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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

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