Atomistry » Potassium » PDB 6hae-6i4g » 6hsg
Atomistry »
  Potassium »
    PDB 6hae-6i4g »
      6hsg »

Potassium in PDB 6hsg: Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149, PDB code: 6hsg was solved by T.B.Shaik, M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.48 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.800, 70.830, 98.350, 78.31, 75.80, 85.98
R / Rfree (%) 20.7 / 25.3

Other elements in 6hsg:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149 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 H292M Mutant Complexed with Ncc-149 (pdb code 6hsg). 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 H292M Mutant Complexed with Ncc-149, PDB code: 6hsg:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6hsg

Go back to Potassium Binding Sites List in 6hsg
Potassium binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:17.2
occ:1.00
 OD1 A:ASP184 2.6 14.5 1.0
O A:ASP186 2.6 15.8 1.0
O A:VAL208 2.7 19.4 1.0
O A:HIS188 2.7 14.0 1.0
OG A:SER207 2.8 13.8 1.0
O A:ASP184 2.8 19.4 1.0
N A:ASP186 3.3 15.6 1.0
CG A:ASP184 3.3 24.8 1.0
C A:ASP186 3.4 19.1 1.0
C A:ASP184 3.5 13.9 1.0
CA A:ASP186 3.6 17.2 1.0
CB A:ASP186 3.7 6.8 1.0
C A:HIS188 3.7 15.2 1.0
C A:VAL208 3.7 16.0 1.0
CB A:ASP184 3.8 16.6 1.0
C A:LEU185 3.9 17.1 1.0
CB A:HIS209 3.9 14.6 1.0
N A:VAL208 4.0 14.7 1.0
CB A:SER207 4.0 15.9 1.0
N A:LEU185 4.1 17.8 1.0
OD2 A:ASP184 4.2 23.9 1.0
CA A:ASP184 4.3 10.8 1.0
CA A:LEU185 4.3 16.5 1.0
N A:GLY190 4.3 15.9 1.0
CA A:SER207 4.4 17.5 1.0
ND1 A:HIS209 4.4 19.4 1.0
CA A:HIS189 4.4 12.8 1.0
N A:HIS188 4.4 20.0 1.0
N A:HIS189 4.4 11.2 1.0
CA A:HIS209 4.5 19.0 1.0
C A:SER207 4.6 15.8 1.0
CA A:VAL208 4.6 21.5 1.0
N A:HIS209 4.6 20.9 1.0
O A:LEU185 4.6 15.8 1.0
N A:LEU187 4.6 17.0 1.0
CG A:HIS209 4.6 14.6 1.0
C A:HIS189 4.7 13.7 1.0
C A:LEU187 4.7 19.7 1.0
CA A:HIS188 4.7 16.3 1.0
CE1 A:HIS141 4.8 21.5 1.0
O A:HOH688 4.8 22.6 1.0
CG A:ASP186 5.0 13.4 1.0

Potassium binding site 2 out of 8 in 6hsg

Go back to Potassium Binding Sites List in 6hsg
Potassium binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:22.3
occ:1.00
 OG A:SER243 2.6 20.0 1.0
O A:PHE197 2.6 15.1 1.0
O A:VAL203 2.7 25.6 1.0
O A:SER200 2.8 18.9 1.0
O A:HOH708 2.9 15.9 1.0
CB A:SER243 3.3 20.2 1.0
O A:SER243 3.4 20.5 1.0
C A:PHE197 3.6 20.8 1.0
C A:SER243 3.8 21.5 1.0
C A:VAL203 3.9 18.3 1.0
C A:SER200 3.9 17.8 1.0
CB A:PHE197 4.0 18.6 1.0
CA A:SER243 4.2 23.1 1.0
N A:SER200 4.4 16.2 1.0
CA A:PHE197 4.4 17.0 1.0
N A:TRP198 4.5 14.4 1.0
CA A:VAL204 4.5 16.1 1.0
N A:ALA244 4.5 20.9 1.0
CA A:SER200 4.6 22.4 1.0
CA A:TRP198 4.6 13.1 1.0
N A:VAL204 4.7 19.9 1.0
N A:THR205 4.7 22.2 1.0
C A:TRP198 4.7 11.1 1.0
CB A:SER200 4.7 21.5 1.0
OG1 A:THR205 4.8 18.4 1.0
O A:GLY240 4.8 24.6 1.0
O A:TRP198 4.8 14.7 1.0
CA A:VAL203 4.8 17.4 1.0
OG A:SER200 4.9 34.1 1.0
CG2 A:THR205 4.9 15.7 1.0
N A:PRO201 4.9 17.0 1.0
CB A:VAL203 5.0 19.4 1.0
N A:VAL203 5.0 18.7 1.0
CA A:ALA244 5.0 20.4 1.0

Potassium binding site 3 out of 8 in 6hsg

Go back to Potassium Binding Sites List in 6hsg
Potassium binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:25.1
occ:1.00
 O B:PHE197 2.5 16.9 1.0
O B:VAL203 2.6 24.9 1.0
OG B:SER243 2.6 26.4 1.0
O B:SER200 2.9 25.8 1.0
O B:HOH732 2.9 13.3 1.0
CB B:SER243 3.3 23.8 1.0
O B:SER243 3.5 25.6 1.0
C B:PHE197 3.5 21.6 1.0
C B:VAL203 3.8 15.7 1.0
C B:SER243 3.9 18.1 1.0
CB B:PHE197 3.9 17.9 1.0
C B:SER200 4.0 25.9 1.0
CA B:SER243 4.3 18.1 1.0
CA B:PHE197 4.4 25.3 1.0
N B:TRP198 4.4 16.9 1.0
N B:SER200 4.5 21.4 1.0
CA B:TRP198 4.5 15.3 1.0
CA B:VAL204 4.6 18.8 1.0
N B:ALA244 4.6 15.1 1.0
O B:TRP198 4.6 18.3 1.0
N B:VAL204 4.6 17.1 1.0
C B:TRP198 4.6 17.9 1.0
CG2 B:THR205 4.6 12.5 1.0
CA B:SER200 4.7 25.2 0.3
CA B:SER200 4.7 26.4 0.7
N B:THR205 4.7 21.3 1.0
CA B:VAL203 4.8 19.5 1.0
OG1 B:THR205 4.8 17.5 1.0
O B:GLY240 4.9 17.6 1.0
CB B:VAL203 4.9 19.2 1.0
N B:VAL203 4.9 22.3 1.0
N B:PRO201 4.9 25.2 1.0
CB B:SER200 5.0 24.0 0.7
CA B:ALA244 5.0 22.4 1.0
CB B:SER200 5.0 24.6 0.3

Potassium binding site 4 out of 8 in 6hsg

Go back to Potassium Binding Sites List in 6hsg
Potassium binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:14.9
occ:1.00
 O B:VAL208 2.6 13.0 1.0
OD1 B:ASP184 2.6 13.3 1.0
O B:ASP186 2.6 21.3 1.0
O B:ASP184 2.7 12.2 1.0
O B:HIS188 2.8 12.2 1.0
OG B:SER207 2.9 16.2 1.0
N B:ASP186 3.3 12.2 1.0
CG B:ASP184 3.3 22.6 1.0
C B:ASP184 3.4 11.4 1.0
C B:ASP186 3.5 15.4 1.0
C B:VAL208 3.7 12.3 1.0
CA B:ASP186 3.7 10.9 1.0
CB B:ASP184 3.7 14.2 1.0
C B:HIS188 3.8 6.5 1.0
CB B:ASP186 3.8 15.3 1.0
C B:LEU185 3.8 13.8 1.0
CB B:HIS209 3.9 6.8 1.0
N B:VAL208 4.0 9.1 1.0
CB B:SER207 4.0 16.0 1.0
N B:LEU185 4.0 14.6 1.0
CA B:ASP184 4.1 14.6 1.0
CA B:LEU185 4.2 10.9 1.0
OD2 B:ASP184 4.2 18.3 1.0
ND1 B:HIS209 4.3 11.1 1.0
N B:GLY190 4.4 9.0 1.0
CA B:SER207 4.4 15.9 1.0
N B:HIS188 4.4 18.7 1.0
CA B:HIS209 4.5 11.1 1.0
C B:SER207 4.5 11.2 1.0
CA B:VAL208 4.5 9.9 1.0
CA B:HIS189 4.5 7.8 1.0
N B:HIS189 4.5 11.1 1.0
N B:HIS209 4.5 11.8 1.0
O B:LEU185 4.5 12.9 1.0
CG B:HIS209 4.6 13.5 1.0
N B:LEU187 4.7 15.5 1.0
C B:LEU187 4.7 15.8 1.0
CA B:HIS188 4.8 11.8 1.0
C B:HIS189 4.8 16.8 1.0
O B:HOH734 4.8 14.0 1.0

Potassium binding site 5 out of 8 in 6hsg

Go back to Potassium Binding Sites List in 6hsg
Potassium binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:19.5
occ:1.00
 O C:PHE197 2.5 17.7 1.0
O C:VAL203 2.7 23.7 1.0
OG C:SER243 2.7 27.3 1.0
O C:HOH736 2.8 14.9 1.0
O C:SER200 3.0 25.2 1.0
O C:SER243 3.4 27.8 1.0
C C:PHE197 3.5 22.9 1.0
CB C:SER243 3.6 22.8 1.0
CB C:PHE197 3.9 19.6 1.0
C C:VAL203 3.9 24.4 1.0
C C:SER243 3.9 25.8 1.0
C C:SER200 4.1 28.8 1.0
CA C:PHE197 4.3 17.9 1.0
N C:TRP198 4.3 16.8 1.0
CA C:TRP198 4.4 18.3 1.0
CA C:SER243 4.4 22.0 1.0
N C:SER200 4.4 22.3 1.0
C C:TRP198 4.5 16.6 1.0
O C:TRP198 4.5 14.9 1.0
N C:ALA244 4.6 14.9 1.0
CA C:VAL204 4.6 24.4 1.0
N C:THR205 4.6 18.8 1.0
OG1 C:THR205 4.7 16.5 1.0
N C:VAL204 4.7 19.1 1.0
CA C:SER200 4.7 28.9 1.0
CG2 C:THR205 4.7 10.2 1.0
CA C:VAL203 4.9 19.2 1.0
CA C:ALA244 4.9 20.3 1.0
O C:GLY240 4.9 18.7 1.0
CB C:ALA244 4.9 23.8 1.0
CB C:SER200 4.9 33.1 1.0
CB C:VAL203 5.0 19.3 1.0

Potassium binding site 6 out of 8 in 6hsg

Go back to Potassium Binding Sites List in 6hsg
Potassium binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:16.0
occ:1.00
 O C:VAL208 2.6 12.1 1.0
OD1 C:ASP184 2.6 15.4 1.0
O C:ASP186 2.6 15.9 1.0
O C:HIS188 2.8 15.9 1.0
O C:ASP184 2.8 12.4 1.0
OG C:SER207 2.9 16.7 1.0
CG C:ASP184 3.3 17.7 1.0
N C:ASP186 3.4 10.2 1.0
C C:ASP184 3.5 10.5 1.0
C C:ASP186 3.5 13.1 1.0
C C:VAL208 3.7 13.7 1.0
CB C:ASP184 3.8 13.1 1.0
CA C:ASP186 3.8 15.3 1.0
C C:HIS188 3.8 7.9 1.0
CB C:HIS209 3.8 8.9 1.0
CB C:ASP186 3.9 14.4 1.0
C C:LEU185 3.9 12.2 1.0
N C:VAL208 4.0 13.7 1.0
CB C:SER207 4.0 17.7 1.0
N C:LEU185 4.1 12.3 1.0
CA C:ASP184 4.2 11.9 1.0
OD2 C:ASP184 4.2 18.7 1.0
ND1 C:HIS209 4.3 10.3 1.0
CA C:LEU185 4.3 13.2 1.0
N C:GLY190 4.4 9.0 1.0
CA C:SER207 4.4 22.9 1.0
N C:HIS188 4.4 15.8 1.0
CA C:HIS209 4.4 8.7 1.0
C C:SER207 4.5 12.6 1.0
CA C:VAL208 4.5 5.5 1.0
CA C:HIS189 4.5 8.7 1.0
N C:HIS209 4.5 14.1 1.0
N C:HIS189 4.5 9.1 1.0
O C:LEU185 4.5 15.3 1.0
CG C:HIS209 4.5 8.8 1.0
N C:LEU187 4.6 16.0 1.0
C C:LEU187 4.7 18.2 1.0
CA C:HIS188 4.7 13.6 1.0
C C:HIS189 4.8 9.1 1.0
O C:HOH735 4.9 16.6 1.0
CG1 C:VAL208 4.9 18.0 1.0

Potassium binding site 7 out of 8 in 6hsg

Go back to Potassium Binding Sites List in 6hsg
Potassium binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:23.4
occ:1.00
 OG D:SER243 2.6 29.0 1.0
O D:PHE197 2.6 15.7 1.0
O D:VAL203 2.6 20.5 1.0
O D:HOH716 2.8 18.0 1.0
O D:SER200 2.8 26.1 1.0
CB D:SER243 3.4 25.5 1.0
O D:SER243 3.4 25.9 1.0
C D:PHE197 3.6 17.4 1.0
C D:SER243 3.8 22.4 1.0
C D:VAL203 3.9 17.9 1.0
C D:SER200 3.9 20.9 1.0
CB D:PHE197 3.9 17.3 1.0
CA D:SER243 4.2 16.2 1.0
N D:SER200 4.4 23.9 1.0
CA D:PHE197 4.4 15.2 1.0
N D:ALA244 4.5 24.1 1.0
N D:TRP198 4.5 18.6 1.0
CA D:VAL204 4.5 18.2 1.0
CA D:SER200 4.6 22.7 0.5
CA D:SER200 4.6 22.7 0.5
N D:THR205 4.6 21.9 1.0
CA D:TRP198 4.6 16.6 1.0
OG1 D:THR205 4.6 17.9 1.0
O D:TRP198 4.6 20.1 1.0
C D:TRP198 4.7 16.4 1.0
N D:VAL204 4.7 17.3 1.0
CB D:SER200 4.7 21.7 0.5
CB D:SER200 4.8 21.7 0.5
O D:GLY240 4.8 23.3 1.0
CG2 D:THR205 4.8 8.6 1.0
CA D:VAL203 4.8 22.1 1.0
CA D:ALA244 4.9 18.8 1.0
N D:PRO201 4.9 23.3 1.0
CB D:VAL203 4.9 26.4 1.0
CB D:ALA244 5.0 16.7 1.0
N D:VAL203 5.0 22.9 1.0

Potassium binding site 8 out of 8 in 6hsg

Go back to Potassium Binding Sites List in 6hsg
Potassium binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:18.2
occ:1.00
 OD1 D:ASP184 2.6 14.7 1.0
O D:HIS188 2.6 12.4 1.0
O D:ASP186 2.6 22.9 1.0
O D:VAL208 2.7 16.9 1.0
OG D:SER207 2.8 13.7 1.0
O D:ASP184 3.0 18.4 1.0
CG D:ASP184 3.4 21.4 1.0
N D:ASP186 3.4 16.0 1.0
C D:ASP186 3.5 18.3 1.0
C D:ASP184 3.5 18.0 1.0
C D:HIS188 3.7 13.6 1.0
C D:VAL208 3.7 16.7 1.0
CA D:ASP186 3.7 12.6 1.0
CB D:ASP186 3.8 12.6 1.0
CB D:ASP184 3.8 12.2 1.0
CB D:HIS209 3.9 13.5 1.0
CB D:SER207 4.0 16.3 1.0
C D:LEU185 4.0 16.6 1.0
N D:VAL208 4.0 18.5 1.0
N D:LEU185 4.1 14.0 1.0
N D:GLY190 4.3 21.1 1.0
OD2 D:ASP184 4.3 26.6 1.0
CA D:ASP184 4.3 11.5 1.0
N D:HIS188 4.3 19.3 1.0
CA D:HIS189 4.3 10.1 1.0
CA D:SER207 4.4 18.4 1.0
N D:HIS189 4.4 13.4 1.0
ND1 D:HIS209 4.4 18.4 1.0
CA D:LEU185 4.4 15.8 1.0
CA D:HIS209 4.4 14.7 1.0
C D:SER207 4.5 20.3 1.0
N D:HIS209 4.5 20.0 1.0
CA D:VAL208 4.6 20.6 1.0
C D:HIS189 4.6 14.4 1.0
C D:LEU187 4.6 25.7 1.0
N D:LEU187 4.6 13.8 1.0
CA D:HIS188 4.6 17.4 1.0
CG D:HIS209 4.6 18.1 1.0
O D:LEU185 4.7 20.4 1.0
CE1 D:HIS141 4.7 14.8 1.0
O D:HOH708 4.8 21.5 1.0
O D:LEU187 5.0 16.2 1.0
CG D:ASP186 5.0 16.4 1.0

Reference:

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087
Page generated: Mon Aug 12 16:23:46 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy