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Potassium in PDB 6ht8: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3, PDB code: 6ht8 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) 35.63 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.788, 70.921, 98.342, 77.90, 75.58, 85.33
R / Rfree (%) 15.8 / 23.6

Other elements in 6ht8:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3 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 3 (pdb code 6ht8). 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 3, PDB code: 6ht8:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6ht8

Go back to Potassium Binding Sites List in 6ht8
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3


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

b:25.9
occ:1.00
 OD1 A:ASP184 2.6 19.1 1.0
O A:HIS188 2.7 13.3 1.0
O A:ASP186 2.7 23.6 1.0
O A:VAL208 2.7 22.1 1.0
O A:ASP184 2.8 9.0 1.0
OG A:SER207 2.9 10.9 1.0
CG A:ASP184 3.3 23.4 1.0
N A:ASP186 3.4 20.2 1.0
C A:ASP184 3.5 15.2 1.0
C A:ASP186 3.5 21.4 1.0
C A:HIS188 3.7 15.2 1.0
CB A:ASP184 3.7 18.5 1.0
C A:VAL208 3.7 20.4 1.0
CA A:ASP186 3.7 16.8 1.0
CB A:ASP186 3.8 18.0 1.0
CB A:HIS209 3.8 11.4 1.0
N A:VAL208 3.9 20.6 1.0
C A:LEU185 4.0 22.0 1.0
CB A:SER207 4.0 18.9 1.0
ND1 A:HIS209 4.1 27.7 1.0
N A:LEU185 4.2 17.1 1.0
CA A:ASP184 4.2 15.5 1.0
OD2 A:ASP184 4.2 25.0 1.0
N A:GLY190 4.2 18.8 1.0
CA A:HIS189 4.3 22.4 1.0
N A:HIS188 4.3 24.8 1.0
CA A:SER207 4.4 31.7 1.0
N A:HIS189 4.4 16.4 1.0
CA A:HIS209 4.4 17.7 1.0
CA A:LEU185 4.4 22.2 1.0
CG A:HIS209 4.5 21.6 1.0
CA A:VAL208 4.5 20.7 1.0
N A:HIS209 4.5 14.7 1.0
C A:SER207 4.5 24.7 1.0
O A:LEU185 4.6 21.3 1.0
C A:HIS189 4.6 23.1 1.0
N A:LEU187 4.7 16.8 1.0
CA A:HIS188 4.7 19.8 1.0
C A:LEU187 4.7 17.7 1.0
CE1 A:HIS141 4.9 21.5 1.0
O A:HOH652 4.9 20.7 1.0
CG A:ASP186 5.0 15.1 1.0

Potassium binding site 2 out of 8 in 6ht8

Go back to Potassium Binding Sites List in 6ht8
Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3


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

b:26.0
occ:1.00
 OG A:SER243 2.5 21.1 1.0
O A:PHE197 2.6 23.6 1.0
O A:VAL203 2.6 27.2 1.0
O A:SER200 2.9 18.6 1.0
O A:HOH641 3.0 12.9 1.0
CB A:SER243 3.2 22.5 1.0
O A:SER243 3.3 15.3 1.0
C A:PHE197 3.6 20.9 1.0
C A:SER243 3.7 14.2 1.0
C A:VAL203 3.8 26.4 1.0
CB A:PHE197 4.1 10.7 1.0
C A:SER200 4.1 26.1 1.0
CA A:SER243 4.1 22.0 1.0
N A:ALA244 4.3 10.2 1.0
CA A:VAL204 4.4 24.6 1.0
CA A:PHE197 4.5 12.3 1.0
N A:TRP198 4.5 26.8 1.0
N A:THR205 4.5 26.6 1.0
N A:SER200 4.6 26.1 1.0
N A:VAL204 4.6 21.6 1.0
CA A:TRP198 4.6 16.0 1.0
C A:TRP198 4.7 14.5 1.0
O A:GLY240 4.8 27.5 1.0
O A:TRP198 4.8 17.6 1.0
OG1 A:THR205 4.8 29.7 1.0
CA A:SER200 4.8 26.4 1.0
CG2 A:THR205 4.8 30.0 1.0
CA A:ALA244 4.8 22.0 1.0
CA A:VAL203 4.9 21.8 1.0
C A:VAL204 4.9 22.6 1.0
CB A:ALA244 5.0 8.5 1.0

Potassium binding site 3 out of 8 in 6ht8

Go back to Potassium Binding Sites List in 6ht8
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3


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

b:21.4
occ:1.00
 O B:VAL208 2.5 15.4 1.0
O B:ASP186 2.6 15.6 1.0
OD1 B:ASP184 2.7 17.3 1.0
O B:ASP184 2.7 20.7 1.0
O B:HIS188 2.8 10.7 1.0
OG B:SER207 3.0 16.4 1.0
CG B:ASP184 3.3 23.0 1.0
N B:ASP186 3.4 11.7 1.0
C B:ASP184 3.4 21.0 1.0
C B:ASP186 3.5 14.1 1.0
C B:VAL208 3.6 13.2 1.0
CB B:ASP184 3.7 16.2 1.0
C B:HIS188 3.8 13.5 1.0
CA B:ASP186 3.8 5.4 1.0
C B:LEU185 3.8 11.5 1.0
CB B:HIS209 3.8 5.7 1.0
N B:VAL208 3.9 16.4 1.0
CB B:ASP186 3.9 7.5 1.0
N B:LEU185 4.1 17.4 1.0
OD2 B:ASP184 4.2 15.5 1.0
CA B:ASP184 4.2 19.4 1.0
CB B:SER207 4.2 14.6 1.0
CA B:LEU185 4.3 16.7 1.0
N B:GLY190 4.3 8.1 1.0
N B:HIS188 4.4 13.0 1.0
CA B:HIS209 4.4 18.2 1.0
O B:LEU185 4.4 18.2 1.0
CA B:VAL208 4.4 11.4 1.0
ND1 B:HIS209 4.5 8.2 1.0
CA B:SER207 4.5 20.1 1.0
N B:HIS209 4.5 8.7 1.0
N B:HIS189 4.5 14.4 1.0
C B:SER207 4.5 17.4 1.0
CA B:HIS189 4.6 9.9 1.0
CG B:HIS209 4.6 11.9 1.0
CA B:HIS188 4.7 14.8 1.0
C B:LEU187 4.7 11.2 1.0
N B:LEU187 4.7 8.8 1.0
O B:HOH685 4.8 15.8 1.0
C B:HIS189 4.8 13.7 1.0
CG1 B:VAL208 5.0 11.8 1.0

Potassium binding site 4 out of 8 in 6ht8

Go back to Potassium Binding Sites List in 6ht8
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3


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

b:18.0
occ:1.00
 O B:PHE197 2.5 16.5 1.0
OG B:SER243 2.6 17.3 1.0
O B:VAL203 2.7 28.6 1.0
O B:HOH687 2.9 22.7 1.0
O B:SER200 3.0 30.2 1.0
CB B:SER243 3.5 15.9 1.0
C B:PHE197 3.5 25.9 1.0
O B:SER243 3.8 20.2 1.0
CB B:PHE197 3.9 27.6 1.0
C B:VAL203 3.9 23.3 1.0
C B:SER200 4.0 29.4 1.0
C B:SER243 4.0 16.4 1.0
CA B:PHE197 4.3 25.0 1.0
N B:TRP198 4.4 17.4 1.0
N B:SER200 4.4 28.2 1.0
CA B:SER243 4.4 18.5 1.0
CA B:TRP198 4.4 21.5 1.0
O B:TRP198 4.5 15.3 1.0
CA B:VAL204 4.5 17.4 1.0
C B:TRP198 4.5 26.6 1.0
CA B:SER200 4.6 32.1 1.0
N B:ALA244 4.6 18.5 1.0
N B:VAL204 4.6 22.1 1.0
N B:THR205 4.7 27.5 1.0
O B:GLY240 4.7 32.1 1.0
OG1 B:THR205 4.7 12.4 1.0
CG2 B:THR205 4.8 5.9 1.0
CA B:VAL203 4.9 21.3 1.0
CB B:SER200 4.9 33.5 1.0
N B:PRO201 5.0 19.8 1.0

Potassium binding site 5 out of 8 in 6ht8

Go back to Potassium Binding Sites List in 6ht8
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3


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

b:20.3
occ:1.00
 O C:ASP186 2.5 13.2 1.0
O C:VAL208 2.6 14.4 1.0
OD1 C:ASP184 2.7 18.0 1.0
O C:HIS188 2.8 17.4 1.0
O C:ASP184 2.8 14.4 1.0
OG C:SER207 3.0 16.7 1.0
CG C:ASP184 3.4 20.8 1.0
N C:ASP186 3.4 12.9 1.0
C C:ASP186 3.4 12.3 1.0
C C:ASP184 3.4 14.8 1.0
C C:VAL208 3.6 13.7 1.0
CA C:ASP186 3.7 10.9 1.0
CB C:ASP184 3.7 10.4 1.0
C C:HIS188 3.8 18.4 1.0
CB C:HIS209 3.8 6.6 1.0
C C:LEU185 3.8 15.5 1.0
CB C:ASP186 3.9 11.7 1.0
N C:VAL208 3.9 13.3 1.0
N C:LEU185 4.1 16.0 1.0
CA C:ASP184 4.2 12.4 1.0
CB C:SER207 4.2 15.2 1.0
CA C:LEU185 4.3 19.5 1.0
OD2 C:ASP184 4.3 16.4 1.0
N C:HIS188 4.3 16.5 1.0
ND1 C:HIS209 4.3 6.8 1.0
CA C:HIS209 4.3 13.6 1.0
O C:LEU185 4.4 17.3 1.0
N C:GLY190 4.4 14.2 1.0
CA C:SER207 4.4 20.9 1.0
N C:HIS209 4.4 13.3 1.0
CA C:VAL208 4.5 8.5 1.0
C C:SER207 4.5 18.0 1.0
N C:HIS189 4.5 18.4 1.0
CA C:HIS189 4.5 12.6 1.0
CG C:HIS209 4.6 6.7 1.0
N C:LEU187 4.6 15.2 1.0
CA C:HIS188 4.7 16.5 1.0
C C:LEU187 4.7 14.5 1.0
C C:HIS189 4.8 13.4 1.0
O C:HOH685 5.0 16.4 1.0

Potassium binding site 6 out of 8 in 6ht8

Go back to Potassium Binding Sites List in 6ht8
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3


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

b:21.8
occ:1.00
 O C:PHE197 2.5 16.5 1.0
O C:VAL203 2.6 19.4 1.0
OG C:SER243 2.6 27.4 1.0
O C:HOH658 2.9 15.9 1.0
O C:SER200 3.0 26.9 1.0
O C:SER243 3.4 21.2 1.0
C C:PHE197 3.5 24.6 1.0
CB C:SER243 3.5 23.0 1.0
C C:VAL203 3.8 22.8 1.0
CB C:PHE197 3.9 10.2 1.0
C C:SER243 3.9 16.0 1.0
C C:SER200 4.1 35.0 1.0
CA C:PHE197 4.3 16.0 1.0
N C:TRP198 4.3 22.0 1.0
CA C:SER243 4.4 20.9 1.0
CA C:TRP198 4.4 15.1 1.0
N C:SER200 4.5 26.6 1.0
CA C:VAL204 4.5 25.8 1.0
N C:ALA244 4.5 14.7 1.0
N C:THR205 4.5 22.4 1.0
C C:TRP198 4.6 21.8 1.0
OG1 C:THR205 4.6 15.3 1.0
O C:TRP198 4.6 16.1 1.0
N C:VAL204 4.6 24.4 1.0
CG2 C:THR205 4.7 23.4 1.0
CA C:SER200 4.7 31.6 1.0
CA C:VAL203 4.9 18.7 1.0
CB C:SER200 4.9 38.5 1.0
O C:GLY240 4.9 27.5 1.0
CB C:VAL203 4.9 20.2 1.0
CA C:ALA244 4.9 16.8 1.0
C C:VAL204 5.0 26.0 1.0

Potassium binding site 7 out of 8 in 6ht8

Go back to Potassium Binding Sites List in 6ht8
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3


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

b:21.2
occ:1.00
 OD1 D:ASP184 2.6 17.6 1.0
O D:ASP186 2.6 26.6 1.0
O D:VAL208 2.7 22.1 1.0
O D:ASP184 2.7 14.9 1.0
OG D:SER207 2.8 19.0 1.0
O D:HIS188 2.8 17.7 1.0
CG D:ASP184 3.3 25.4 1.0
C D:ASP184 3.4 19.7 1.0
C D:ASP186 3.5 22.8 1.0
N D:ASP186 3.6 20.1 1.0
C D:VAL208 3.6 19.8 1.0
CB D:ASP186 3.7 11.4 1.0
CB D:ASP184 3.8 11.2 1.0
CA D:ASP186 3.8 12.3 1.0
C D:HIS188 3.8 19.3 1.0
CB D:HIS209 3.8 19.4 1.0
CB D:SER207 3.9 19.6 1.0
C D:LEU185 4.0 21.9 1.0
N D:VAL208 4.0 22.4 1.0
N D:LEU185 4.1 20.8 1.0
CA D:ASP184 4.2 13.8 1.0
ND1 D:HIS209 4.2 28.9 1.0
CA D:SER207 4.3 26.8 1.0
CA D:HIS209 4.3 20.8 1.0
OD2 D:ASP184 4.3 27.2 1.0
N D:GLY190 4.3 13.8 1.0
CA D:LEU185 4.4 20.6 1.0
N D:HIS209 4.4 17.8 1.0
CA D:HIS189 4.4 22.9 1.0
N D:HIS188 4.4 20.9 1.0
C D:SER207 4.5 24.9 1.0
N D:HIS189 4.5 17.7 1.0
CA D:VAL208 4.5 16.7 1.0
CG D:HIS209 4.5 23.2 1.0
O D:LEU185 4.6 17.5 1.0
N D:LEU187 4.6 15.6 1.0
C D:LEU187 4.7 19.6 1.0
CA D:HIS188 4.7 24.2 1.0
C D:HIS189 4.8 15.4 1.0
CE1 D:HIS141 4.8 20.3 1.0
O D:HOH644 4.9 16.3 1.0
CG D:ASP186 4.9 13.9 1.0

Potassium binding site 8 out of 8 in 6ht8

Go back to Potassium Binding Sites List in 6ht8
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 3


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

b:23.9
occ:1.00
 OG D:SER243 2.5 28.3 1.0
O D:PHE197 2.6 12.2 1.0
O D:VAL203 2.6 21.8 1.0
O D:SER200 2.7 30.5 1.0
O D:HOH661 2.8 9.6 1.0
CB D:SER243 3.2 27.8 1.0
O D:SER243 3.4 24.1 1.0
C D:PHE197 3.6 15.6 1.0
C D:SER243 3.7 23.1 1.0
C D:VAL203 3.9 25.4 1.0
C D:SER200 3.9 26.4 1.0
CB D:PHE197 4.0 17.8 1.0
CA D:SER243 4.1 25.0 1.0
N D:ALA244 4.3 18.8 1.0
CA D:PHE197 4.4 16.6 1.0
N D:TRP198 4.5 16.8 1.0
N D:SER200 4.6 28.2 1.0
CA D:VAL204 4.6 25.4 1.0
CA D:TRP198 4.6 13.8 1.0
O D:GLY240 4.6 32.5 1.0
N D:THR205 4.6 25.9 1.0
N D:VAL204 4.7 23.4 1.0
C D:TRP198 4.7 17.7 1.0
O D:TRP198 4.7 17.7 1.0
CA D:SER200 4.7 30.9 1.0
OG1 D:THR205 4.8 19.3 1.0
CA D:VAL203 4.8 26.6 1.0
N D:PRO201 4.9 23.1 1.0
CA D:ALA244 4.9 18.2 1.0
CA D:PRO201 4.9 24.1 1.0
CB D:VAL203 4.9 24.6 1.0
CB D:SER200 4.9 31.5 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 16:27:35 2024

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