Atomistry » Potassium » PDB 6hae-6i4g » 6hu2
Atomistry »
  Potassium »
    PDB 6hae-6i4g »
      6hu2 »

Potassium in PDB 6hu2: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11, PDB code: 6hu2 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) 48.43 / 1.99
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.290, 71.330, 99.080, 75.72, 78.17, 85.61
R / Rfree (%) 15.6 / 19.7

Other elements in 6hu2:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11 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 11 (pdb code 6hu2). 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 11, PDB code: 6hu2:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6hu2

Go back to Potassium Binding Sites List in 6hu2
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11


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

b:22.7
occ:1.00
 O A:VAL208 2.6 17.9 1.0
O A:ASP186 2.6 21.5 1.0
OD1 A:ASP184 2.7 22.6 1.0
O A:HIS188 2.8 19.8 1.0
O A:ASP184 2.9 20.8 1.0
OG A:SER207 2.9 19.8 1.0
N A:ASP186 3.3 21.5 1.0
CG A:ASP184 3.4 24.5 1.0
C A:ASP186 3.5 24.1 1.0
C A:ASP184 3.5 19.4 1.0
C A:VAL208 3.6 19.8 1.0
CA A:ASP186 3.7 21.6 1.0
CB A:HIS209 3.8 16.7 1.0
C A:HIS188 3.8 18.6 1.0
CB A:ASP186 3.8 16.6 1.0
CB A:ASP184 3.8 22.7 1.0
C A:LEU185 3.9 25.3 1.0
N A:VAL208 3.9 25.1 1.0
N A:LEU185 4.1 17.5 1.0
CB A:SER207 4.1 15.9 1.0
ND1 A:HIS209 4.2 21.5 1.0
CA A:ASP184 4.3 21.5 1.0
CA A:LEU185 4.3 20.8 1.0
OD2 A:ASP184 4.3 24.2 1.0
CA A:HIS209 4.4 21.3 1.0
CA A:SER207 4.4 23.9 1.0
N A:GLY190 4.4 22.5 1.0
CA A:VAL208 4.4 20.1 1.0
N A:HIS188 4.5 20.5 1.0
N A:HIS209 4.5 23.6 1.0
CA A:HIS189 4.5 16.1 1.0
C A:SER207 4.5 27.3 1.0
CG A:HIS209 4.5 25.1 1.0
N A:HIS189 4.5 16.7 1.0
O A:LEU185 4.5 21.0 1.0
N A:LEU187 4.6 21.8 1.0
C A:LEU187 4.7 19.1 1.0
C A:HIS189 4.8 22.8 1.0
CA A:HIS188 4.8 18.5 1.0
O A:HOH714 4.8 23.7 1.0
CE1 A:HIS141 4.9 14.5 1.0

Potassium binding site 2 out of 8 in 6hu2

Go back to Potassium Binding Sites List in 6hu2
Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11


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

b:25.8
occ:1.00
 O A:PHE197 2.6 23.2 1.0
O A:VAL203 2.6 23.6 1.0
OG A:SER243 2.6 24.1 1.0
O A:SER200 2.9 27.3 1.0
O A:HOH701 2.9 22.1 1.0
O A:SER243 3.4 28.9 1.0
CB A:SER243 3.5 24.8 1.0
C A:PHE197 3.6 23.6 1.0
C A:VAL203 3.8 27.1 1.0
C A:SER243 3.9 23.9 1.0
C A:SER200 4.0 32.6 1.0
CB A:PHE197 4.0 24.9 1.0
CA A:SER243 4.3 24.9 1.0
N A:SER200 4.4 29.1 1.0
CA A:PHE197 4.4 22.3 1.0
N A:TRP198 4.5 20.5 1.0
CA A:VAL204 4.5 23.9 1.0
N A:ALA244 4.5 23.3 1.0
CA A:TRP198 4.6 22.1 1.0
CA A:SER200 4.6 33.7 1.0
C A:TRP198 4.6 24.8 1.0
N A:VAL204 4.6 19.5 1.0
N A:THR205 4.7 27.5 1.0
O A:TRP198 4.7 21.1 1.0
OG1 A:THR205 4.7 21.1 1.0
CA A:VAL203 4.8 26.0 1.0
CB A:SER200 4.8 35.3 1.0
O A:GLY240 4.9 27.9 1.0
CG2 A:THR205 4.9 18.9 1.0
CB A:VAL203 4.9 29.0 1.0
N A:PRO201 4.9 28.9 1.0
CA A:ALA244 5.0 22.7 1.0
CB A:ALA244 5.0 20.1 1.0
N A:VAL203 5.0 25.8 1.0

Potassium binding site 3 out of 8 in 6hu2

Go back to Potassium Binding Sites List in 6hu2
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11


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

b:19.2
occ:1.00
 O B:ASP186 2.6 20.8 1.0
O B:VAL208 2.6 14.7 1.0
OD1 B:ASP184 2.7 19.3 1.0
O B:HIS188 2.7 19.2 1.0
O B:ASP184 2.8 17.5 1.0
OG B:SER207 2.9 20.4 1.0
N B:ASP186 3.4 15.3 1.0
CG B:ASP184 3.4 21.5 1.0
C B:ASP184 3.4 16.4 1.0
C B:ASP186 3.4 17.7 1.0
C B:VAL208 3.6 20.4 1.0
CA B:ASP186 3.8 14.7 1.0
C B:HIS188 3.8 19.7 1.0
CB B:ASP184 3.8 14.7 1.0
C B:LEU185 3.8 18.9 1.0
CB B:HIS209 3.9 15.6 1.0
CB B:ASP186 3.9 18.2 1.0
N B:VAL208 3.9 20.1 1.0
N B:LEU185 4.0 15.0 1.0
CB B:SER207 4.1 19.4 1.0
CA B:LEU185 4.2 15.9 1.0
CA B:ASP184 4.2 15.6 1.0
ND1 B:HIS209 4.3 14.2 1.0
OD2 B:ASP184 4.3 21.0 1.0
CA B:HIS209 4.4 18.3 1.0
N B:GLY190 4.4 17.4 1.0
N B:HIS188 4.4 18.4 1.0
CA B:SER207 4.4 20.8 1.0
CA B:VAL208 4.5 19.2 1.0
N B:HIS209 4.5 19.9 1.0
C B:SER207 4.5 22.7 1.0
CA B:HIS189 4.5 19.6 1.0
N B:HIS189 4.5 19.1 1.0
O B:LEU185 4.5 18.9 1.0
CG B:HIS209 4.6 17.9 1.0
N B:LEU187 4.6 19.7 1.0
C B:LEU187 4.7 19.4 1.0
O B:HOH721 4.7 21.9 1.0
CA B:HIS188 4.7 19.8 1.0
C B:HIS189 4.8 21.2 1.0

Potassium binding site 4 out of 8 in 6hu2

Go back to Potassium Binding Sites List in 6hu2
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11


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

b:26.4
occ:1.00
 O B:PHE197 2.6 21.9 1.0
O B:VAL203 2.6 29.6 1.0
OG B:SER243 2.6 30.1 1.0
O B:HOH738 2.8 24.6 1.0
O B:SER200 2.9 29.7 1.0
CB B:SER243 3.5 32.3 1.0
O B:SER243 3.5 25.6 1.0
C B:PHE197 3.6 23.6 1.0
C B:VAL203 3.8 29.7 1.0
CB B:PHE197 3.9 23.3 1.0
C B:SER243 3.9 24.6 1.0
C B:SER200 4.0 35.2 1.0
CA B:SER243 4.4 25.1 1.0
CA B:PHE197 4.4 26.0 1.0
N B:SER200 4.4 31.1 1.0
N B:TRP198 4.5 22.1 1.0
CA B:VAL204 4.5 23.4 1.0
N B:ALA244 4.5 17.8 1.0
CA B:TRP198 4.6 22.1 1.0
C B:TRP198 4.6 28.8 1.0
N B:THR205 4.6 19.9 1.0
N B:VAL204 4.6 27.0 1.0
O B:TRP198 4.6 25.5 1.0
CA B:SER200 4.7 37.1 1.0
OG1 B:THR205 4.8 20.4 1.0
CG2 B:THR205 4.8 24.8 1.0
CA B:VAL203 4.8 27.4 1.0
O B:GLY240 4.8 23.3 1.0
CB B:SER200 4.9 39.7 1.0
CA B:ALA244 5.0 19.7 1.0
CB B:VAL203 5.0 20.8 1.0
N B:VAL203 5.0 24.6 1.0

Potassium binding site 5 out of 8 in 6hu2

Go back to Potassium Binding Sites List in 6hu2
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11


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

b:20.3
occ:1.00
 O C:ASP186 2.6 18.1 1.0
O C:VAL208 2.7 19.1 1.0
OD1 C:ASP184 2.7 18.1 1.0
O C:HIS188 2.8 17.5 1.0
O C:ASP184 2.8 16.8 1.0
OG C:SER207 2.9 18.4 1.0
N C:ASP186 3.3 21.9 1.0
CG C:ASP184 3.4 21.2 1.0
C C:ASP184 3.4 21.6 1.0
C C:ASP186 3.5 18.7 1.0
C C:VAL208 3.7 18.6 1.0
CA C:ASP186 3.7 20.6 1.0
C C:HIS188 3.8 19.4 1.0
CB C:ASP184 3.8 18.6 1.0
C C:LEU185 3.8 21.8 1.0
CB C:HIS209 3.8 16.5 1.0
CB C:ASP186 3.9 15.3 1.0
N C:VAL208 3.9 16.5 1.0
N C:LEU185 4.0 18.8 1.0
CB C:SER207 4.1 21.9 1.0
CA C:LEU185 4.2 18.8 1.0
CA C:ASP184 4.2 16.9 1.0
ND1 C:HIS209 4.3 21.4 1.0
OD2 C:ASP184 4.3 20.0 1.0
N C:GLY190 4.4 15.3 1.0
CA C:HIS209 4.4 15.1 1.0
CA C:SER207 4.4 23.0 1.0
N C:HIS188 4.4 17.8 1.0
CA C:VAL208 4.5 18.1 1.0
N C:HIS209 4.5 18.9 1.0
C C:SER207 4.5 23.4 1.0
CA C:HIS189 4.5 20.4 1.0
O C:LEU185 4.6 19.3 1.0
CG C:HIS209 4.6 23.4 1.0
N C:HIS189 4.6 17.2 1.0
N C:LEU187 4.7 17.8 1.0
C C:LEU187 4.7 20.5 1.0
O C:HOH726 4.7 24.1 1.0
C C:HIS189 4.8 20.9 1.0
CA C:HIS188 4.8 22.3 1.0

Potassium binding site 6 out of 8 in 6hu2

Go back to Potassium Binding Sites List in 6hu2
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11


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

b:25.4
occ:1.00
 O C:VAL203 2.6 24.9 1.0
O C:PHE197 2.7 23.5 1.0
OG C:SER243 2.7 33.3 1.0
O C:HOH727 2.9 21.8 1.0
O C:SER200 2.9 33.7 1.0
CB C:SER243 3.5 27.4 1.0
C C:PHE197 3.6 20.6 1.0
O C:SER243 3.7 22.7 1.0
C C:VAL203 3.8 24.2 1.0
CB C:PHE197 3.8 21.6 1.0
C C:SER243 4.0 22.8 1.0
C C:SER200 4.1 31.0 1.0
CA C:PHE197 4.3 27.3 1.0
CA C:SER243 4.4 21.4 1.0
N C:TRP198 4.4 19.7 1.0
N C:SER200 4.5 24.5 1.0
CA C:VAL204 4.6 22.8 1.0
CA C:TRP198 4.6 26.8 1.0
N C:VAL204 4.6 20.6 1.0
O C:TRP198 4.6 24.6 1.0
C C:TRP198 4.6 27.3 1.0
N C:ALA244 4.6 21.0 1.0
N C:THR205 4.7 23.3 1.0
CA C:SER200 4.7 33.1 1.0
CG2 C:THR205 4.8 19.5 1.0
CA C:VAL203 4.8 23.6 1.0
OG1 C:THR205 4.8 21.4 1.0
CB C:VAL203 4.9 22.2 1.0
O C:GLY240 4.9 20.4 1.0
N C:VAL203 4.9 26.0 1.0
CB C:SER200 4.9 39.3 1.0

Potassium binding site 7 out of 8 in 6hu2

Go back to Potassium Binding Sites List in 6hu2
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11


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

b:22.6
occ:1.00
 OD1 D:ASP184 2.6 21.6 1.0
O D:ASP186 2.6 19.8 1.0
O D:VAL208 2.7 17.0 1.0
O D:HIS188 2.8 21.4 1.0
O D:ASP184 2.8 19.1 1.0
OG D:SER207 2.8 20.2 1.0
N D:ASP186 3.3 18.0 1.0
CG D:ASP184 3.4 26.6 1.0
C D:ASP184 3.5 21.2 1.0
C D:ASP186 3.5 22.6 1.0
C D:VAL208 3.7 19.3 1.0
CA D:ASP186 3.7 17.3 1.0
C D:HIS188 3.8 22.5 1.0
CB D:ASP184 3.8 19.4 1.0
CB D:ASP186 3.8 18.4 1.0
CB D:HIS209 3.9 15.6 1.0
C D:LEU185 3.9 24.8 1.0
N D:VAL208 3.9 22.1 1.0
CB D:SER207 4.0 20.1 1.0
N D:LEU185 4.1 17.9 1.0
ND1 D:HIS209 4.2 21.4 1.0
CA D:ASP184 4.3 20.3 1.0
CA D:LEU185 4.3 21.3 1.0
OD2 D:ASP184 4.3 22.9 1.0
CA D:SER207 4.3 22.6 1.0
N D:GLY190 4.4 24.7 1.0
CA D:HIS209 4.4 19.1 1.0
C D:SER207 4.5 22.8 1.0
N D:HIS209 4.5 22.2 1.0
CA D:VAL208 4.5 20.0 1.0
CG D:HIS209 4.5 23.3 1.0
N D:HIS188 4.5 19.8 1.0
CA D:HIS189 4.5 17.3 1.0
N D:HIS189 4.5 17.5 1.0
O D:LEU185 4.6 21.5 1.0
N D:LEU187 4.7 19.8 1.0
O D:HOH669 4.7 22.3 1.0
C D:LEU187 4.8 21.1 1.0
C D:HIS189 4.8 22.6 1.0
CA D:HIS188 4.8 20.5 1.0
CE1 D:HIS141 4.9 22.5 1.0

Potassium binding site 8 out of 8 in 6hu2

Go back to Potassium Binding Sites List in 6hu2
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 11


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

b:24.6
occ:1.00
 O D:VAL203 2.6 31.1 1.0
O D:PHE197 2.6 24.4 1.0
OG D:SER243 2.6 25.5 1.0
O D:HOH715 2.7 20.5 1.0
O D:SER200 2.9 28.1 1.0
O D:SER243 3.4 26.6 1.0
CB D:SER243 3.6 24.6 1.0
C D:PHE197 3.6 21.6 1.0
C D:VAL203 3.8 26.0 1.0
C D:SER243 3.9 27.7 1.0
CB D:PHE197 3.9 17.8 1.0
C D:SER200 4.0 28.5 1.0
CA D:PHE197 4.4 21.9 1.0
CA D:SER243 4.4 25.1 1.0
N D:TRP198 4.4 23.2 1.0
N D:SER200 4.5 25.2 1.0
CA D:VAL204 4.5 27.0 1.0
CA D:TRP198 4.6 22.8 1.0
N D:VAL204 4.6 26.0 1.0
N D:ALA244 4.6 22.8 1.0
C D:TRP198 4.6 24.0 1.0
N D:THR205 4.6 23.4 1.0
OG1 D:THR205 4.7 18.3 1.0
O D:TRP198 4.7 20.0 1.0
CA D:SER200 4.7 28.9 0.5
CA D:SER200 4.7 28.9 0.5
CA D:VAL203 4.8 21.4 1.0
CG2 D:THR205 4.8 15.0 1.0
CB D:SER200 4.9 29.7 0.5
CB D:SER200 4.9 29.8 0.5
CA D:ALA244 5.0 24.6 1.0
CB D:VAL203 5.0 19.8 1.0
CB D:ALA244 5.0 20.3 1.0
O D:GLY240 5.0 27.5 1.0
N D:VAL203 5.0 23.8 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 16:33:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy