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

Go back to Potassium Binding Sites List in 7p3s
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy