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Potassium in PDB 6gxw: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4, PDB code: 6gxw 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 / 2.07
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.800, 70.990, 98.200, 75.58, 77.93, 85.56
R / Rfree (%) 18.9 / 24.7

Other elements in 6gxw:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4 also contains other interesting chemical elements:

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

Potassium binding site 1 out of 8 in 6gxw

Go back to Potassium Binding Sites List in 6gxw
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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

b:22.0
occ:1.00
 OD1 A:ASP184 2.6 23.5 1.0
O A:VAL208 2.6 20.9 1.0
O A:ASP186 2.6 19.9 1.0
OG A:SER207 2.7 15.5 1.0
O A:HIS188 2.8 22.2 1.0
O A:ASP184 2.9 22.3 1.0
CG A:ASP184 3.3 28.5 1.0
C A:ASP184 3.4 18.7 1.0
N A:ASP186 3.5 16.4 1.0
C A:ASP186 3.5 19.9 1.0
C A:VAL208 3.7 23.6 1.0
CB A:ASP184 3.7 9.8 1.0
CB A:HIS209 3.7 16.9 1.0
C A:HIS188 3.8 29.4 1.0
CA A:ASP186 3.8 13.5 1.0
CB A:SER207 3.9 21.6 1.0
CB A:ASP186 3.9 12.9 1.0
C A:LEU185 4.0 23.4 1.0
N A:VAL208 4.0 21.1 1.0
N A:LEU185 4.1 16.3 1.0
CA A:ASP184 4.2 17.8 1.0
ND1 A:HIS209 4.2 16.1 1.0
N A:GLY190 4.3 20.1 1.0
OD2 A:ASP184 4.3 20.9 1.0
CA A:SER207 4.3 24.5 1.0
CA A:HIS209 4.3 24.4 1.0
CA A:LEU185 4.3 27.6 1.0
CA A:HIS189 4.4 18.4 1.0
N A:HIS188 4.4 21.0 1.0
C A:SER207 4.4 24.2 1.0
N A:HIS209 4.4 17.7 1.0
CG A:HIS209 4.5 18.8 1.0
N A:HIS189 4.5 16.2 1.0
CA A:VAL208 4.5 19.9 1.0
C A:HIS189 4.7 24.4 1.0
O A:LEU185 4.7 18.2 1.0
C A:LEU187 4.7 25.2 1.0
N A:LEU187 4.7 20.0 1.0
CA A:HIS188 4.8 24.1 1.0
CE1 A:HIS141 4.9 32.3 1.0
O A:HOH660 4.9 27.1 1.0

Potassium binding site 2 out of 8 in 6gxw

Go back to Potassium Binding Sites List in 6gxw
Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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

b:25.4
occ:1.00
 O A:VAL203 2.5 25.3 1.0
O A:PHE197 2.6 20.6 1.0
OG A:SER243 2.7 25.8 1.0
O A:SER200 2.9 34.2 1.0
O A:HOH634 2.9 18.2 1.0
CB A:SER243 3.4 17.1 1.0
O A:SER243 3.6 22.9 1.0
C A:PHE197 3.6 24.6 1.0
C A:VAL203 3.7 25.4 1.0
CB A:PHE197 3.9 21.6 1.0
C A:SER243 3.9 18.9 1.0
C A:SER200 4.0 29.1 1.0
CA A:SER243 4.3 22.3 1.0
OG1 A:THR205 4.3 20.9 1.0
CA A:PHE197 4.4 22.9 1.0
CA A:VAL204 4.4 25.2 1.0
N A:SER200 4.5 25.5 1.0
N A:TRP198 4.5 18.6 1.0
N A:VAL204 4.5 24.5 1.0
N A:THR205 4.5 31.0 1.0
N A:ALA244 4.6 16.8 1.0
CA A:TRP198 4.7 22.4 1.0
CA A:SER200 4.7 24.6 1.0
C A:TRP198 4.7 24.3 1.0
O A:TRP198 4.8 23.4 1.0
CA A:VAL203 4.8 15.3 1.0
CG2 A:THR205 4.8 14.6 1.0
CB A:VAL203 4.9 20.8 1.0
C A:VAL204 4.9 24.6 1.0
CB A:SER200 4.9 25.3 1.0
N A:VAL203 4.9 22.9 1.0
O A:GLY240 4.9 19.5 1.0
CA A:ALA244 5.0 17.0 1.0
N A:PRO201 5.0 32.0 1.0

Potassium binding site 3 out of 8 in 6gxw

Go back to Potassium Binding Sites List in 6gxw
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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

b:23.2
occ:1.00
 O B:VAL208 2.5 11.8 1.0
O B:ASP186 2.6 16.0 1.0
OD1 B:ASP184 2.7 25.5 1.0
O B:HIS188 2.7 15.4 1.0
O B:ASP184 2.8 19.1 1.0
OG B:SER207 3.0 15.5 1.0
N B:ASP186 3.3 9.3 1.0
C B:ASP184 3.4 23.2 1.0
C B:ASP186 3.4 22.2 1.0
CG B:ASP184 3.4 16.0 1.0
C B:VAL208 3.6 13.1 1.0
CB B:HIS209 3.7 19.0 1.0
CA B:ASP186 3.7 17.9 1.0
C B:HIS188 3.8 19.8 1.0
C B:LEU185 3.8 10.8 1.0
CB B:ASP184 3.8 10.2 1.0
CB B:ASP186 3.9 19.9 1.0
N B:VAL208 4.1 19.7 1.0
N B:LEU185 4.1 9.1 1.0
CB B:SER207 4.1 19.8 1.0
CA B:ASP184 4.2 16.4 1.0
CA B:LEU185 4.2 11.5 1.0
CA B:HIS209 4.2 14.4 1.0
OD2 B:ASP184 4.3 23.9 1.0
CA B:SER207 4.4 16.1 1.0
N B:HIS209 4.4 14.9 1.0
O B:LEU185 4.4 20.7 1.0
N B:HIS188 4.4 25.9 1.0
ND1 B:HIS209 4.4 20.6 1.0
N B:GLY190 4.5 19.1 1.0
C B:SER207 4.5 18.0 1.0
CA B:HIS189 4.5 23.9 1.0
CA B:VAL208 4.5 17.0 1.0
N B:HIS189 4.5 18.6 1.0
CG B:HIS209 4.6 17.9 1.0
N B:LEU187 4.6 26.3 1.0
C B:LEU187 4.7 27.1 1.0
CA B:HIS188 4.7 26.9 1.0
O B:HOH696 4.8 16.2 1.0
C B:HIS189 4.8 20.0 1.0
CG1 B:VAL208 5.0 24.6 1.0

Potassium binding site 4 out of 8 in 6gxw

Go back to Potassium Binding Sites List in 6gxw
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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

b:26.3
occ:1.00
 O B:PHE197 2.5 26.2 1.0
O B:VAL203 2.6 24.5 1.0
OG B:SER243 2.7 18.2 1.0
O B:HOH657 2.8 24.4 1.0
O B:SER200 2.8 26.5 1.0
CB B:SER243 3.3 22.2 1.0
O B:SER243 3.5 24.5 1.0
C B:PHE197 3.6 26.7 1.0
C B:VAL203 3.8 24.8 1.0
CB B:PHE197 3.9 21.1 1.0
C B:SER200 3.9 27.7 1.0
C B:SER243 3.9 23.4 1.0
CA B:SER243 4.3 22.1 1.0
N B:SER200 4.3 24.2 1.0
CA B:PHE197 4.4 19.0 1.0
CA B:VAL204 4.4 23.5 1.0
CA B:SER200 4.5 27.2 1.0
N B:TRP198 4.5 22.9 1.0
N B:THR205 4.6 15.8 1.0
N B:VAL204 4.6 23.4 1.0
CG2 B:THR205 4.6 21.5 1.0
N B:ALA244 4.6 18.4 1.0
CB B:SER200 4.6 34.5 1.0
CA B:TRP198 4.6 21.0 1.0
C B:TRP198 4.7 24.8 1.0
O B:TRP198 4.7 26.4 1.0
OG1 B:THR205 4.7 22.4 1.0
CA B:VAL203 4.8 15.4 1.0
O B:GLY240 4.9 21.0 1.0
N B:PRO201 4.9 30.0 1.0
CB B:VAL203 5.0 14.1 1.0
C B:VAL204 5.0 14.3 1.0
N B:VAL203 5.0 24.2 1.0

Potassium binding site 5 out of 8 in 6gxw

Go back to Potassium Binding Sites List in 6gxw
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K803

b:22.1
occ:1.00
 O C:VAL208 2.6 16.1 1.0
O C:ASP186 2.6 17.8 1.0
OD1 C:ASP184 2.7 27.9 1.0
O C:ASP184 2.7 19.7 1.0
O C:HIS188 2.8 14.6 1.0
OG C:SER207 3.1 16.0 1.0
N C:ASP186 3.2 19.0 1.0
CG C:ASP184 3.3 17.5 1.0
C C:ASP184 3.4 18.4 1.0
C C:ASP186 3.4 17.5 1.0
C C:VAL208 3.6 13.5 1.0
CA C:ASP186 3.6 20.5 1.0
CB C:ASP186 3.7 18.6 1.0
CB C:ASP184 3.7 9.5 1.0
C C:HIS188 3.8 15.6 1.0
C C:LEU185 3.8 20.0 1.0
CB C:HIS209 3.9 14.3 1.0
N C:VAL208 3.9 22.7 1.0
N C:LEU185 4.0 12.3 1.0
CA C:ASP184 4.2 10.8 1.0
OD2 C:ASP184 4.2 19.9 1.0
CA C:LEU185 4.2 8.5 1.0
CB C:SER207 4.2 20.9 1.0
CA C:HIS209 4.3 16.3 1.0
N C:HIS188 4.4 20.0 1.0
N C:GLY190 4.4 25.1 1.0
N C:HIS209 4.4 19.0 1.0
CA C:VAL208 4.4 14.5 1.0
ND1 C:HIS209 4.4 10.3 1.0
CA C:SER207 4.5 21.1 1.0
N C:HIS189 4.5 18.5 1.0
CA C:HIS189 4.5 23.1 1.0
C C:SER207 4.5 23.4 1.0
O C:LEU185 4.6 21.1 1.0
N C:LEU187 4.6 21.3 1.0
CG C:HIS209 4.6 14.0 1.0
C C:LEU187 4.7 19.8 1.0
CA C:HIS188 4.7 25.2 1.0
C C:HIS189 4.8 26.0 1.0
CG C:ASP186 5.0 18.0 1.0
CG1 C:VAL208 5.0 18.5 1.0

Potassium binding site 6 out of 8 in 6gxw

Go back to Potassium Binding Sites List in 6gxw
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K804

b:25.6
occ:1.00
 O C:PHE197 2.5 18.8 1.0
O C:VAL203 2.6 20.1 1.0
OG C:SER243 2.6 14.4 1.0
O C:HOH982 2.7 17.4 1.0
O C:SER200 2.8 33.9 1.0
C C:PHE197 3.4 23.5 1.0
O C:SER243 3.5 22.9 1.0
CB C:SER243 3.6 17.1 1.0
CB C:PHE197 3.8 27.0 1.0
C C:VAL203 3.8 23.1 1.0
C C:SER243 3.9 20.2 1.0
C C:SER200 4.0 30.6 1.0
CA C:PHE197 4.2 25.7 1.0
N C:TRP198 4.3 25.6 1.0
CA C:SER243 4.4 14.7 1.0
N C:SER200 4.4 32.2 1.0
CA C:TRP198 4.5 20.7 1.0
CA C:VAL204 4.5 22.5 1.0
O C:TRP198 4.6 29.9 1.0
C C:TRP198 4.6 28.6 1.0
N C:ALA244 4.6 24.3 1.0
N C:VAL204 4.6 21.4 1.0
CA C:SER200 4.7 31.9 1.0
N C:THR205 4.7 19.6 1.0
CG2 C:THR205 4.7 17.4 1.0
O C:GLY240 4.8 19.1 1.0
CA C:VAL203 4.8 20.4 1.0
OG1 C:THR205 4.9 20.8 1.0
N C:PRO201 4.9 21.7 1.0
CB C:SER200 4.9 27.9 1.0
CA C:ALA244 5.0 16.4 1.0
N C:VAL203 5.0 25.3 1.0
CB C:VAL203 5.0 19.6 1.0

Potassium binding site 7 out of 8 in 6gxw

Go back to Potassium Binding Sites List in 6gxw
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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

b:20.7
occ:1.00
 OD1 D:ASP184 2.6 28.9 1.0
O D:ASP186 2.7 30.6 1.0
O D:VAL208 2.7 20.6 1.0
O D:HIS188 2.8 24.1 1.0
O D:ASP184 2.8 20.9 1.0
OG D:SER207 2.9 24.4 1.0
CG D:ASP184 3.3 24.2 1.0
N D:ASP186 3.3 22.1 1.0
C D:ASP186 3.5 25.6 1.0
C D:ASP184 3.5 17.8 1.0
CB D:ASP184 3.7 18.8 1.0
CA D:ASP186 3.7 20.0 1.0
C D:VAL208 3.7 18.3 1.0
C D:HIS188 3.8 25.3 1.0
CB D:ASP186 3.8 21.8 1.0
CB D:HIS209 3.8 11.9 1.0
C D:LEU185 3.9 18.3 1.0
CB D:SER207 4.0 24.3 1.0
N D:VAL208 4.0 24.5 1.0
OD2 D:ASP184 4.1 28.1 1.0
N D:LEU185 4.1 13.8 1.0
CA D:ASP184 4.2 17.3 1.0
N D:GLY190 4.3 25.0 1.0
CA D:SER207 4.3 23.9 1.0
ND1 D:HIS209 4.3 22.9 1.0
CA D:HIS189 4.3 24.0 1.0
CA D:LEU185 4.4 13.5 1.0
CA D:HIS209 4.4 13.9 1.0
C D:SER207 4.4 17.2 1.0
N D:HIS189 4.4 14.7 1.0
N D:HIS209 4.5 18.4 1.0
N D:HIS188 4.5 15.1 1.0
CG D:HIS209 4.5 15.8 1.0
CA D:VAL208 4.6 14.8 1.0
C D:HIS189 4.6 29.6 1.0
N D:LEU187 4.6 20.1 1.0
O D:LEU185 4.7 17.0 1.0
CE1 D:HIS141 4.7 23.1 1.0
CA D:HIS188 4.8 22.1 1.0
C D:LEU187 4.8 21.3 1.0
O D:HOH637 4.8 27.4 1.0
CG D:ASP186 5.0 26.6 1.0
OD1 D:ASP186 5.0 20.1 1.0

Potassium binding site 8 out of 8 in 6gxw

Go back to Potassium Binding Sites List in 6gxw
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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

b:22.2
occ:1.00
 O D:PHE197 2.5 21.6 1.0
OG D:SER243 2.6 28.5 1.0
O D:VAL203 2.7 35.0 1.0
O D:HOH622 2.8 19.0 1.0
O D:SER200 2.9 21.1 1.0
C D:PHE197 3.4 20.7 1.0
CB D:SER243 3.4 27.2 1.0
O D:SER243 3.6 18.4 1.0
CB D:PHE197 3.9 14.6 1.0
C D:SER200 3.9 23.4 1.0
C D:VAL203 3.9 27.5 1.0
C D:SER243 3.9 26.0 1.0
N D:TRP198 4.2 19.3 1.0
N D:SER200 4.3 26.9 1.0
CA D:PHE197 4.3 20.3 1.0
CA D:SER243 4.4 27.7 1.0
CA D:TRP198 4.4 17.1 1.0
C D:TRP198 4.5 22.7 1.0
O D:TRP198 4.5 23.2 1.0
CA D:SER200 4.5 36.6 1.0
N D:ALA244 4.5 20.3 1.0
OG1 D:THR205 4.6 23.4 1.0
CA D:VAL204 4.7 28.2 1.0
N D:VAL204 4.7 29.1 1.0
N D:THR205 4.7 22.4 1.0
CB D:SER200 4.8 40.8 1.0
O D:GLY240 4.8 27.2 1.0
CG2 D:THR205 4.8 21.7 1.0
N D:PRO201 4.9 20.9 1.0
CA D:VAL203 4.9 25.1 1.0
CA D:ALA244 5.0 25.3 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 16:15:54 2024

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