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Potassium in PDB 5fue: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate, PDB code: 5fue was solved by M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.145 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.955, 70.669, 98.656, 77.99, 75.41, 85.40
R / Rfree (%) 14.76 / 19.57

Other elements in 5fue:

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

Potassium binding site 1 out of 8 in 5fue

Go back to Potassium Binding Sites List in 5fue
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K600

b:17.2
occ:1.00
 O A:VAL208 2.7 15.9 1.0
OD1 A:ASP184 2.7 20.1 1.0
O A:ASP186 2.7 21.6 1.0
O A:HIS188 2.8 14.2 1.0
O A:ASP184 2.8 15.6 1.0
OG A:SER207 2.9 12.7 1.0
N A:ASP186 3.4 15.0 1.0
CG A:ASP184 3.4 21.7 1.0
C A:ASP184 3.4 20.4 1.0
C A:ASP186 3.5 18.3 1.0
C A:VAL208 3.6 17.5 1.0
C A:HIS188 3.8 16.0 1.0
CA A:ASP186 3.8 12.9 1.0
CB A:ASP184 3.8 20.9 1.0
CB A:HIS209 3.8 12.6 1.0
C A:LEU185 3.9 20.0 1.0
N A:VAL208 3.9 17.6 1.0
CB A:ASP186 3.9 15.8 1.0
N A:LEU185 4.0 15.0 1.0
CB A:SER207 4.0 15.0 1.0
CA A:ASP184 4.2 17.6 1.0
CA A:LEU185 4.3 15.0 1.0
ND1 A:HIS209 4.3 17.1 1.0
N A:GLY190 4.3 17.1 1.0
OD2 A:ASP184 4.3 18.0 1.0
CA A:SER207 4.3 15.5 1.0
CA A:HIS189 4.4 17.2 1.0
CA A:HIS209 4.4 17.8 1.0
C A:SER207 4.4 18.2 1.0
N A:HIS189 4.5 10.2 1.0
CA A:VAL208 4.5 15.8 1.0
N A:HIS209 4.5 16.5 1.0
N A:HIS188 4.5 13.1 1.0
CG A:HIS209 4.6 14.9 1.0
O A:LEU185 4.6 19.2 1.0
C A:HIS189 4.7 17.6 1.0
N A:LEU187 4.7 17.2 1.0
O A:HOH2084 4.7 21.5 1.0
CA A:HIS188 4.8 15.8 1.0
C A:LEU187 4.8 17.9 1.0
CE1 A:HIS141 4.9 18.8 1.0

Potassium binding site 2 out of 8 in 5fue

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Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:20.7
occ:1.00
 O A:VAL203 2.6 24.1 1.0
O A:PHE197 2.6 19.1 1.0
OG A:SER243 2.6 17.8 1.0
O A:HOH2089 2.8 14.8 1.0
O A:SER200 2.8 22.5 1.0
CB A:SER243 3.4 16.9 1.0
O A:SER243 3.5 21.0 1.0
C A:PHE197 3.5 18.1 1.0
C A:VAL203 3.8 25.1 1.0
C A:SER243 3.9 18.7 1.0
CB A:PHE197 3.9 16.1 1.0
C A:SER200 4.0 24.5 1.0
CA A:SER243 4.3 20.5 1.0
CA A:PHE197 4.4 15.3 1.0
N A:TRP198 4.4 20.4 1.0
N A:SER200 4.5 21.4 1.0
CA A:VAL204 4.5 19.9 1.0
N A:ALA244 4.5 16.4 1.0
CA A:TRP198 4.6 22.9 1.0
N A:THR205 4.6 17.1 1.0
N A:VAL204 4.6 21.2 1.0
CG2 A:THR205 4.6 17.0 1.0
C A:TRP198 4.7 17.4 1.0
CA A:SER200 4.7 24.8 1.0
O A:TRP198 4.7 15.6 1.0
OG1 A:THR205 4.8 20.1 1.0
CA A:VAL203 4.8 21.7 1.0
O A:GLY240 4.8 16.9 1.0
CB A:VAL203 4.9 19.4 1.0
CA A:ALA244 4.9 17.4 1.0
CB A:SER200 5.0 27.1 1.0
N A:PRO201 5.0 21.5 1.0
N A:VAL203 5.0 16.6 1.0
CB A:ALA244 5.0 14.6 1.0

Potassium binding site 3 out of 8 in 5fue

Go back to Potassium Binding Sites List in 5fue
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K600

b:16.4
occ:1.00
 O B:ASP186 2.6 13.3 1.0
O B:VAL208 2.7 15.1 1.0
O B:ASP184 2.7 16.7 1.0
OD1 B:ASP184 2.7 14.2 1.0
O B:HIS188 2.8 13.8 1.0
OG B:SER207 3.0 12.0 1.0
N B:ASP186 3.3 12.4 1.0
C B:ASP184 3.4 14.9 1.0
CG B:ASP184 3.4 16.9 1.0
C B:ASP186 3.5 18.9 1.0
C B:VAL208 3.7 15.9 1.0
CA B:ASP186 3.7 17.3 1.0
CB B:ASP184 3.8 14.2 1.0
C B:HIS188 3.8 15.8 1.0
CB B:ASP186 3.8 13.2 1.0
C B:LEU185 3.9 19.7 1.0
CB B:HIS209 3.9 5.6 1.0
N B:VAL208 3.9 17.6 1.0
N B:LEU185 4.0 9.9 1.0
CB B:SER207 4.1 16.3 1.0
CA B:ASP184 4.2 16.1 1.0
ND1 B:HIS209 4.2 9.7 1.0
CA B:LEU185 4.2 13.9 1.0
OD2 B:ASP184 4.3 19.6 1.0
N B:GLY190 4.4 13.7 1.0
N B:HIS188 4.4 12.8 1.0
CA B:HIS209 4.4 14.3 1.0
CA B:SER207 4.5 18.3 1.0
CA B:HIS189 4.5 13.8 1.0
N B:HIS189 4.5 12.8 1.0
CA B:VAL208 4.5 15.0 1.0
N B:HIS209 4.5 10.7 1.0
CG B:HIS209 4.5 10.7 1.0
C B:SER207 4.5 21.2 1.0
O B:LEU185 4.6 19.6 1.0
N B:LEU187 4.7 14.8 1.0
O B:HOH2065 4.7 20.1 1.0
CA B:HIS188 4.7 14.6 1.0
C B:HIS189 4.7 13.9 1.0
C B:LEU187 4.7 18.8 1.0
CE1 B:HIS141 4.9 13.8 1.0

Potassium binding site 4 out of 8 in 5fue

Go back to Potassium Binding Sites List in 5fue
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:17.4
occ:1.00
 O B:PHE197 2.5 16.2 1.0
O B:VAL203 2.6 18.8 1.0
OG B:SER243 2.6 19.5 1.0
O B:HOH2068 2.8 17.6 1.0
O B:SER200 2.9 26.1 1.0
C B:PHE197 3.5 17.7 1.0
CB B:SER243 3.5 14.0 1.0
O B:SER243 3.6 16.1 1.0
C B:VAL203 3.8 18.3 1.0
CB B:PHE197 3.9 12.6 1.0
C B:SER243 4.0 19.1 1.0
C B:SER200 4.0 23.9 1.0
CA B:PHE197 4.3 20.1 1.0
N B:TRP198 4.4 18.9 1.0
CA B:SER243 4.4 16.9 1.0
N B:SER200 4.5 21.4 1.0
CA B:TRP198 4.5 21.9 1.0
CA B:VAL204 4.6 16.7 1.0
N B:ALA244 4.6 20.1 1.0
O B:TRP198 4.6 19.4 1.0
C B:TRP198 4.6 24.5 1.0
N B:THR205 4.6 17.6 1.0
N B:VAL204 4.6 15.9 1.0
CA B:SER200 4.6 30.8 1.0
CA B:VAL203 4.7 18.4 1.0
CG2 B:THR205 4.8 10.2 1.0
O B:GLY240 4.8 19.1 1.0
CB B:VAL203 4.8 15.2 1.0
OG1 B:THR205 4.8 13.9 1.0
CB B:SER200 4.9 35.2 1.0
N B:VAL203 4.9 17.6 1.0

Potassium binding site 5 out of 8 in 5fue

Go back to Potassium Binding Sites List in 5fue
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K600

b:14.1
occ:1.00
 O C:ASP186 2.6 15.0 1.0
OD1 C:ASP184 2.6 14.6 1.0
O C:VAL208 2.7 14.0 1.0
O C:HIS188 2.8 13.1 1.0
O C:ASP184 2.8 14.3 1.0
OG C:SER207 2.9 14.9 1.0
CG C:ASP184 3.4 13.4 1.0
C C:ASP184 3.4 15.2 1.0
N C:ASP186 3.4 16.3 1.0
C C:ASP186 3.5 19.1 1.0
C C:VAL208 3.7 15.1 1.0
CA C:ASP186 3.7 16.4 1.0
CB C:ASP184 3.8 13.2 1.0
C C:HIS188 3.8 14.3 1.0
C C:LEU185 3.8 17.7 1.0
CB C:ASP186 3.8 10.2 1.0
CB C:HIS209 3.8 10.8 1.0
N C:LEU185 4.0 13.6 1.0
N C:VAL208 4.0 14.7 1.0
CB C:SER207 4.1 17.6 1.0
CA C:ASP184 4.2 16.8 1.0
CA C:LEU185 4.2 14.8 1.0
OD2 C:ASP184 4.3 21.6 1.0
ND1 C:HIS209 4.3 15.0 1.0
N C:GLY190 4.4 13.6 1.0
CA C:HIS209 4.4 14.0 1.0
CA C:SER207 4.4 14.5 1.0
CA C:HIS189 4.5 16.3 1.0
N C:HIS188 4.5 14.7 1.0
N C:HIS189 4.5 10.0 1.0
N C:HIS209 4.5 13.9 1.0
O C:LEU185 4.5 19.2 1.0
CA C:VAL208 4.6 14.1 1.0
C C:SER207 4.6 16.9 1.0
CG C:HIS209 4.6 16.5 1.0
N C:LEU187 4.7 17.9 1.0
C C:HIS189 4.8 18.5 1.0
CA C:HIS188 4.8 17.9 1.0
C C:LEU187 4.8 22.0 1.0
O C:HOH2056 4.8 20.3 1.0

Potassium binding site 6 out of 8 in 5fue

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


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 3-Benzamido-Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K601

b:19.7
occ:1.00
 O C:PHE197 2.6 20.7 1.0
O C:VAL203 2.6 23.6 1.0
OG C:SER243 2.7 18.2 1.0
O C:HOH2061 2.8 19.8 1.0
O C:SER200 2.8 24.6 1.0
O C:SER243 3.4 20.4 1.0
CB C:SER243 3.5 14.1 1.0
C C:PHE197 3.5 18.6 1.0
C C:VAL203 3.8 25.2 1.0
C C:SER243 3.9 20.0 1.0
C C:SER200 3.9 20.7 1.0
CB C:PHE197 3.9 18.4 1.0
CA C:SER243 4.4 17.4 1.0
N C:TRP198 4.4 23.2 1.0
CA C:PHE197 4.4 20.9 1.0
N C:SER200 4.4 23.9 1.0
CA C:VAL204 4.4 14.8 1.0
CA C:TRP198 4.5 16.3 1.0
N C:THR205 4.5 15.6 1.0
N C:ALA244 4.5 19.2 1.0
N C:VAL204 4.6 20.1 1.0
CA C:SER200 4.6 26.1 1.0
C C:TRP198 4.6 26.6 1.0
CG2 C:THR205 4.6 16.5 1.0
OG1 C:THR205 4.6 15.3 1.0
O C:TRP198 4.7 19.4 1.0
CA C:VAL203 4.8 22.5 1.0
CB C:SER200 4.8 35.2 1.0
O C:GLY240 4.8 24.9 1.0
CB C:VAL203 4.9 18.6 1.0
CA C:ALA244 4.9 19.6 1.0
CB C:ALA244 4.9 23.8 1.0
C C:VAL204 4.9 16.1 1.0
N C:VAL203 5.0 20.9 1.0
N C:PRO201 5.0 23.3 1.0

Potassium binding site 7 out of 8 in 5fue

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Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K600

b:16.6
occ:1.00
 O D:VAL208 2.6 17.1 1.0
O D:ASP186 2.6 20.0 1.0
OD1 D:ASP184 2.7 21.6 1.0
O D:HIS188 2.8 15.0 1.0
OG D:SER207 2.8 17.4 1.0
O D:ASP184 2.8 19.3 1.0
N D:ASP186 3.4 18.4 1.0
C D:ASP184 3.4 19.6 1.0
CG D:ASP184 3.5 21.1 1.0
C D:ASP186 3.5 23.4 1.0
C D:VAL208 3.6 19.5 1.0
C D:HIS188 3.8 14.7 1.0
CA D:ASP186 3.8 17.6 1.0
CB D:HIS209 3.8 15.5 1.0
C D:LEU185 3.9 18.8 1.0
CB D:ASP184 3.9 12.6 1.0
CB D:ASP186 3.9 15.2 1.0
N D:VAL208 3.9 19.1 1.0
CB D:SER207 4.0 14.5 1.0
N D:LEU185 4.0 17.6 1.0
ND1 D:HIS209 4.3 16.7 1.0
CA D:LEU185 4.3 21.1 1.0
CA D:ASP184 4.3 18.6 1.0
CA D:SER207 4.4 17.8 1.0
N D:GLY190 4.4 16.4 1.0
CA D:HIS209 4.4 19.6 1.0
OD2 D:ASP184 4.4 25.0 1.0
CA D:HIS189 4.4 18.7 1.0
N D:HIS209 4.4 20.4 1.0
N D:HIS189 4.5 12.7 1.0
CA D:VAL208 4.5 20.0 1.0
N D:HIS188 4.5 20.8 1.0
C D:SER207 4.5 21.6 1.0
O D:LEU185 4.5 21.9 1.0
CG D:HIS209 4.5 17.1 1.0
N D:LEU187 4.7 18.5 1.0
C D:LEU187 4.7 22.9 1.0
C D:HIS189 4.7 15.8 1.0
CA D:HIS188 4.8 19.6 1.0
O D:HOH2068 4.8 21.0 1.0
CE1 D:HIS141 4.9 19.6 1.0

Potassium binding site 8 out of 8 in 5fue

Go back to Potassium Binding Sites List in 5fue
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K601

b:20.2
occ:1.00
 O D:VAL203 2.6 23.1 1.0
O D:PHE197 2.6 22.9 1.0
OG D:SER243 2.6 22.9 1.0
O D:HOH2073 2.8 17.2 1.0
O D:SER200 2.8 25.1 1.0
CB D:SER243 3.4 24.5 1.0
O D:SER243 3.4 22.1 1.0
C D:PHE197 3.6 21.1 1.0
C D:VAL203 3.8 24.2 1.0
C D:SER243 3.8 23.3 1.0
C D:SER200 3.9 24.9 1.0
CB D:PHE197 4.0 16.4 1.0
CA D:SER243 4.3 25.3 1.0
CA D:PHE197 4.4 15.2 1.0
N D:SER200 4.4 24.6 1.0
CA D:VAL204 4.4 24.7 1.0
N D:ALA244 4.5 18.9 1.0
N D:TRP198 4.5 19.0 1.0
N D:THR205 4.5 23.0 1.0
N D:VAL204 4.6 21.8 1.0
CA D:SER200 4.6 27.6 1.0
CA D:TRP198 4.6 20.7 1.0
CB D:SER200 4.7 25.4 1.0
C D:TRP198 4.7 22.8 1.0
OG1 D:THR205 4.7 18.4 1.0
O D:GLY240 4.7 18.6 1.0
CA D:VAL203 4.8 18.5 1.0
O D:TRP198 4.8 22.6 1.0
CG2 D:THR205 4.8 10.5 1.0
CA D:ALA244 4.9 19.2 1.0
CB D:VAL203 4.9 21.8 1.0
CB D:ALA244 4.9 16.3 1.0
C D:VAL204 5.0 23.9 1.0
N D:VAL203 5.0 20.1 1.0
N D:PRO201 5.0 28.4 1.0

Reference:

T.Heimburg, A.Chakrabarti, J.Lancelot, M.Marek, J.Melesina, A.T.Hauser, T.B.Shaik, S.Duclaud, D.Robaa, F.Erdmann, M.Schmidt, C.Romier, R.J.Pierce, M.Jung, W.Sippl. Structure-Based Design and Synthesis of Novel Inhibitors Targeting HDAC8 From Schistosoma Mansoni For the Treatment of Schistosomiasis. J.Med.Chem. V. 59 2423 2016.
ISSN: ISSN 0022-2623
PubMed: 26937828
DOI: 10.1021/ACS.JMEDCHEM.5B01478
Page generated: Sun Dec 13 23:57:22 2020

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