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Potassium in PDB 7p3s: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12, PDB code: 7p3s was solved by T.B.Shaik, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.52 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.39, 70.39, 97.94, 78.05, 75.57, 85.69
R / Rfree (%) 16.9 / 19.3

Other elements in 7p3s:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 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 12 (pdb code 7p3s). 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 12, PDB code: 7p3s:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 7p3s

Go back to Potassium Binding Sites List in 7p3s
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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

b:16.4
occ:1.00
 O A:VAL208 2.6 15.9 1.0
O A:ASP186 2.6 15.3 1.0
OD1 A:ASP184 2.7 14.0 1.0
O A:ASP184 2.8 14.7 1.0
O A:HIS188 2.8 14.7 1.0
OG A:SER207 2.9 13.9 1.0
N A:ASP186 3.4 14.6 1.0
CG A:ASP184 3.4 17.4 1.0
C A:ASP184 3.4 15.6 1.0
C A:ASP186 3.5 16.9 1.0
C A:VAL208 3.6 13.6 1.0
CA A:ASP186 3.8 12.5 1.0
CB A:ASP184 3.8 13.5 1.0
C A:HIS188 3.8 13.1 1.0
CB A:HIS209 3.8 13.8 1.0
C A:LEU185 3.9 14.7 1.0
CB A:ASP186 3.9 12.6 1.0
N A:VAL208 3.9 14.0 1.0
N A:LEU185 4.0 14.5 1.0
CB A:SER207 4.1 13.4 1.0
CA A:ASP184 4.2 14.1 1.0
ND1 A:HIS209 4.3 15.2 1.0
CA A:LEU185 4.3 15.1 1.0
CA A:HIS209 4.3 14.8 1.0
OD2 A:ASP184 4.3 14.6 1.0
N A:GLY190 4.3 14.4 1.0
CA A:SER207 4.4 13.5 1.0
N A:HIS209 4.4 14.4 1.0
CA A:HIS189 4.4 12.2 1.0
CA A:VAL208 4.4 14.8 1.0
N A:HIS189 4.4 12.6 1.0
N A:HIS188 4.5 14.6 1.0
C A:SER207 4.5 14.0 1.0
CG A:HIS209 4.5 14.9 1.0
O A:LEU185 4.5 14.9 1.0
N A:LEU187 4.7 14.5 1.0
C A:HIS189 4.7 14.1 1.0
C A:LEU187 4.7 15.9 1.0
CA A:HIS188 4.8 14.5 1.0
O A:HOH783 4.8 18.0 1.0
CE1 A:HIS141 4.9 14.7 1.0

Potassium binding site 2 out of 8 in 7p3s

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Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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

b:17.3
occ:1.00
 O A:VAL203 2.5 17.9 1.0
O A:PHE197 2.6 16.9 1.0
OG A:SER243 2.6 18.9 1.0
O A:HOH781 2.7 15.9 1.0
O A:SER200 2.8 21.0 1.0
O A:SER243 3.4 18.1 1.0
CB A:SER243 3.5 16.6 1.0
C A:PHE197 3.5 16.9 1.0
C A:VAL203 3.7 14.5 1.0
C A:SER243 3.9 17.3 1.0
CB A:PHE197 3.9 14.1 1.0
C A:SER200 3.9 20.0 1.0
CA A:SER243 4.3 17.9 1.0
CA A:PHE197 4.4 13.7 1.0
N A:SER200 4.4 18.9 1.0
CA A:VAL204 4.4 17.8 1.0
N A:TRP198 4.4 17.6 1.0
N A:VAL204 4.5 16.3 1.0
CA A:TRP198 4.5 16.1 1.0
N A:THR205 4.6 14.4 1.0
C A:TRP198 4.6 18.1 1.0
N A:ALA244 4.6 16.6 1.0
O A:TRP198 4.6 18.0 1.0
CA A:SER200 4.6 24.8 0.5
CA A:SER200 4.6 24.9 0.5
OG1 A:THR205 4.7 14.2 1.0
CA A:VAL203 4.8 14.5 1.0
CG2 A:THR205 4.8 16.6 1.0
CB A:SER200 4.8 24.5 0.5
CB A:VAL203 4.9 16.9 1.0
N A:VAL203 4.9 15.6 1.0
O A:GLY240 4.9 18.2 1.0
C A:VAL204 4.9 15.6 1.0
N A:PRO201 4.9 15.4 1.0
CB A:SER200 4.9 25.3 0.5
CA A:ALA244 5.0 16.8 1.0

Potassium binding site 3 out of 8 in 7p3s

Go back to Potassium Binding Sites List in 7p3s
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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

b:15.2
occ:1.00
 O B:VAL208 2.6 15.0 1.0
O B:ASP186 2.6 13.4 1.0
OD1 B:ASP184 2.6 13.0 1.0
O B:ASP184 2.8 12.7 1.0
O B:HIS188 2.8 12.9 1.0
OG B:SER207 2.9 13.5 1.0
CG B:ASP184 3.3 13.8 1.0
N B:ASP186 3.4 12.4 1.0
C B:ASP184 3.4 11.7 1.0
C B:ASP186 3.5 11.6 1.0
C B:VAL208 3.6 13.0 1.0
CB B:ASP184 3.7 11.3 1.0
C B:HIS188 3.8 12.5 1.0
CB B:HIS209 3.8 13.2 1.0
CA B:ASP186 3.8 11.6 1.0
C B:LEU185 3.9 15.4 1.0
CB B:ASP186 3.9 11.8 1.0
N B:VAL208 3.9 11.9 1.0
N B:LEU185 4.0 11.5 1.0
CB B:SER207 4.0 17.8 1.0
CA B:ASP184 4.2 13.0 1.0
ND1 B:HIS209 4.2 14.3 1.0
CA B:LEU185 4.2 12.1 1.0
OD2 B:ASP184 4.3 13.1 1.0
CA B:HIS209 4.3 13.6 1.0
N B:GLY190 4.3 11.3 1.0
CA B:SER207 4.3 14.7 1.0
N B:HIS209 4.4 13.4 1.0
N B:HIS188 4.4 11.6 1.0
CA B:HIS189 4.4 12.6 1.0
CA B:VAL208 4.4 13.6 1.0
C B:SER207 4.4 14.0 1.0
N B:HIS189 4.5 11.5 1.0
CG B:HIS209 4.5 12.8 1.0
O B:LEU185 4.6 12.9 1.0
N B:LEU187 4.7 11.6 1.0
C B:HIS189 4.7 13.0 1.0
C B:LEU187 4.7 13.6 1.0
CA B:HIS188 4.7 13.0 1.0
O B:HOH810 4.8 16.8 1.0
CE1 B:HIS141 5.0 11.9 1.0

Potassium binding site 4 out of 8 in 7p3s

Go back to Potassium Binding Sites List in 7p3s
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:17.4
occ:1.00
 O B:VAL203 2.5 18.6 1.0
O B:PHE197 2.6 15.5 1.0
OG B:SER243 2.6 19.2 1.0
O B:SER200 2.8 25.8 1.0
O B:HOH805 2.8 14.0 1.0
CB B:SER243 3.4 18.4 1.0
C B:PHE197 3.5 15.8 1.0
O B:SER243 3.6 17.2 1.0
C B:VAL203 3.8 15.6 1.0
CB B:PHE197 3.8 14.0 1.0
C B:SER200 3.9 24.1 1.0
C B:SER243 3.9 16.5 1.0
CA B:PHE197 4.3 15.9 1.0
CA B:SER243 4.4 15.1 1.0
N B:TRP198 4.4 17.4 1.0
N B:SER200 4.5 19.5 1.0
CA B:VAL204 4.5 13.1 1.0
CA B:TRP198 4.5 18.3 1.0
N B:ALA244 4.6 16.6 1.0
N B:VAL204 4.6 13.2 1.0
C B:TRP198 4.6 16.9 1.0
CA B:SER200 4.6 23.3 0.6
N B:THR205 4.6 15.3 1.0
CA B:SER200 4.7 23.8 0.4
O B:TRP198 4.7 17.6 1.0
OG1 B:THR205 4.7 15.0 1.0
CA B:VAL203 4.7 14.3 1.0
CB B:SER200 4.8 26.9 0.6
CG2 B:THR205 4.8 14.4 1.0
CB B:VAL203 4.9 16.1 1.0
O B:GLY240 4.9 17.0 1.0
N B:VAL203 4.9 16.5 1.0
CB B:SER200 4.9 26.5 0.4
N B:PRO201 4.9 19.8 1.0
CA B:ALA244 5.0 14.7 1.0

Potassium binding site 5 out of 8 in 7p3s

Go back to Potassium Binding Sites List in 7p3s
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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

b:15.4
occ:1.00
 O C:VAL208 2.5 13.7 1.0
O C:ASP186 2.6 14.6 1.0
OD1 C:ASP184 2.6 12.6 1.0
O C:ASP184 2.8 13.2 1.0
O C:HIS188 2.8 12.8 1.0
OG C:SER207 2.9 13.6 1.0
CG C:ASP184 3.3 13.5 1.0
C C:ASP184 3.4 10.9 1.0
N C:ASP186 3.4 11.1 1.0
C C:ASP186 3.5 13.5 1.0
C C:VAL208 3.6 10.4 1.0
CB C:HIS209 3.8 9.8 1.0
CB C:ASP184 3.8 10.7 1.0
C C:HIS188 3.8 11.8 1.0
CA C:ASP186 3.8 10.6 1.0
C C:LEU185 3.9 10.9 1.0
CB C:ASP186 3.9 10.5 1.0
N C:VAL208 3.9 11.8 1.0
N C:LEU185 4.0 11.4 1.0
CB C:SER207 4.1 15.8 1.0
CA C:ASP184 4.2 10.9 1.0
ND1 C:HIS209 4.2 13.5 1.0
CA C:LEU185 4.2 11.3 1.0
OD2 C:ASP184 4.3 14.0 1.0
CA C:HIS209 4.3 12.4 1.0
N C:GLY190 4.3 11.9 1.0
CA C:SER207 4.3 15.9 1.0
N C:HIS209 4.4 12.7 1.0
N C:HIS188 4.4 10.4 1.0
CA C:HIS189 4.4 10.9 1.0
CA C:VAL208 4.4 13.4 1.0
N C:HIS189 4.5 11.6 1.0
CG C:HIS209 4.5 12.9 1.0
C C:SER207 4.5 14.3 1.0
O C:LEU185 4.5 12.9 1.0
N C:LEU187 4.7 12.6 1.0
C C:HIS189 4.7 13.2 1.0
C C:LEU187 4.7 13.0 1.0
O C:HOH803 4.7 15.8 1.0
CA C:HIS188 4.7 12.1 1.0
CE1 C:HIS141 5.0 12.8 1.0

Potassium binding site 6 out of 8 in 7p3s

Go back to Potassium Binding Sites List in 7p3s
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:18.0
occ:1.00
 O C:VAL203 2.5 19.7 1.0
O C:PHE197 2.6 18.7 1.0
OG C:SER243 2.6 20.2 1.0
O C:HOH782 2.7 16.4 1.0
O C:SER200 2.9 21.6 1.0
O C:SER243 3.4 16.5 1.0
CB C:SER243 3.5 18.3 1.0
C C:PHE197 3.6 19.4 1.0
C C:VAL203 3.8 15.8 1.0
C C:SER243 3.8 15.9 1.0
CB C:PHE197 3.9 17.2 1.0
C C:SER200 3.9 21.1 1.0
CA C:SER243 4.3 16.9 1.0
CA C:PHE197 4.4 17.8 1.0
N C:SER200 4.4 21.3 1.0
CA C:VAL204 4.4 13.6 1.0
N C:TRP198 4.5 16.1 1.0
N C:ALA244 4.5 16.3 1.0
N C:THR205 4.5 14.1 1.0
N C:VAL204 4.6 14.9 1.0
CA C:TRP198 4.6 19.9 1.0
CA C:SER200 4.6 22.6 0.5
CA C:SER200 4.6 22.6 0.5
C C:TRP198 4.6 19.3 1.0
O C:TRP198 4.6 18.8 1.0
OG1 C:THR205 4.6 16.7 1.0
CG2 C:THR205 4.8 15.2 1.0
CB C:SER200 4.8 25.7 0.5
CA C:VAL203 4.8 17.0 1.0
CB C:SER200 4.8 25.8 0.5
CA C:ALA244 4.9 16.1 1.0
CB C:VAL203 4.9 18.2 1.0
O C:GLY240 4.9 17.6 1.0
N C:PRO201 4.9 18.7 1.0
C C:VAL204 4.9 14.6 1.0
CB C:ALA244 4.9 17.8 1.0
N C:VAL203 5.0 17.0 1.0

Potassium binding site 7 out of 8 in 7p3s

Go back to Potassium Binding Sites List in 7p3s
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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

b:16.6
occ:1.00
 O D:VAL208 2.6 14.4 1.0
O D:ASP186 2.6 16.6 1.0
OD1 D:ASP184 2.6 15.3 1.0
O D:HIS188 2.8 14.3 1.0
O D:ASP184 2.8 14.3 1.0
OG D:SER207 2.9 16.1 1.0
N D:ASP186 3.3 15.0 1.0
CG D:ASP184 3.4 15.0 1.0
C D:ASP184 3.4 16.5 1.0
C D:ASP186 3.5 16.3 1.0
C D:VAL208 3.6 15.7 1.0
CA D:ASP186 3.7 14.5 1.0
C D:HIS188 3.8 14.8 1.0
CB D:ASP184 3.8 12.7 1.0
CB D:HIS209 3.8 13.4 1.0
CB D:ASP186 3.8 13.0 1.0
C D:LEU185 3.8 15.1 1.0
N D:VAL208 3.9 14.0 1.0
N D:LEU185 4.0 15.0 1.0
CB D:SER207 4.1 17.6 1.0
CA D:ASP184 4.2 14.2 1.0
ND1 D:HIS209 4.2 16.4 1.0
CA D:LEU185 4.2 15.9 1.0
OD2 D:ASP184 4.3 16.1 1.0
CA D:HIS209 4.3 14.4 1.0
N D:GLY190 4.3 15.1 1.0
CA D:SER207 4.4 15.4 1.0
N D:HIS209 4.4 16.3 1.0
N D:HIS188 4.4 14.4 1.0
CA D:VAL208 4.4 14.3 1.0
CA D:HIS189 4.4 16.6 1.0
C D:SER207 4.5 15.3 1.0
N D:HIS189 4.5 15.0 1.0
CG D:HIS209 4.5 14.5 1.0
O D:LEU185 4.5 15.7 1.0
N D:LEU187 4.7 13.8 1.0
C D:HIS189 4.7 16.1 1.0
C D:LEU187 4.7 15.6 1.0
CA D:HIS188 4.7 15.0 1.0
O D:HOH786 4.8 17.8 1.0
CE1 D:HIS141 4.9 14.8 1.0
CG1 D:VAL208 5.0 18.2 1.0

Potassium binding site 8 out of 8 in 7p3s

Go back to Potassium Binding Sites List in 7p3s
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K504

b:18.3
occ:1.00
 O D:VAL203 2.5 17.4 1.0
OG D:SER243 2.6 18.2 1.0
O D:PHE197 2.6 16.9 1.0
O D:HOH776 2.8 16.8 1.0
O D:SER200 2.8 20.2 1.0
CB D:SER243 3.4 18.7 1.0
O D:SER243 3.5 18.6 1.0
C D:PHE197 3.6 16.2 1.0
C D:VAL203 3.7 14.9 1.0
C D:SER243 3.9 18.2 1.0
CB D:PHE197 3.9 15.5 1.0
C D:SER200 4.0 18.6 1.0
CA D:SER243 4.3 16.8 1.0
CA D:PHE197 4.4 14.4 1.0
CA D:VAL204 4.4 17.9 1.0
N D:SER200 4.4 18.7 1.0
N D:TRP198 4.4 16.8 1.0
N D:VAL204 4.5 18.0 1.0
N D:THR205 4.5 17.4 1.0
N D:ALA244 4.6 15.8 1.0
CA D:TRP198 4.6 16.7 1.0
C D:TRP198 4.6 18.4 1.0
CA D:SER200 4.6 19.0 0.5
CA D:SER200 4.7 19.0 0.5
O D:TRP198 4.7 18.0 1.0
OG1 D:THR205 4.7 16.8 1.0
CA D:VAL203 4.8 15.1 1.0
CB D:SER200 4.8 21.1 0.5
CG2 D:THR205 4.8 14.4 1.0
O D:GLY240 4.9 19.9 1.0
CB D:VAL203 4.9 19.4 1.0
CB D:SER200 4.9 21.4 0.5
C D:VAL204 4.9 16.6 1.0
CA D:ALA244 4.9 17.2 1.0
N D:VAL203 5.0 20.0 1.0
N D:PRO201 5.0 17.4 1.0
CB D:ALA244 5.0 15.2 1.0

Reference:

T.B.Shaik, C.Romier. Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 To Be Published.
Page generated: Mon Aug 12 19:51:21 2024

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