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Potassium in PDB 4bz8: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038, PDB code: 4bz8 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) 32.36 / 2.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.655, 70.721, 98.391, 77.98, 75.51, 85.80
R / Rfree (%) 17.77 / 22.21

Other elements in 4bz8:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038 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 J1038 (pdb code 4bz8). 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 J1038, PDB code: 4bz8:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 4bz8

Go back to Potassium Binding Sites List in 4bz8
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038


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 J1038 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K600

b:30.9
occ:1.00
 O A:VAL203 2.4 19.6 1.0
O A:PHE197 2.4 16.1 1.0
OG A:SER243 2.5 21.4 1.0
O A:SER200 2.7 24.2 1.0
O A:HOH2082 3.0 17.9 1.0
CB A:SER243 3.3 16.9 1.0
C A:PHE197 3.4 16.6 1.0
C A:VAL203 3.6 20.0 1.0
O A:SER243 3.7 18.0 1.0
CB A:PHE197 3.8 14.2 1.0
C A:SER200 3.8 23.3 1.0
C A:SER243 4.0 18.2 1.0
CA A:PHE197 4.2 12.9 1.0
N A:TRP198 4.3 14.4 1.0
CA A:SER243 4.3 16.2 1.0
CA A:VAL204 4.4 17.5 1.0
N A:SER200 4.4 17.5 1.0
N A:VAL204 4.4 17.8 1.0
CA A:VAL203 4.5 15.2 1.0
CA A:SER200 4.5 18.1 1.0
CA A:TRP198 4.6 14.8 1.0
CB A:VAL203 4.7 18.2 1.0
C A:TRP198 4.7 17.4 1.0
N A:THR205 4.7 15.8 1.0
N A:VAL203 4.7 15.8 1.0
O A:TRP198 4.8 15.6 1.0
N A:ALA244 4.8 12.6 1.0
CB A:SER200 4.8 22.4 1.0
N A:PRO201 4.9 18.1 1.0
O A:GLY240 4.9 18.9 1.0
OG1 A:THR205 4.9 15.4 1.0
CG2 A:THR205 5.0 11.0 1.0
CA A:PRO201 5.0 17.3 1.0

Potassium binding site 2 out of 8 in 4bz8

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Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038


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 J1038 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:17.6
occ:1.00
 O A:ASP186 2.5 16.8 1.0
OD1 A:ASP184 2.6 20.3 1.0
O A:VAL208 2.7 19.5 1.0
OG A:SER207 2.8 16.8 1.0
O A:HIS188 2.8 15.4 1.0
O A:ASP184 2.9 16.3 1.0
CG A:ASP184 3.3 21.1 1.0
C A:ASP186 3.5 17.2 1.0
N A:ASP186 3.5 13.4 1.0
C A:ASP184 3.5 16.1 1.0
C A:VAL208 3.7 19.3 1.0
CB A:ASP184 3.7 15.0 1.0
CB A:HIS209 3.8 14.1 1.0
CA A:ASP186 3.9 12.6 1.0
C A:HIS188 3.9 16.0 1.0
N A:VAL208 3.9 14.9 1.0
C A:LEU185 4.0 17.5 1.0
CB A:SER207 4.0 17.3 1.0
CB A:ASP186 4.0 13.3 1.0
N A:LEU185 4.2 11.8 1.0
OD2 A:ASP184 4.2 20.0 1.0
ND1 A:HIS209 4.2 18.3 1.0
CA A:ASP184 4.3 13.2 1.0
CA A:SER207 4.3 15.0 1.0
CA A:LEU185 4.4 12.2 1.0
CA A:HIS209 4.4 15.0 1.0
N A:GLY190 4.4 13.3 1.0
N A:HIS209 4.4 15.8 1.0
C A:SER207 4.4 17.6 1.0
CA A:HIS189 4.5 12.9 1.0
CA A:VAL208 4.5 14.5 1.0
CG A:HIS209 4.5 16.8 1.0
N A:HIS188 4.6 13.8 1.0
O A:LEU185 4.6 19.1 1.0
N A:HIS189 4.6 13.1 1.0
N A:LEU187 4.6 13.0 1.0
C A:HIS189 4.8 16.8 1.0
C A:LEU187 4.8 17.4 1.0
CE1 A:HIS141 4.9 20.4 1.0
CA A:HIS188 4.9 13.1 1.0
O A:HOH2080 4.9 18.7 1.0

Potassium binding site 3 out of 8 in 4bz8

Go back to Potassium Binding Sites List in 4bz8
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038


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 J1038 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K600

b:29.7
occ:1.00
 OG B:SER243 2.4 19.4 1.0
O B:VAL203 2.5 18.6 1.0
O B:PHE197 2.5 15.9 1.0
O B:SER200 2.8 25.7 1.0
O B:HOH2060 2.8 19.8 1.0
CB B:SER243 3.4 15.7 1.0
C B:PHE197 3.5 16.8 1.0
O B:SER243 3.6 19.9 1.0
C B:VAL203 3.7 18.5 1.0
CB B:PHE197 3.9 14.8 1.0
C B:SER200 3.9 24.4 1.0
C B:SER243 4.0 19.8 1.0
CA B:SER243 4.3 14.2 1.0
CA B:PHE197 4.3 13.6 1.0
N B:TRP198 4.3 14.0 1.0
N B:SER200 4.4 19.7 1.0
CA B:VAL204 4.5 13.5 1.0
N B:VAL204 4.5 14.1 1.0
CA B:TRP198 4.5 14.7 1.0
CA B:SER200 4.6 20.3 1.0
O B:TRP198 4.6 18.7 1.0
C B:TRP198 4.6 19.8 1.0
CA B:VAL203 4.7 14.0 1.0
N B:THR205 4.7 13.9 1.0
N B:ALA244 4.7 16.9 1.0
O B:GLY240 4.7 20.2 1.0
CB B:VAL203 4.8 16.5 1.0
N B:VAL203 4.8 16.2 1.0
OG1 B:THR205 4.9 19.4 1.0
CG2 B:THR205 4.9 13.1 1.0
N B:PRO201 5.0 20.6 1.0
CB B:SER200 5.0 25.0 1.0

Potassium binding site 4 out of 8 in 4bz8

Go back to Potassium Binding Sites List in 4bz8
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038


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 J1038 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:11.5
occ:1.00
 O B:ASP186 2.6 14.0 1.0
O B:VAL208 2.6 11.7 1.0
O B:HIS188 2.6 11.3 1.0
OD1 B:ASP184 2.7 18.0 1.0
O B:ASP184 2.8 12.9 1.0
OG B:SER207 3.0 11.6 1.0
CG B:ASP184 3.4 17.8 1.0
C B:ASP186 3.5 15.3 1.0
C B:ASP184 3.5 13.9 1.0
N B:ASP186 3.5 11.5 1.0
C B:VAL208 3.6 13.2 1.0
C B:HIS188 3.7 13.0 1.0
CB B:HIS209 3.8 9.9 1.0
CB B:ASP184 3.8 12.5 1.0
CA B:ASP186 3.8 11.9 1.0
N B:VAL208 3.9 11.8 1.0
CB B:ASP186 3.9 13.5 1.0
C B:LEU185 4.0 15.3 1.0
ND1 B:HIS209 4.2 12.2 1.0
N B:LEU185 4.2 10.6 1.0
CB B:SER207 4.2 13.4 1.0
CA B:ASP184 4.3 11.0 1.0
CA B:HIS209 4.4 10.4 1.0
OD2 B:ASP184 4.4 17.1 1.0
CA B:HIS189 4.4 10.6 1.0
N B:HIS189 4.4 10.2 1.0
N B:HIS188 4.4 10.4 1.0
N B:HIS209 4.4 10.5 1.0
N B:GLY190 4.4 11.9 1.0
CA B:LEU185 4.4 10.8 1.0
CA B:SER207 4.5 11.2 1.0
CG B:HIS209 4.5 11.6 1.0
CA B:VAL208 4.5 11.7 1.0
C B:SER207 4.5 14.0 1.0
N B:LEU187 4.6 11.2 1.0
O B:LEU185 4.7 15.3 1.0
CA B:HIS188 4.7 10.7 1.0
C B:LEU187 4.7 13.3 1.0
C B:HIS189 4.8 13.9 1.0
O B:HOH2056 4.8 20.7 1.0

Potassium binding site 5 out of 8 in 4bz8

Go back to Potassium Binding Sites List in 4bz8
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038


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 J1038 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K600

b:12.9
occ:1.00
 O C:ASP186 2.5 11.9 1.0
O C:VAL208 2.6 10.4 1.0
OD1 C:ASP184 2.7 13.3 1.0
O C:HIS188 2.7 11.8 1.0
O C:ASP184 2.8 15.6 1.0
OG C:SER207 2.9 12.1 1.0
CG C:ASP184 3.4 14.2 1.0
C C:ASP184 3.4 15.7 1.0
N C:ASP186 3.4 11.2 1.0
C C:ASP186 3.5 12.9 1.0
C C:VAL208 3.6 10.8 1.0
C C:HIS188 3.8 12.8 1.0
CB C:ASP184 3.8 12.9 1.0
CA C:ASP186 3.8 10.8 1.0
CB C:HIS209 3.8 7.6 1.0
N C:VAL208 3.9 9.9 1.0
C C:LEU185 4.0 14.0 1.0
CB C:ASP186 4.0 11.5 1.0
N C:LEU185 4.0 12.4 1.0
CB C:SER207 4.1 11.3 1.0
CA C:ASP184 4.2 12.2 1.0
ND1 C:HIS209 4.3 9.4 1.0
CA C:LEU185 4.3 11.0 1.0
OD2 C:ASP184 4.3 18.5 1.0
CA C:HIS209 4.4 7.9 1.0
N C:HIS209 4.4 8.8 1.0
CA C:SER207 4.4 10.3 1.0
CA C:HIS189 4.5 11.4 1.0
CA C:VAL208 4.5 9.1 1.0
N C:GLY190 4.5 12.3 1.0
C C:SER207 4.5 12.9 1.0
N C:HIS189 4.5 11.2 1.0
N C:HIS188 4.5 10.7 1.0
CG C:HIS209 4.6 9.1 1.0
N C:LEU187 4.6 10.7 1.0
O C:LEU185 4.7 14.6 1.0
O C:HOH2075 4.7 11.0 1.0
C C:LEU187 4.7 13.2 1.0
CA C:HIS188 4.8 11.5 1.0
C C:HIS189 4.8 14.6 1.0

Potassium binding site 6 out of 8 in 4bz8

Go back to Potassium Binding Sites List in 4bz8
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038


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 J1038 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K601

b:31.7
occ:1.00
 O C:VAL203 2.3 19.9 1.0
O C:PHE197 2.5 19.6 1.0
OG C:SER243 2.6 19.1 1.0
O C:SER200 2.8 23.8 1.0
O C:HOH2080 2.9 19.1 1.0
CB C:SER243 3.4 16.5 1.0
C C:PHE197 3.5 19.7 1.0
C C:VAL203 3.6 20.1 1.0
O C:SER243 3.6 17.8 1.0
CB C:PHE197 3.9 16.9 1.0
C C:SER243 3.9 17.1 1.0
C C:SER200 4.0 24.5 1.0
CA C:SER243 4.3 13.6 1.0
CA C:PHE197 4.3 15.7 1.0
N C:TRP198 4.4 16.7 1.0
CA C:VAL204 4.4 14.8 1.0
N C:VAL204 4.4 15.9 1.0
N C:SER200 4.5 21.5 1.0
CA C:VAL203 4.6 15.8 1.0
N C:ALA244 4.6 14.1 1.0
CA C:TRP198 4.6 16.9 1.0
CA C:SER200 4.6 21.7 1.0
N C:THR205 4.6 15.0 1.0
C C:TRP198 4.7 19.9 1.0
O C:GLY240 4.7 19.6 1.0
O C:TRP198 4.7 16.7 1.0
CB C:VAL203 4.8 18.1 1.0
N C:VAL203 4.8 17.2 1.0
OG1 C:THR205 4.8 20.2 1.0
CB C:SER200 4.9 26.2 1.0
CG2 C:THR205 4.9 16.9 1.0
C C:VAL204 5.0 18.5 1.0

Potassium binding site 7 out of 8 in 4bz8

Go back to Potassium Binding Sites List in 4bz8
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038


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 J1038 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K600

b:30.4
occ:1.00
 O D:VAL203 2.4 19.1 1.0
O D:PHE197 2.5 20.1 1.0
OG D:SER243 2.6 21.8 1.0
O D:SER200 2.9 29.0 1.0
O D:HOH2073 2.9 17.7 1.0
CB D:SER243 3.3 20.0 1.0
C D:PHE197 3.5 20.8 1.0
C D:VAL203 3.7 20.9 1.0
O D:SER243 3.7 22.9 1.0
CB D:PHE197 3.9 17.7 1.0
C D:SER200 3.9 27.6 1.0
C D:SER243 3.9 23.3 1.0
CA D:SER243 4.3 19.8 1.0
CA D:PHE197 4.3 16.1 1.0
N D:TRP198 4.3 19.3 1.0
CA D:VAL204 4.5 16.1 1.0
N D:VAL204 4.5 16.3 1.0
N D:SER200 4.5 21.0 1.0
CA D:SER200 4.6 21.4 1.0
N D:ALA244 4.6 19.8 1.0
CA D:TRP198 4.6 20.8 1.0
CA D:VAL203 4.7 19.3 1.0
N D:THR205 4.7 17.4 1.0
O D:GLY240 4.7 22.7 1.0
C D:TRP198 4.8 24.8 1.0
OG1 D:THR205 4.8 20.1 1.0
CB D:SER200 4.8 24.1 1.0
CB D:VAL203 4.8 22.1 1.0
O D:TRP198 4.8 24.3 1.0
CG2 D:THR205 4.9 14.3 1.0
N D:VAL203 4.9 20.6 1.0
N D:PRO201 5.0 23.7 1.0
C D:VAL204 5.0 20.5 1.0

Potassium binding site 8 out of 8 in 4bz8

Go back to Potassium Binding Sites List in 4bz8
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1038


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 J1038 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K601

b:16.5
occ:1.00
 O D:ASP186 2.5 18.5 1.0
O D:HIS188 2.7 11.7 1.0
O D:VAL208 2.7 19.0 1.0
O D:ASP184 2.9 15.1 1.0
OD1 D:ASP184 2.9 16.6 1.0
OG D:SER207 2.9 18.8 1.0
C D:ASP186 3.4 17.5 1.0
N D:ASP186 3.4 13.2 1.0
C D:ASP184 3.5 15.5 1.0
CG D:ASP184 3.5 17.9 1.0
C D:VAL208 3.8 19.6 1.0
C D:HIS188 3.8 13.2 1.0
CA D:ASP186 3.8 12.9 1.0
CB D:ASP184 3.8 13.9 1.0
CB D:HIS209 3.9 15.6 1.0
C D:LEU185 3.9 16.2 1.0
CB D:ASP186 3.9 13.9 1.0
N D:VAL208 4.0 16.3 1.0
N D:LEU185 4.1 12.7 1.0
CB D:SER207 4.1 15.7 1.0
CA D:ASP184 4.2 13.3 1.0
ND1 D:HIS209 4.2 20.4 1.0
CA D:LEU185 4.3 13.4 1.0
OD2 D:ASP184 4.3 17.7 1.0
CA D:SER207 4.4 15.7 1.0
CA D:HIS189 4.4 11.9 1.0
N D:GLY190 4.4 16.9 1.0
N D:HIS188 4.5 10.9 1.0
CA D:HIS209 4.5 15.5 1.0
N D:HIS189 4.5 11.7 1.0
N D:HIS209 4.5 16.1 1.0
C D:SER207 4.6 19.1 1.0
N D:LEU187 4.6 12.2 1.0
CG D:HIS209 4.6 18.6 1.0
CA D:VAL208 4.6 16.2 1.0
O D:LEU185 4.6 15.5 1.0
C D:LEU187 4.7 15.3 1.0
CA D:HIS188 4.8 10.6 1.0
C D:HIS189 4.8 17.9 1.0
CE1 D:HIS141 4.8 18.2 1.0
O D:HOH2070 4.9 15.1 1.0

Reference:

M.Marek, S.Kannan, A.Hauser, M.Moraes Mourao, S.Caby, V.Cura, D.A.Stolfa, K.Schmidtkunz, J.Lancelot, L.Andrade, J.Renaud, G.Oliveira, W.Sippl, M.Jung, J.Cavarelli, R.J.Pierce, C.Romier. Structural Basis For the Inhibition of Histone Deacetylase 8 (HDAC8), A Key Epigenetic Player in the Blood Fluke Schistosoma Mansoni. Plos Pathog. V. 9 03645 2013.
ISSN: ISSN 1553-7366
PubMed: 24086136
DOI: 10.1371/JOURNAL.PPAT.1003645
Page generated: Mon Aug 12 10:17:20 2024

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