Atomistry » Potassium » PDB 6hae-6i4g » 6hti
Atomistry »
  Potassium »
    PDB 6hae-6i4g »
      6hti »

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

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 6

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 6:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 6, PDB code: 6hti 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) 48.13 / 1.69
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.730, 70.730, 98.350, 75.70, 78.01, 85.80
R / Rfree (%) 19.7 / 22.9

Other elements in 6hti:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 6 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
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 6 (pdb code 6hti). 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 6, PDB code: 6hti:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6hti

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


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

b:20.4
occ:1.00
 O A:VAL208 2.5 20.0 1.0
OD1 A:ASP184 2.6 17.9 1.0
O A:ASP186 2.7 18.8 1.0
O A:HIS188 2.7 17.0 1.0
OG A:SER207 2.8 18.9 1.0
O A:ASP184 2.9 21.4 1.0
N A:ASP186 3.3 17.3 1.0
CG A:ASP184 3.4 25.5 1.0
C A:ASP186 3.5 21.1 1.0
C A:ASP184 3.5 20.5 1.0
C A:VAL208 3.6 18.1 1.0
CA A:ASP186 3.7 18.7 1.0
C A:HIS188 3.8 17.0 1.0
CB A:ASP184 3.8 23.3 1.0
CB A:ASP186 3.8 18.4 1.0
CB A:HIS209 3.8 18.3 1.0
C A:LEU185 3.9 18.2 1.0
N A:VAL208 3.9 21.6 1.0
N A:LEU185 4.0 21.5 1.0
CB A:SER207 4.1 20.3 1.0
CA A:ASP184 4.3 19.7 1.0
ND1 A:HIS209 4.3 20.0 1.0
CA A:LEU185 4.3 23.3 1.0
OD2 A:ASP184 4.3 21.6 1.0
CA A:HIS209 4.3 17.2 1.0
N A:GLY190 4.4 19.8 1.0
CA A:SER207 4.4 20.9 1.0
N A:HIS209 4.4 19.9 1.0
N A:HIS188 4.4 20.5 1.0
CA A:VAL208 4.4 20.1 1.0
CA A:HIS189 4.5 22.1 1.0
N A:HIS189 4.5 20.6 1.0
C A:SER207 4.5 21.4 1.0
CG A:HIS209 4.5 20.5 1.0
O A:LEU185 4.6 18.1 1.0
N A:LEU187 4.7 19.0 1.0
O A:HOH687 4.7 27.2 1.0
C A:LEU187 4.7 19.4 1.0
CA A:HIS188 4.7 18.7 1.0
C A:HIS189 4.7 23.4 1.0
CE1 A:HIS141 4.9 25.8 1.0

Potassium binding site 2 out of 8 in 6hti

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


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

b:22.4
occ:1.00
 O A:VAL203 2.5 22.8 1.0
O A:PHE197 2.6 19.1 1.0
OG A:SER243 2.7 24.3 1.0
O A:HOH672 2.8 19.4 1.0
O A:SER200 2.9 27.8 1.0
O A:SER243 3.4 25.9 1.0
CB A:SER243 3.5 20.9 1.0
C A:PHE197 3.6 21.2 1.0
C A:VAL203 3.8 21.5 1.0
C A:SER243 3.9 23.2 1.0
CB A:PHE197 3.9 22.0 1.0
C A:SER200 4.0 25.5 1.0
CA A:SER243 4.3 22.8 1.0
CA A:PHE197 4.4 22.0 1.0
N A:SER200 4.4 21.7 1.0
N A:TRP198 4.4 19.4 1.0
CA A:VAL204 4.5 20.2 1.0
N A:ALA244 4.5 20.8 1.0
N A:VAL204 4.6 20.3 1.0
CA A:TRP198 4.6 21.1 1.0
N A:THR205 4.6 20.5 1.0
C A:TRP198 4.6 22.1 1.0
O A:TRP198 4.7 25.2 1.0
CA A:SER200 4.7 26.5 0.5
CA A:SER200 4.7 26.5 0.5
CG2 A:THR205 4.7 20.3 1.0
OG1 A:THR205 4.7 21.7 1.0
CA A:VAL203 4.7 22.5 1.0
CB A:VAL203 4.8 20.3 1.0
CB A:SER200 4.9 28.0 0.5
O A:GLY240 4.9 22.3 1.0
CB A:ALA244 4.9 20.5 1.0
CA A:ALA244 4.9 19.6 1.0
CB A:SER200 4.9 28.1 0.5
N A:VAL203 5.0 23.8 1.0
N A:PRO201 5.0 26.2 1.0
C A:VAL204 5.0 22.4 1.0

Potassium binding site 3 out of 8 in 6hti

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


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

b:17.8
occ:1.00
 O B:VAL208 2.6 18.8 1.0
O B:ASP186 2.7 16.6 1.0
OD1 B:ASP184 2.7 17.3 1.0
O B:ASP184 2.8 17.3 1.0
O B:HIS188 2.8 17.6 1.0
OG B:SER207 2.9 15.8 1.0
N B:ASP186 3.3 19.1 1.0
C B:ASP184 3.4 13.8 1.0
CG B:ASP184 3.4 19.8 1.0
C B:ASP186 3.5 10.7 1.0
C B:VAL208 3.6 14.7 1.0
CA B:ASP186 3.7 17.1 1.0
C B:HIS188 3.8 16.5 1.0
CB B:ASP184 3.8 15.9 1.0
CB B:ASP186 3.8 16.4 1.0
C B:LEU185 3.8 13.5 1.0
CB B:HIS209 3.8 14.9 1.0
N B:VAL208 3.9 18.2 1.0
N B:LEU185 4.0 16.6 1.0
CB B:SER207 4.1 20.7 1.0
CA B:ASP184 4.2 14.0 1.0
CA B:LEU185 4.2 14.4 1.0
ND1 B:HIS209 4.3 15.6 1.0
OD2 B:ASP184 4.3 18.9 1.0
CA B:HIS209 4.4 14.5 1.0
N B:GLY190 4.4 16.5 1.0
CA B:SER207 4.4 24.2 1.0
N B:HIS188 4.4 16.7 1.0
N B:HIS209 4.5 15.3 1.0
CA B:VAL208 4.5 20.4 1.0
CA B:HIS189 4.5 15.9 1.0
C B:SER207 4.5 16.9 1.0
N B:HIS189 4.5 15.1 1.0
O B:LEU185 4.6 16.1 1.0
CG B:HIS209 4.6 15.8 1.0
N B:LEU187 4.6 15.8 1.0
C B:HIS189 4.7 19.1 1.0
CA B:HIS188 4.8 16.4 1.0
C B:LEU187 4.8 16.8 1.0
O B:HOH714 4.8 20.4 1.0

Potassium binding site 4 out of 8 in 6hti

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


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:23.0
occ:1.00
 O B:PHE197 2.5 21.3 1.0
O B:VAL203 2.6 22.3 1.0
O B:HOH675 2.7 22.7 1.0
OG B:SER243 2.8 23.2 1.0
O B:SER200 2.9 25.8 1.0
O B:SER243 3.4 20.6 1.0
C B:PHE197 3.5 20.0 1.0
CB B:SER243 3.5 19.7 1.0
CB B:PHE197 3.8 20.1 1.0
C B:VAL203 3.8 20.0 1.0
C B:SER243 3.9 22.4 1.0
C B:SER200 4.0 25.6 1.0
CA B:PHE197 4.2 21.4 1.0
N B:SER200 4.3 23.6 1.0
CA B:SER243 4.4 21.6 1.0
N B:TRP198 4.4 19.4 1.0
CA B:VAL204 4.5 20.6 1.0
N B:THR205 4.5 19.4 1.0
CA B:SER200 4.6 27.9 0.6
CA B:SER200 4.6 27.6 0.4
N B:VAL204 4.6 19.1 1.0
CA B:TRP198 4.6 19.6 1.0
N B:ALA244 4.6 21.3 1.0
C B:TRP198 4.6 24.9 1.0
O B:TRP198 4.6 19.2 1.0
OG1 B:THR205 4.7 18.9 1.0
CB B:SER200 4.7 29.8 0.6
CB B:SER200 4.7 29.7 0.4
CA B:VAL203 4.8 23.0 1.0
CG2 B:THR205 4.9 23.8 1.0
O B:GLY240 4.9 22.8 1.0
CB B:VAL203 4.9 22.3 1.0
CA B:ALA244 4.9 21.9 1.0
C B:VAL204 5.0 21.4 1.0
CB B:ALA244 5.0 20.4 1.0
N B:PRO201 5.0 23.0 1.0

Potassium binding site 5 out of 8 in 6hti

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


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

b:18.1
occ:1.00
 O C:VAL208 2.6 15.1 1.0
O C:ASP186 2.7 16.7 1.0
OD1 C:ASP184 2.7 18.0 1.0
O C:HIS188 2.8 16.6 1.0
O C:ASP184 2.8 17.7 1.0
OG C:SER207 3.0 16.3 1.0
N C:ASP186 3.4 14.6 1.0
C C:ASP184 3.4 17.0 1.0
CG C:ASP184 3.5 20.6 1.0
C C:ASP186 3.5 14.1 1.0
C C:VAL208 3.6 16.6 1.0
C C:HIS188 3.8 16.0 1.0
CA C:ASP186 3.8 15.4 1.0
CB C:HIS209 3.8 13.5 1.0
CB C:ASP184 3.9 18.6 1.0
C C:LEU185 3.9 18.0 1.0
CB C:ASP186 3.9 16.0 1.0
N C:VAL208 3.9 18.2 1.0
N C:LEU185 4.0 18.5 1.0
CB C:SER207 4.1 20.8 1.0
CA C:ASP184 4.2 13.8 1.0
CA C:LEU185 4.3 16.6 1.0
ND1 C:HIS209 4.3 15.6 1.0
CA C:HIS209 4.3 16.2 1.0
OD2 C:ASP184 4.4 18.5 1.0
CA C:SER207 4.4 16.5 1.0
N C:GLY190 4.4 15.2 1.0
N C:HIS209 4.5 16.2 1.0
CA C:VAL208 4.5 18.8 1.0
N C:HIS188 4.5 17.8 1.0
C C:SER207 4.5 15.2 1.0
CA C:HIS189 4.5 16.7 1.0
N C:HIS189 4.5 17.8 1.0
CG C:HIS209 4.5 17.7 1.0
O C:LEU185 4.6 20.4 1.0
N C:LEU187 4.7 14.2 1.0
O C:HOH697 4.7 23.8 1.0
C C:HIS189 4.7 16.9 1.0
C C:LEU187 4.7 20.9 1.0
CA C:HIS188 4.8 16.7 1.0

Potassium binding site 6 out of 8 in 6hti

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


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:21.7
occ:1.00
 O C:VAL203 2.5 20.9 1.0
O C:PHE197 2.6 19.2 1.0
OG C:SER243 2.7 23.6 1.0
O C:HOH701 2.8 21.7 1.0
O C:SER200 2.9 26.6 1.0
CB C:SER243 3.4 18.8 1.0
C C:PHE197 3.5 21.7 1.0
O C:SER243 3.6 26.9 1.0
C C:VAL203 3.8 20.5 1.0
CB C:PHE197 3.8 23.2 1.0
C C:SER243 4.0 24.1 1.0
C C:SER200 4.0 23.1 1.0
CA C:PHE197 4.3 20.9 1.0
CA C:SER243 4.3 17.3 1.0
N C:TRP198 4.4 19.7 1.0
N C:SER200 4.4 20.4 1.0
CA C:TRP198 4.5 20.1 1.0
CA C:VAL204 4.5 19.6 1.0
N C:VAL204 4.6 20.1 1.0
N C:THR205 4.6 17.6 1.0
N C:ALA244 4.6 21.9 1.0
C C:TRP198 4.6 21.6 1.0
O C:TRP198 4.7 19.1 1.0
CA C:SER200 4.7 25.1 1.0
CA C:VAL203 4.7 20.0 1.0
OG1 C:THR205 4.8 20.0 1.0
CB C:VAL203 4.9 18.1 1.0
CG2 C:THR205 4.9 18.0 1.0
CB C:SER200 4.9 33.3 1.0
O C:GLY240 4.9 21.9 1.0
N C:VAL203 4.9 17.8 1.0
N C:PRO201 5.0 22.1 1.0

Potassium binding site 7 out of 8 in 6hti

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


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

b:18.9
occ:1.00
 O D:VAL208 2.6 17.3 1.0
OD1 D:ASP184 2.6 18.4 1.0
O D:ASP186 2.7 18.2 1.0
O D:HIS188 2.8 18.2 1.0
OG D:SER207 2.8 20.5 1.0
O D:ASP184 2.9 17.0 1.0
N D:ASP186 3.3 15.3 1.0
CG D:ASP184 3.4 22.6 1.0
C D:ASP184 3.4 16.1 1.0
C D:ASP186 3.5 15.7 1.0
C D:VAL208 3.6 20.0 1.0
CA D:ASP186 3.7 14.9 1.0
CB D:ASP186 3.8 15.7 1.0
C D:HIS188 3.8 18.8 1.0
CB D:HIS209 3.8 13.2 1.0
CB D:ASP184 3.8 18.9 1.0
C D:LEU185 3.8 22.4 1.0
N D:VAL208 3.9 20.7 1.0
CB D:SER207 4.0 23.3 1.0
N D:LEU185 4.0 17.1 1.0
CA D:ASP184 4.2 18.8 1.0
OD2 D:ASP184 4.2 20.0 1.0
CA D:LEU185 4.3 21.0 1.0
ND1 D:HIS209 4.3 20.1 1.0
CA D:SER207 4.3 19.3 1.0
CA D:HIS209 4.3 16.6 1.0
N D:HIS209 4.4 21.5 1.0
N D:GLY190 4.4 19.4 1.0
CA D:VAL208 4.4 20.6 1.0
C D:SER207 4.5 19.5 1.0
N D:HIS188 4.5 17.0 1.0
CA D:HIS189 4.5 14.9 1.0
N D:HIS189 4.5 17.2 1.0
CG D:HIS209 4.5 18.6 1.0
O D:LEU185 4.5 20.1 1.0
N D:LEU187 4.7 15.8 1.0
CA D:HIS188 4.7 19.0 1.0
O D:HOH658 4.8 22.8 1.0
C D:HIS189 4.8 19.4 1.0
C D:LEU187 4.8 14.7 1.0
CE1 D:HIS141 4.8 19.9 1.0

Potassium binding site 8 out of 8 in 6hti

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


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K504

b:20.0
occ:1.00
 O D:VAL203 2.5 21.6 1.0
O D:PHE197 2.6 19.3 1.0
OG D:SER243 2.6 24.8 1.0
O D:SER200 2.9 23.6 1.0
O D:HOH649 2.9 21.6 1.0
O D:SER243 3.4 22.8 1.0
CB D:SER243 3.4 20.6 1.0
C D:PHE197 3.6 16.5 1.0
C D:VAL203 3.8 18.2 1.0
C D:SER243 3.8 21.0 1.0
CB D:PHE197 3.9 20.6 1.0
C D:SER200 4.0 20.8 1.0
CA D:SER243 4.3 23.6 1.0
CA D:PHE197 4.4 15.1 1.0
CA D:VAL204 4.4 20.7 1.0
N D:SER200 4.4 21.9 1.0
N D:TRP198 4.4 21.3 1.0
N D:ALA244 4.5 19.1 1.0
N D:VAL204 4.5 19.9 1.0
N D:THR205 4.6 19.8 1.0
CA D:TRP198 4.6 20.1 1.0
C D:TRP198 4.6 17.1 1.0
O D:TRP198 4.6 21.5 1.0
CA D:SER200 4.6 22.3 1.0
CG2 D:THR205 4.7 18.9 1.0
OG1 D:THR205 4.7 21.5 1.0
CA D:VAL203 4.8 15.3 1.0
O D:GLY240 4.9 21.8 1.0
CB D:VAL203 4.9 18.2 1.0
N D:PRO201 4.9 22.9 1.0
CB D:SER200 4.9 35.3 1.0
C D:VAL204 4.9 22.2 1.0
CA D:ALA244 4.9 21.7 1.0
N D:VAL203 5.0 15.3 1.0
CA D:PRO201 5.0 19.2 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 16:28:58 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy