.6 19.1 1.0
CA C:VAL204 4.6 16.7 1.0
N C:THR205 4.6 15.2 1.0
CA C:SER200 4.6 23.1 0.5
CG2 C:THR205 4.6 9.9 1.0
CA C:SER200 4.6 23.1 0.5
OG1 C:THR205 4.6 14.0 1.0
N C:VAL204 4.7 17.5 1.0
CB C:SER200 4.7 23.1 0.5
CB C:SER200 4.8 23.1 0.5
CA C:VAL203 4.8 12.2 1.0
O C:GLY240 4.8 13.2 1.0
CB C:VAL203 4.9 11.2 1.0
N C:VAL203 5.0 15.5 1.0

Potassium binding site 7 out of 8 in 6hth

Go back to Potassium Binding Sites List in 6hth
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:13.4
occ:1.00
 OD1 D:ASP184 2.5 7.8 1.0
O D:ASP186 2.6 15.4 1.0
O D:HIS188 2.6 13.2 1.0
O D:VAL208 2.7 11.0 1.0
OG D:SER207 2.8 11.1 1.0
O D:ASP184 2.9 7.7 1.0
CG D:ASP184 3.3 17.2 1.0
N D:ASP186 3.4 9.7 1.0
C D:ASP186 3.4 16.9 1.0
C D:ASP184 3.5 8.1 1.0
C D:HIS188 3.7 13.1 1.0
CA D:ASP186 3.7 10.3 1.0
C D:VAL208 3.7 16.5 1.0
CB D:ASP186 3.8 11.7 1.0
CB D:HIS209 3.8 8.6 1.0
CB D:ASP184 3.9 11.2 1.0
C D:LEU185 3.9 11.4 1.0
N D:VAL208 4.0 12.1 1.0
CB D:SER207 4.0 15.0 1.0
N D:LEU185 4.1 9.2 1.0
OD2 D:ASP184 4.2 15.7 1.0
CA D:HIS189 4.3 12.6 1.0
CA D:ASP184 4.3 11.0 1.0
N D:HIS189 4.3 9.1 1.0
N D:GLY190 4.3 12.8 1.0
ND1 D:HIS209 4.3 18.5 1.0
N D:HIS188 4.3 11.2 1.0
CA D:HIS209 4.3 12.8 1.0
CA D:LEU185 4.4 14.9 1.0
CA D:SER207 4.4 13.2 1.0
N D:HIS209 4.5 10.8 1.0
C D:SER207 4.5 12.5 1.0
CG D:HIS209 4.6 17.4 1.0
CA D:VAL208 4.6 13.8 1.0
O D:LEU185 4.6 15.1 1.0
C D:HIS189 4.6 16.5 1.0
N D:LEU187 4.6 12.2 1.0
C D:LEU187 4.6 15.1 1.0
CA D:HIS188 4.7 9.2 1.0
O D:HOH675 4.8 12.8 1.0
CE1 D:HIS141 4.8 15.9 1.0
O D:LEU187 5.0 16.1 1.0
CG D:ASP186 5.0 12.3 1.0

Potassium binding site 8 out of 8 in 6hth

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:18.1
occ:1.00
 O D:PHE197 2.5 10.9 1.0
O D:VAL203 2.6 21.1 1.0
OG D:SER243 2.7 17.1 1.0
O D:SER200 2.8 20.1 1.0
O D:HOH677 2.9 14.0 1.0
CB D:SER243 3.4 13.9 1.0
C D:PHE197 3.5 4.9 1.0
O D:SER243 3.7 13.4 1.0
C D:VAL203 3.8 15.9 1.0
C D:SER200 3.9 15.2 1.0
CB D:PHE197 3.9 13.2 1.0
C D:SER243 3.9 18.1 1.0
CA D:PHE197 4.3 6.3 1.0
N D:SER200 4.3 12.5 1.0
N D:TRP198 4.3 7.8 1.0
CA D:SER243 4.3 17.3 1.0
N D:ALA244 4.5 13.7 1.0
CA D:TRP198 4.5 13.3 1.0
CA D:SER200 4.5 16.1 0.5
CA D:SER200 4.5 16.1 0.5
C D:TRP198 4.5 14.0 1.0
CA D:VAL204 4.6 14.0 1.0
O D:TRP198 4.6 12.8 1.0
CB D:SER200 4.6 14.7 0.5
N D:VAL204 4.7 14.8 1.0
CB D:SER200 4.7 14.8 0.5
N D:THR205 4.7 20.4 1.0
O D:GLY240 4.8 16.3 1.0
OG1 D:THR205 4.8 12.0 1.0
OG D:SER200 4.8 20.1 0.5
CA D:VAL203 4.8 14.6 1.0
N D:PRO201 4.9 18.4 1.0
CA D:ALA244 4.9 15.8 1.0
N D:VAL203 5.0 14.2 1.0
CB D:VAL203 5.0 12.3 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 16:28:43 2024

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