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Potassium in PDB 6fu1: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate, PDB code: 6fu1 was solved by M.Marek, T.B.Shaik, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.96 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.710, 70.690, 99.190, 75.33, 77.78, 84.80
R / Rfree (%) 19.9 / 22.3

Other elements in 6fu1:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate (pdb code 6fu1). 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 N- Alkyl Hydroxamate, PDB code: 6fu1:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6fu1

Go back to Potassium Binding Sites List in 6fu1
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:17.5
occ:1.00
 O A:VAL208 2.6 19.2 1.0
O A:ASP186 2.6 19.6 1.0
OD1 A:ASP184 2.7 18.6 1.0
O A:HIS188 2.7 17.2 1.0
OG A:SER207 2.8 16.5 1.0
O A:ASP184 2.8 17.0 1.0
CG A:ASP184 3.4 18.8 1.0
N A:ASP186 3.4 19.0 1.0
C A:ASP184 3.5 17.1 1.0
C A:ASP186 3.5 17.1 1.0
C A:VAL208 3.6 17.2 1.0
C A:HIS188 3.7 17.3 1.0
CA A:ASP186 3.8 18.5 1.0
CB A:ASP184 3.8 13.9 1.0
CB A:HIS209 3.8 15.8 1.0
CB A:ASP186 3.8 20.6 1.0
C A:LEU185 3.9 19.7 1.0
N A:VAL208 3.9 14.8 1.0
CB A:SER207 4.0 16.2 1.0
N A:LEU185 4.1 17.0 1.0
CA A:ASP184 4.3 14.1 1.0
CA A:LEU185 4.3 14.7 1.0
OD2 A:ASP184 4.3 18.8 1.0
N A:GLY190 4.3 15.8 1.0
ND1 A:HIS209 4.3 19.9 1.0
CA A:SER207 4.3 16.3 1.0
CA A:HIS209 4.3 16.1 1.0
CA A:HIS189 4.4 14.6 1.0
N A:HIS209 4.4 18.1 1.0
N A:HIS188 4.4 17.8 1.0
N A:HIS189 4.4 15.9 1.0
CA A:VAL208 4.5 15.7 1.0
C A:SER207 4.5 18.2 1.0
CG A:HIS209 4.5 18.0 1.0
O A:LEU185 4.6 20.0 1.0
C A:HIS189 4.6 17.5 1.0
N A:LEU187 4.7 17.1 1.0
C A:LEU187 4.7 18.5 1.0
CA A:HIS188 4.7 15.8 1.0
O A:HOH711 4.8 23.3 1.0
CE1 A:HIS141 4.9 20.2 1.0

Potassium binding site 2 out of 8 in 6fu1

Go back to Potassium Binding Sites List in 6fu1
Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:27.5
occ:1.00
 O A:VAL203 2.4 20.3 1.0
O A:PHE197 2.4 19.9 1.0
OG A:SER243 2.4 21.1 1.0
O A:SER200 2.6 23.6 1.0
O A:HOH694 2.8 25.4 1.0
CB A:SER243 3.4 23.1 1.0
C A:PHE197 3.4 16.1 1.0
C A:VAL203 3.6 19.1 1.0
C A:SER200 3.7 21.0 1.0
O A:SER243 3.7 20.5 1.0
CB A:PHE197 3.8 16.4 1.0
C A:SER243 4.1 20.9 1.0
N A:SER200 4.2 21.4 1.0
CA A:PHE197 4.2 16.3 1.0
N A:TRP198 4.3 17.8 1.0
CA A:SER200 4.3 21.9 0.5
CA A:SER200 4.4 22.0 0.5
CA A:SER243 4.4 19.6 1.0
CA A:VAL204 4.5 18.4 1.0
CB A:SER200 4.5 27.2 0.5
N A:VAL204 4.5 18.6 1.0
C A:TRP198 4.5 19.1 1.0
CB A:SER200 4.5 27.4 0.5
CA A:TRP198 4.5 21.7 1.0
O A:TRP198 4.6 18.7 1.0
CA A:VAL203 4.6 16.0 1.0
CB A:VAL203 4.7 18.7 1.0
N A:VAL203 4.7 18.6 1.0
N A:PRO201 4.8 21.1 1.0
O A:GLY240 4.8 20.5 1.0
N A:THR205 4.8 18.2 1.0
N A:ALA244 4.8 18.8 1.0
OG1 A:THR205 4.9 18.2 1.0
CA A:PRO201 4.9 19.7 1.0

Potassium binding site 3 out of 8 in 6fu1

Go back to Potassium Binding Sites List in 6fu1
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:17.2
occ:1.00
 O B:VAL208 2.6 16.9 1.0
OD1 B:ASP184 2.6 16.6 1.0
O B:ASP186 2.6 18.1 1.0
O B:ASP184 2.8 17.3 1.0
O B:HIS188 2.8 17.2 1.0
OG B:SER207 2.9 17.6 1.0
CG B:ASP184 3.3 18.4 1.0
N B:ASP186 3.4 16.2 1.0
C B:ASP184 3.4 17.3 1.0
C B:ASP186 3.5 16.9 1.0
C B:VAL208 3.6 16.7 1.0
CB B:ASP184 3.8 16.0 1.0
CA B:ASP186 3.8 16.9 1.0
C B:HIS188 3.8 19.0 1.0
CB B:HIS209 3.8 16.6 1.0
CB B:ASP186 3.9 18.2 1.0
C B:LEU185 3.9 16.0 1.0
N B:VAL208 3.9 15.3 1.0
N B:LEU185 4.0 15.6 1.0
CB B:SER207 4.1 17.2 1.0
CA B:ASP184 4.2 13.6 1.0
OD2 B:ASP184 4.2 18.4 1.0
ND1 B:HIS209 4.3 18.1 1.0
CA B:LEU185 4.3 14.9 1.0
CA B:HIS209 4.3 19.8 1.0
N B:GLY190 4.3 17.4 1.0
CA B:SER207 4.3 16.9 1.0
CA B:HIS189 4.4 11.9 1.0
N B:HIS209 4.4 18.8 1.0
CA B:VAL208 4.5 14.5 1.0
N B:HIS189 4.5 15.7 1.0
C B:SER207 4.5 16.8 1.0
N B:HIS188 4.5 16.3 1.0
CG B:HIS209 4.5 18.6 1.0
O B:LEU185 4.6 18.6 1.0
C B:HIS189 4.7 16.8 1.0
N B:LEU187 4.7 14.9 1.0
C B:LEU187 4.7 15.2 1.0
CA B:HIS188 4.8 17.6 1.0
O B:HOH735 4.9 20.1 1.0
CG1 B:VAL208 5.0 20.0 1.0
CE1 B:HIS141 5.0 18.6 1.0

Potassium binding site 4 out of 8 in 6fu1

Go back to Potassium Binding Sites List in 6fu1
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:31.1
occ:1.00
 O B:PHE197 2.4 24.3 1.0
O B:VAL203 2.4 22.8 1.0
OG B:SER243 2.4 23.2 1.0
O B:SER200 2.6 27.5 1.0
O B:HOH701 3.0 26.6 1.0
CB B:SER243 3.3 20.8 1.0
C B:PHE197 3.4 20.5 1.0
C B:VAL203 3.6 20.8 1.0
C B:SER200 3.8 28.1 1.0
CB B:PHE197 3.8 21.5 1.0
O B:SER243 3.9 20.8 1.0
C B:SER243 4.1 21.5 1.0
CA B:PHE197 4.2 22.1 1.0
N B:SER200 4.2 24.6 1.0
N B:TRP198 4.3 19.8 1.0
CA B:SER243 4.4 18.9 1.0
CA B:SER200 4.4 29.1 0.5
CA B:SER200 4.4 29.1 0.5
CA B:VAL204 4.5 17.4 1.0
CA B:TRP198 4.5 21.7 1.0
N B:VAL204 4.5 18.7 1.0
C B:TRP198 4.5 21.9 1.0
CB B:SER200 4.6 31.6 0.5
CA B:VAL203 4.6 21.7 1.0
CB B:SER200 4.6 31.9 0.5
O B:TRP198 4.6 22.4 1.0
CB B:VAL203 4.7 20.5 1.0
N B:VAL203 4.8 19.4 1.0
O B:GLY240 4.8 21.5 1.0
N B:PRO201 4.8 25.3 1.0
N B:ALA244 4.8 19.9 1.0
N B:THR205 4.8 17.2 1.0
OG1 B:THR205 4.9 19.7 1.0
CA B:PRO201 5.0 25.8 1.0

Potassium binding site 5 out of 8 in 6fu1

Go back to Potassium Binding Sites List in 6fu1
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:17.3
occ:1.00
 O C:VAL208 2.6 16.1 1.0
OD1 C:ASP184 2.6 16.8 1.0
O C:ASP186 2.6 18.6 1.0
O C:HIS188 2.7 17.8 1.0
O C:ASP184 2.8 15.6 1.0
OG C:SER207 2.9 18.6 1.0
N C:ASP186 3.4 15.2 1.0
CG C:ASP184 3.4 19.3 1.0
C C:ASP184 3.4 16.6 1.0
C C:ASP186 3.5 17.7 1.0
C C:VAL208 3.6 14.7 1.0
C C:HIS188 3.7 13.8 1.0
CA C:ASP186 3.8 15.1 1.0
CB C:ASP184 3.8 17.4 1.0
CB C:HIS209 3.8 14.4 1.0
C C:LEU185 3.9 15.6 1.0
CB C:ASP186 3.9 15.9 1.0
N C:VAL208 3.9 16.2 1.0
N C:LEU185 4.0 15.9 1.0
CB C:SER207 4.1 19.4 1.0
CA C:ASP184 4.2 13.5 1.0
CA C:LEU185 4.3 17.6 1.0
OD2 C:ASP184 4.3 19.2 1.0
ND1 C:HIS209 4.3 18.2 1.0
N C:GLY190 4.3 18.0 1.0
CA C:HIS209 4.3 16.8 1.0
CA C:SER207 4.4 17.3 1.0
CA C:HIS189 4.4 17.1 1.0
N C:HIS189 4.4 18.8 1.0
N C:HIS209 4.4 16.6 1.0
N C:HIS188 4.5 15.6 1.0
CA C:VAL208 4.5 15.2 1.0
C C:SER207 4.5 16.2 1.0
CG C:HIS209 4.5 15.1 1.0
O C:LEU185 4.6 18.2 1.0
C C:HIS189 4.7 18.4 1.0
N C:LEU187 4.7 15.8 1.0
C C:LEU187 4.7 17.4 1.0
CA C:HIS188 4.7 16.1 1.0
O C:HOH735 4.8 20.1 1.0
CE1 C:HIS141 5.0 21.4 1.0

Potassium binding site 6 out of 8 in 6fu1

Go back to Potassium Binding Sites List in 6fu1
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:27.6
occ:1.00
 O C:PHE197 2.4 21.3 1.0
O C:VAL203 2.4 20.8 1.0
OG C:SER243 2.5 22.9 1.0
O C:SER200 2.6 28.1 1.0
O C:HOH699 3.1 26.2 1.0
CB C:SER243 3.3 20.9 1.0
C C:PHE197 3.5 23.5 1.0
C C:VAL203 3.7 19.9 1.0
C C:SER200 3.7 29.2 1.0
CB C:PHE197 3.9 19.1 1.0
O C:SER243 3.9 21.2 1.0
C C:SER243 4.2 21.9 1.0
N C:SER200 4.2 20.8 1.0
CA C:PHE197 4.3 21.2 1.0
CA C:SER243 4.4 21.5 1.0
N C:TRP198 4.4 21.0 1.0
CA C:SER200 4.4 28.5 0.5
CA C:SER200 4.4 28.5 0.5
CA C:TRP198 4.5 20.8 1.0
CA C:VAL204 4.5 18.2 1.0
C C:TRP198 4.5 22.4 1.0
N C:VAL204 4.5 17.4 1.0
CB C:SER200 4.5 30.5 0.5
CB C:SER200 4.6 30.9 0.5
O C:TRP198 4.6 23.1 1.0
CA C:VAL203 4.6 17.2 1.0
O C:GLY240 4.7 22.4 1.0
N C:VAL203 4.7 17.7 1.0
CB C:VAL203 4.7 20.0 1.0
N C:PRO201 4.7 27.6 1.0
N C:ALA244 4.8 22.2 1.0
CA C:PRO201 4.9 26.8 1.0
N C:THR205 4.9 17.5 1.0
OG C:SER200 5.0 29.3 0.5
CA C:GLY240 5.0 20.8 1.0

Potassium binding site 7 out of 8 in 6fu1

Go back to Potassium Binding Sites List in 6fu1
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:17.6
occ:1.00
 O D:VAL208 2.6 19.6 1.0
O D:ASP186 2.6 18.9 1.0
OD1 D:ASP184 2.7 19.0 1.0
O D:HIS188 2.8 18.9 1.0
O D:ASP184 2.8 15.6 1.0
OG D:SER207 2.8 17.6 1.0
N D:ASP186 3.3 16.5 1.0
CG D:ASP184 3.4 20.0 1.0
C D:ASP184 3.5 16.4 1.0
C D:ASP186 3.5 18.7 1.0
C D:VAL208 3.6 22.4 1.0
CA D:ASP186 3.7 19.8 1.0
C D:HIS188 3.8 17.2 1.0
CB D:ASP184 3.8 16.7 1.0
CB D:HIS209 3.8 15.7 1.0
C D:LEU185 3.8 19.0 1.0
CB D:ASP186 3.9 18.2 1.0
N D:VAL208 3.9 15.7 1.0
CB D:SER207 4.0 17.5 1.0
N D:LEU185 4.1 17.2 1.0
CA D:ASP184 4.2 16.1 1.0
CA D:LEU185 4.3 16.9 1.0
CA D:SER207 4.3 16.2 1.0
ND1 D:HIS209 4.3 19.2 1.0
CA D:HIS209 4.3 15.3 1.0
OD2 D:ASP184 4.3 20.1 1.0
N D:GLY190 4.4 16.8 1.0
N D:HIS209 4.4 18.9 1.0
CA D:HIS189 4.4 15.8 1.0
CA D:VAL208 4.4 19.4 1.0
C D:SER207 4.5 19.6 1.0
N D:HIS188 4.5 18.3 1.0
N D:HIS189 4.5 18.4 1.0
O D:LEU185 4.5 20.3 1.0
CG D:HIS209 4.5 18.6 1.0
N D:LEU187 4.7 17.2 1.0
C D:HIS189 4.7 17.2 1.0
C D:LEU187 4.7 20.4 1.0
O D:HOH692 4.7 22.6 1.0
CA D:HIS188 4.8 15.6 1.0
CE1 D:HIS141 5.0 20.9 1.0

Potassium binding site 8 out of 8 in 6fu1

Go back to Potassium Binding Sites List in 6fu1
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:26.0
occ:1.00
 O D:PHE197 2.4 17.9 1.0
OG D:SER243 2.4 19.5 1.0
O D:VAL203 2.4 22.9 1.0
O D:SER200 2.6 25.4 1.0
O D:HOH699 2.8 25.2 1.0
CB D:SER243 3.3 21.0 1.0
C D:PHE197 3.4 20.1 1.0
C D:VAL203 3.6 23.2 1.0
O D:SER243 3.7 19.4 1.0
C D:SER200 3.8 21.1 1.0
CB D:PHE197 3.9 18.8 1.0
C D:SER243 4.1 21.8 1.0
N D:SER200 4.2 21.3 1.0
CA D:PHE197 4.2 16.0 1.0
N D:TRP198 4.3 19.9 1.0
CA D:SER243 4.3 21.2 1.0
CA D:SER200 4.4 22.3 0.6
CA D:SER200 4.4 22.4 0.4
CB D:SER200 4.4 24.6 0.6
CA D:VAL204 4.5 20.2 1.0
C D:TRP198 4.5 19.7 1.0
CA D:TRP198 4.5 18.6 1.0
N D:VAL204 4.5 19.7 1.0
CB D:SER200 4.5 24.7 0.4
O D:TRP198 4.5 20.7 1.0
CA D:VAL203 4.6 19.1 1.0
CB D:VAL203 4.7 18.2 1.0
O D:GLY240 4.8 20.4 1.0
N D:VAL203 4.8 19.8 1.0
N D:THR205 4.8 17.7 1.0
N D:ALA244 4.8 18.6 1.0
N D:PRO201 4.8 20.9 1.0
OG1 D:THR205 5.0 20.8 1.0
CG2 D:THR205 5.0 20.2 1.0
CA D:PRO201 5.0 22.8 1.0

Reference:

C.V.Simoben, D.Robaa, A.Chakrabarti, K.Schmidtkunz, M.Marek, J.Lancelot, S.Kannan, J.Melesina, T.B.Shaik, R.J.Pierce, C.Romier, M.Jung, W.Sippl. A Novel Class of Schistosoma Mansoni Histone Deacetylase 8 (HDAC8) Inhibitors Identified By Structure-Based Virtual Screening and in Vitro Testing. Molecules V. 23 2018.
ISSN: ESSN 1420-3049
PubMed: 29498707
DOI: 10.3390/MOLECULES23030566
Page generated: Mon Aug 12 16:08:06 2024

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