Atomistry » Potassium » PDB 6f3o-6h6x » 6gxu
Atomistry »
  Potassium »
    PDB 6f3o-6h6x »
      6gxu »

Potassium in PDB 6gxu: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3, PDB code: 6gxu 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) 46.55 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.420, 70.460, 97.910, 77.96, 75.94, 85.97
R / Rfree (%) 20.1 / 24.8

Other elements in 6gxu:

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

Potassium binding site 1 out of 8 in 6gxu

Go back to Potassium Binding Sites List in 6gxu
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 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 An Hydroxamate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:25.8
occ:1.00
 OD1 A:ASP184 2.4 20.1 1.0
O A:ASP186 2.6 29.9 1.0
O A:HIS188 2.7 21.1 1.0
O A:VAL208 2.8 22.3 1.0
OG A:SER207 2.8 21.3 1.0
O A:ASP184 2.9 19.9 1.0
CG A:ASP184 3.2 27.8 1.0
N A:ASP186 3.3 28.2 1.0
C A:ASP184 3.4 23.4 1.0
C A:ASP186 3.5 33.0 1.0
CB A:ASP184 3.6 21.7 1.0
CA A:ASP186 3.7 25.4 1.0
C A:HIS188 3.8 18.0 1.0
C A:VAL208 3.8 21.1 1.0
C A:LEU185 3.9 20.1 1.0
CB A:ASP186 3.9 28.9 1.0
CB A:SER207 4.0 18.6 1.0
N A:VAL208 4.0 24.1 1.0
CB A:HIS209 4.0 13.6 1.0
N A:LEU185 4.0 20.4 1.0
CA A:ASP184 4.1 24.7 1.0
OD2 A:ASP184 4.1 25.5 1.0
N A:GLY190 4.3 20.0 1.0
CA A:LEU185 4.3 17.1 1.0
CA A:SER207 4.3 24.1 1.0
ND1 A:HIS209 4.4 24.1 1.0
CA A:HIS189 4.5 19.4 1.0
N A:HIS188 4.5 17.0 1.0
C A:SER207 4.5 26.9 1.0
N A:HIS189 4.5 15.8 1.0
CA A:HIS209 4.5 20.6 1.0
O A:LEU185 4.6 23.9 1.0
CA A:VAL208 4.6 25.3 1.0
N A:HIS209 4.6 21.6 1.0
C A:HIS189 4.7 19.9 1.0
N A:LEU187 4.7 29.2 1.0
CG A:HIS209 4.7 21.5 1.0
CA A:HIS188 4.8 18.6 1.0
C A:LEU187 4.8 22.7 1.0
CE1 A:HIS141 4.9 27.4 1.0
O A:HOH681 5.0 22.2 1.0

Potassium binding site 2 out of 8 in 6gxu

Go back to Potassium Binding Sites List in 6gxu
Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 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 An Hydroxamate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:31.0
occ:1.00
 O A:VAL203 2.5 25.0 1.0
O A:PHE197 2.6 26.2 1.0
OG A:SER243 2.7 30.3 1.0
O A:SER200 2.8 35.2 0.5
O A:SER200 2.9 35.1 0.5
O A:HOH658 3.0 23.0 1.0
CB A:SER243 3.5 26.2 1.0
O A:SER243 3.5 20.0 1.0
C A:PHE197 3.5 26.6 1.0
C A:VAL203 3.7 24.7 1.0
CB A:PHE197 3.8 24.5 1.0
C A:SER200 3.9 33.5 0.5
C A:SER200 3.9 33.5 0.5
C A:SER243 3.9 25.3 1.0
CA A:PHE197 4.3 20.2 1.0
CA A:SER243 4.4 24.1 1.0
N A:SER200 4.4 22.7 0.5
N A:SER200 4.4 22.3 0.5
CA A:VAL204 4.4 20.3 1.0
N A:TRP198 4.5 25.2 1.0
N A:VAL204 4.5 19.6 1.0
CA A:SER200 4.6 29.6 0.5
CG2 A:THR205 4.6 20.6 1.0
CA A:SER200 4.6 29.7 0.5
OG1 A:THR205 4.6 26.7 1.0
N A:ALA244 4.6 19.9 1.0
N A:THR205 4.6 29.1 1.0
C A:TRP198 4.7 32.4 1.0
CA A:TRP198 4.7 27.1 1.0
O A:TRP198 4.7 26.7 1.0
CA A:VAL203 4.8 21.1 1.0
CB A:SER200 4.8 24.8 0.5
CB A:SER200 4.8 24.9 0.5
CB A:VAL203 4.9 25.6 1.0
N A:PRO201 4.9 34.9 1.0
O A:GLY240 4.9 27.3 1.0
OG A:SER200 5.0 26.8 0.5
N A:VAL203 5.0 25.4 1.0
C A:VAL204 5.0 27.2 1.0

Potassium binding site 3 out of 8 in 6gxu

Go back to Potassium Binding Sites List in 6gxu
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 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 An Hydroxamate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:27.0
occ:1.00
 O B:ASP186 2.5 21.7 1.0
O B:VAL208 2.6 20.5 1.0
OD1 B:ASP184 2.6 25.8 1.0
O B:ASP184 2.7 30.4 1.0
O B:HIS188 2.8 20.3 1.0
OG B:SER207 2.9 25.5 1.0
N B:ASP186 3.3 24.6 1.0
C B:ASP184 3.3 28.3 1.0
C B:ASP186 3.4 19.8 1.0
CG B:ASP184 3.4 31.2 1.0
C B:VAL208 3.6 22.3 1.0
CA B:ASP186 3.7 21.9 1.0
CB B:ASP184 3.8 20.8 1.0
C B:LEU185 3.8 20.4 1.0
C B:HIS188 3.8 25.0 1.0
CB B:HIS209 3.8 19.6 1.0
CB B:ASP186 3.8 25.7 1.0
N B:VAL208 3.9 26.9 1.0
N B:LEU185 4.0 24.6 1.0
CB B:SER207 4.1 20.6 1.0
CA B:ASP184 4.2 28.7 1.0
CA B:LEU185 4.2 21.3 1.0
ND1 B:HIS209 4.3 19.5 1.0
CA B:HIS209 4.3 25.5 1.0
OD2 B:ASP184 4.4 26.2 1.0
CA B:SER207 4.4 28.6 1.0
N B:GLY190 4.4 24.3 1.0
N B:HIS209 4.4 23.6 1.0
N B:HIS188 4.4 18.3 1.0
CA B:VAL208 4.5 24.6 1.0
O B:LEU185 4.5 27.3 1.0
CA B:HIS189 4.5 23.7 1.0
C B:SER207 4.5 31.6 1.0
N B:HIS189 4.5 17.6 1.0
N B:LEU187 4.6 17.6 1.0
CG B:HIS209 4.6 20.1 1.0
O B:HOH684 4.6 25.5 1.0
C B:LEU187 4.6 24.8 1.0
C B:HIS189 4.8 19.8 1.0
CA B:HIS188 4.8 30.0 1.0
O B:LEU187 5.0 26.4 1.0

Potassium binding site 4 out of 8 in 6gxu

Go back to Potassium Binding Sites List in 6gxu
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 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 An Hydroxamate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:27.0
occ:1.00
 O B:VAL203 2.5 25.4 1.0
O B:PHE197 2.6 30.9 1.0
OG B:SER243 2.7 31.1 1.0
O B:HOH694 2.8 21.0 1.0
O B:SER200 2.9 37.0 1.0
CB B:SER243 3.4 36.6 1.0
C B:PHE197 3.5 29.2 1.0
O B:SER243 3.6 26.6 1.0
C B:VAL203 3.8 31.5 1.0
CB B:PHE197 3.8 28.0 1.0
C B:SER243 4.0 29.3 1.0
C B:SER200 4.1 35.2 1.0
CA B:PHE197 4.3 32.6 1.0
CA B:SER243 4.3 29.6 1.0
N B:TRP198 4.4 28.0 1.0
N B:SER200 4.5 27.3 1.0
N B:ALA244 4.6 31.1 1.0
CA B:TRP198 4.6 27.4 1.0
CA B:VAL204 4.6 24.9 1.0
N B:VAL204 4.6 26.4 1.0
N B:THR205 4.7 21.3 1.0
CG2 B:THR205 4.7 26.6 1.0
CA B:VAL203 4.7 22.8 1.0
CA B:SER200 4.7 35.7 1.0
C B:TRP198 4.7 26.4 1.0
CB B:VAL203 4.8 18.4 1.0
O B:TRP198 4.8 24.4 1.0
CB B:SER200 4.9 45.7 1.0
OG1 B:THR205 4.9 21.4 1.0
N B:VAL203 4.9 22.7 1.0
O B:GLY240 4.9 28.3 1.0
CA B:ALA244 5.0 28.8 1.0
CB B:ALA244 5.0 20.6 1.0

Potassium binding site 5 out of 8 in 6gxu

Go back to Potassium Binding Sites List in 6gxu
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 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 An Hydroxamate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:23.6
occ:1.00
 O C:ASP186 2.5 22.8 1.0
O C:VAL208 2.6 19.9 1.0
O C:ASP184 2.6 16.8 1.0
OD1 C:ASP184 2.7 25.7 1.0
O C:HIS188 2.8 20.0 1.0
OG C:SER207 3.0 25.1 1.0
C C:ASP184 3.3 18.4 1.0
N C:ASP186 3.3 18.8 1.0
CG C:ASP184 3.4 23.4 1.0
C C:ASP186 3.4 18.9 1.0
C C:VAL208 3.6 13.2 1.0
CA C:ASP186 3.7 17.2 1.0
C C:HIS188 3.8 21.4 1.0
CB C:ASP184 3.8 12.5 1.0
CB C:ASP186 3.8 17.9 1.0
C C:LEU185 3.8 21.0 1.0
N C:VAL208 3.9 26.7 1.0
CB C:HIS209 3.9 23.8 1.0
N C:LEU185 3.9 18.9 1.0
CA C:ASP184 4.1 17.4 1.0
CB C:SER207 4.1 19.3 1.0
CA C:LEU185 4.2 19.4 1.0
OD2 C:ASP184 4.3 30.1 1.0
CA C:HIS209 4.3 25.2 1.0
CA C:SER207 4.3 16.3 1.0
ND1 C:HIS209 4.4 19.3 1.0
N C:GLY190 4.4 17.2 1.0
C C:SER207 4.4 25.8 1.0
CA C:VAL208 4.4 23.7 1.0
N C:HIS209 4.4 19.2 1.0
CA C:HIS189 4.4 25.2 1.0
N C:HIS189 4.5 19.2 1.0
N C:HIS188 4.5 24.5 1.0
O C:LEU185 4.5 27.5 1.0
CG C:HIS209 4.6 18.9 1.0
N C:LEU187 4.6 21.0 1.0
O C:HOH683 4.7 25.6 1.0
C C:HIS189 4.7 22.7 1.0
C C:LEU187 4.7 26.2 1.0
CA C:HIS188 4.8 22.3 1.0
CG1 C:VAL208 4.9 27.6 1.0

Potassium binding site 6 out of 8 in 6gxu

Go back to Potassium Binding Sites List in 6gxu
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 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 An Hydroxamate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:28.0
occ:1.00
 O C:PHE197 2.5 24.7 1.0
O C:VAL203 2.6 30.5 1.0
OG C:SER243 2.6 28.2 1.0
O C:HOH677 2.7 26.8 1.0
O C:SER200 2.9 26.9 1.0
O C:SER243 3.4 22.4 1.0
CB C:SER243 3.4 22.7 1.0
C C:PHE197 3.5 27.2 1.0
C C:VAL203 3.8 27.4 1.0
CB C:PHE197 3.9 16.4 1.0
C C:SER243 3.9 24.3 1.0
C C:SER200 4.0 30.0 1.0
CA C:PHE197 4.3 22.0 1.0
CA C:SER243 4.3 21.1 1.0
N C:SER200 4.4 29.0 1.0
N C:TRP198 4.4 28.7 1.0
CA C:VAL204 4.5 20.4 1.0
CA C:TRP198 4.5 25.1 1.0
O C:TRP198 4.6 30.7 1.0
C C:TRP198 4.6 26.6 1.0
N C:VAL204 4.6 27.5 1.0
CG2 C:THR205 4.6 25.2 1.0
CA C:SER200 4.6 32.4 1.0
N C:ALA244 4.6 23.6 1.0
N C:THR205 4.7 25.1 1.0
OG1 C:THR205 4.8 20.6 1.0
O C:GLY240 4.8 24.2 1.0
CA C:VAL203 4.8 26.3 1.0
CB C:SER200 4.8 39.6 1.0
CB C:VAL203 4.9 21.7 1.0
CB C:ALA244 4.9 17.7 1.0
CA C:ALA244 4.9 21.0 1.0
N C:PRO201 5.0 30.3 1.0

Potassium binding site 7 out of 8 in 6gxu

Go back to Potassium Binding Sites List in 6gxu
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 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 An Hydroxamate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:26.3
occ:1.00
 O D:ASP186 2.6 23.5 1.0
OD1 D:ASP184 2.6 32.4 1.0
O D:HIS188 2.7 19.1 1.0
O D:VAL208 2.8 23.4 1.0
O D:ASP184 2.9 20.6 1.0
OG D:SER207 2.9 20.6 1.0
N D:ASP186 3.2 30.4 1.0
CG D:ASP184 3.3 32.5 1.0
C D:ASP186 3.4 22.6 1.0
C D:ASP184 3.5 25.1 1.0
CA D:ASP186 3.6 30.4 1.0
C D:HIS188 3.7 21.6 1.0
CB D:ASP186 3.7 30.2 1.0
CB D:ASP184 3.7 21.1 1.0
C D:VAL208 3.8 19.6 1.0
CB D:HIS209 3.9 22.5 1.0
C D:LEU185 3.9 20.9 1.0
N D:VAL208 4.0 25.9 1.0
CB D:SER207 4.1 22.7 1.0
N D:LEU185 4.1 22.0 1.0
OD2 D:ASP184 4.2 27.0 1.0
CA D:ASP184 4.2 29.0 1.0
ND1 D:HIS209 4.3 27.3 1.0
N D:GLY190 4.3 23.8 1.0
CA D:LEU185 4.4 22.3 1.0
CA D:HIS189 4.4 22.6 1.0
N D:HIS189 4.4 19.0 1.0
N D:HIS188 4.4 26.2 1.0
CA D:HIS209 4.4 28.9 1.0
CA D:SER207 4.5 30.1 1.0
CG D:HIS209 4.6 24.3 1.0
N D:LEU187 4.6 15.8 1.0
N D:HIS209 4.6 22.0 1.0
C D:SER207 4.6 28.3 1.0
CA D:VAL208 4.6 27.0 1.0
O D:LEU185 4.6 22.6 1.0
C D:HIS189 4.7 21.6 1.0
CA D:HIS188 4.7 25.5 1.0
C D:LEU187 4.7 24.1 1.0
CE1 D:HIS141 4.8 29.9 1.0
O D:HOH681 4.9 24.9 1.0
CG D:ASP186 4.9 29.0 1.0

Potassium binding site 8 out of 8 in 6gxu

Go back to Potassium Binding Sites List in 6gxu
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 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 An Hydroxamate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:31.1
occ:1.00
 OG D:SER243 2.6 28.2 1.0
O D:VAL203 2.6 22.9 1.0
O D:PHE197 2.7 24.8 1.0
O D:SER200 2.9 29.1 1.0
O D:HOH660 2.9 22.0 1.0
CB D:SER243 3.4 29.6 1.0
O D:SER243 3.4 26.5 1.0
C D:PHE197 3.7 29.9 1.0
C D:VAL203 3.8 28.9 1.0
C D:SER243 3.8 29.6 1.0
C D:SER200 4.0 28.2 1.0
CB D:PHE197 4.0 34.1 1.0
CA D:SER243 4.3 24.4 1.0
N D:ALA244 4.4 21.7 1.0
N D:SER200 4.4 25.5 1.0
CA D:VAL204 4.5 19.9 1.0
CA D:PHE197 4.5 25.6 1.0
N D:TRP198 4.5 22.6 1.0
N D:VAL204 4.6 23.4 1.0
OG1 D:THR205 4.6 26.0 1.0
O D:TRP198 4.6 28.6 1.0
N D:THR205 4.6 23.9 1.0
CA D:TRP198 4.6 32.3 1.0
C D:TRP198 4.6 29.4 1.0
CA D:SER200 4.7 26.2 1.0
CA D:VAL203 4.8 27.2 1.0
CG2 D:THR205 4.8 21.8 1.0
O D:GLY240 4.8 25.0 1.0
CB D:SER200 4.8 23.5 1.0
N D:PRO201 4.9 29.0 1.0
CA D:ALA244 4.9 31.0 1.0
CB D:VAL203 4.9 24.9 1.0
N D:VAL203 4.9 26.4 1.0
CA D:PRO201 5.0 33.1 1.0
C D:VAL204 5.0 29.1 1.0

Reference:

T.Bayer, A.Chakrabarti, J.Lancelot, T.B.Shaik, K.Hausmann, J.Melesina, K.Schmidtkunz, M.Marek, F.Erdmann, M.Schmidt, D.Robaa, C.Romier, R.J.Pierce, M.Jung, W.Sippl. Synthesis, Crystallization Studies, and in Vitro Characterization of Cinnamic Acid Derivatives As SMHDAC8 Inhibitors For the Treatment of Schistosomiasis. Chemmedchem V. 13 1517 2018.
ISSN: ESSN 1860-7187
PubMed: 29806110
DOI: 10.1002/CMDC.201800238
Page generated: Mon Aug 12 16:15:08 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