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Potassium in PDB 2vcg: Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17

Protein crystallography data

The structure of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17, PDB code: 2vcg was solved by A.Dickmanns, A.Strasser, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 117.85 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.664, 93.633, 121.664, 90.00, 103.99, 90.00
R / Rfree (%) 15.6 / 20.6

Other elements in 2vcg:

The structure of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 (pdb code 2vcg). 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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17, PDB code: 2vcg:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 2vcg

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Potassium binding site 1 out of 8 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1376

b:12.7
occ:1.00
 O A:LEU208 2.6 12.6 1.0
O A:ASP186 2.6 10.5 1.0
O A:HIS188 2.6 10.2 1.0
OG A:SER207 2.7 10.9 1.0
OD2 A:ASP184 2.7 9.9 1.0
O A:ASP184 3.0 12.0 1.0
CG A:ASP184 3.1 11.4 1.0
OD1 A:ASP184 3.5 13.3 1.0
C A:LEU208 3.6 12.5 1.0
C A:ASP184 3.6 11.4 1.0
C A:ASP186 3.7 10.0 1.0
C A:HIS188 3.7 10.7 1.0
CB A:SER207 3.8 13.1 1.0
N A:LEU208 3.8 12.5 1.0
CB A:HIS209 4.0 12.2 1.0
N A:GLY190 4.0 12.3 1.0
N A:ASP186 4.0 10.6 1.0
CB A:ASP184 4.0 11.2 1.0
CA A:SER207 4.1 13.0 1.0
C A:SER207 4.2 13.3 1.0
N A:TRP185 4.3 10.3 1.0
ND1 A:HIS209 4.3 12.7 1.0
C A:TRP185 4.3 10.4 1.0
CA A:HIS189 4.3 12.0 1.0
CA A:ASP186 4.3 10.3 1.0
CA A:TRP185 4.3 10.4 1.0
CA A:LEU208 4.4 12.6 1.0
N A:HIS209 4.4 12.8 1.0
N A:HIS188 4.4 9.7 1.0
CB A:ASP186 4.4 10.0 1.0
CA A:ASP184 4.4 11.5 1.0
ND1 A:HIS148 4.4 11.7 1.0
N A:HIS189 4.5 11.5 1.0
CA A:HIS209 4.5 12.4 1.0
C A:HIS189 4.5 12.5 1.0
CE1 A:HIS148 4.5 11.4 1.0
O A:HOH2279 4.6 10.8 1.0
CG A:HIS209 4.6 13.4 1.0
C A:VAL187 4.6 9.6 1.0
CA A:HIS188 4.7 10.4 1.0
N A:VAL187 4.7 9.4 1.0
CA A:GLY190 4.9 12.5 1.0
OD1 A:ASP186 4.9 12.4 1.0

Potassium binding site 2 out of 8 in 2vcg

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Potassium binding site 2 out of 8 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1377

b:31.3
occ:1.00
 O A:HOH2242 2.2 30.2 1.0
O A:ASP200 2.4 18.5 1.0
O A:HOH2269 2.4 16.3 1.0
O A:VAL203 2.4 14.6 1.0
O A:TRP197 2.5 16.3 1.0
O A:TYR232 3.3 17.8 1.0
C A:TRP197 3.4 16.3 1.0
C A:ASP200 3.4 19.2 1.0
CB A:TRP197 3.5 15.8 1.0
C A:VAL203 3.6 14.4 1.0
CB A:TYR232 3.9 18.2 1.0
O A:HOH2229 3.9 34.1 1.0
C A:TYR232 4.0 17.7 1.0
CA A:TRP197 4.1 16.2 1.0
N A:ASP200 4.1 19.4 1.0
CA A:ASP200 4.2 18.9 1.0
N A:PRO201 4.4 18.8 1.0
N A:TRP198 4.5 17.1 1.0
CA A:VAL203 4.5 15.4 1.0
CA A:PRO201 4.5 18.7 1.0
N A:LEU204 4.5 14.4 1.0
OG1 A:THR205 4.5 17.4 1.0
N A:VAL203 4.5 16.0 1.0
CB A:ASP200 4.6 19.0 1.0
CA A:TYR232 4.6 18.2 1.0
O A:TRP198 4.6 18.5 1.0
CA A:LEU204 4.6 13.9 1.0
O A:GLY229 4.7 20.5 1.0
C A:TRP198 4.7 18.1 1.0
CG2 A:THR205 4.7 14.8 1.0
CB A:VAL203 4.7 15.2 1.0
N A:THR205 4.7 14.2 1.0
CA A:TRP198 4.8 18.1 1.0
CG A:TRP197 4.8 15.7 1.0
N A:ASN233 4.9 17.6 1.0
CA A:GLY229 4.9 21.4 1.0
C A:PRO201 4.9 18.1 1.0

Potassium binding site 3 out of 8 in 2vcg

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Potassium binding site 3 out of 8 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1377

b:10.1
occ:1.00
 O B:ASP186 2.5 6.8 1.0
O B:LEU208 2.6 8.4 1.0
O B:HIS188 2.7 6.7 1.0
OG B:SER207 2.7 8.4 1.0
OD1 B:ASP184 2.8 7.8 1.0
O B:ASP184 3.0 6.3 1.0
CG B:ASP184 3.1 8.5 1.0
OD2 B:ASP184 3.5 10.7 1.0
C B:ASP186 3.6 6.7 1.0
C B:ASP184 3.6 6.9 1.0
C B:LEU208 3.6 7.9 1.0
C B:HIS188 3.7 6.7 1.0
N B:LEU208 3.8 7.9 1.0
CB B:SER207 3.9 7.7 1.0
N B:ASP186 3.9 7.4 1.0
CB B:ASP184 3.9 6.9 1.0
N B:GLY190 4.0 7.0 1.0
CB B:HIS209 4.0 6.6 1.0
CA B:SER207 4.1 7.7 1.0
CA B:ASP186 4.2 6.7 1.0
C B:SER207 4.3 7.8 1.0
CD2 B:HIS209 4.3 7.8 1.0
C B:TRP185 4.3 7.5 1.0
N B:TRP185 4.3 6.1 1.0
CA B:TRP185 4.3 7.3 1.0
CA B:HIS189 4.3 6.8 1.0
CE1 B:HIS148 4.3 6.7 1.0
N B:HIS188 4.3 6.5 1.0
ND1 B:HIS148 4.3 7.2 1.0
CB B:ASP186 4.4 6.5 1.0
CA B:ASP184 4.4 6.9 1.0
CA B:LEU208 4.5 8.7 1.0
N B:HIS189 4.5 7.3 1.0
C B:HIS189 4.5 7.0 1.0
N B:HIS209 4.5 7.3 1.0
CA B:HIS209 4.5 7.1 1.0
CG B:HIS209 4.5 7.8 1.0
O B:HOH2318 4.6 6.5 1.0
C B:VAL187 4.6 6.2 1.0
N B:VAL187 4.6 6.4 1.0
CA B:HIS188 4.7 6.9 1.0
CA B:GLY190 4.8 6.5 1.0
OD1 B:ASP186 4.9 6.0 1.0
CA B:VAL187 5.0 6.3 1.0

Potassium binding site 4 out of 8 in 2vcg

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Potassium binding site 4 out of 8 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1378

b:22.9
occ:1.00
 O B:VAL203 2.3 7.1 1.0
O B:ASP200 2.4 11.9 1.0
O B:HOH2308 2.4 9.0 1.0
O B:TRP197 2.5 8.2 1.0
O B:TYR232 3.4 9.9 1.0
CB B:TRP197 3.5 7.1 1.0
C B:ASP200 3.5 11.7 1.0
C B:TRP197 3.5 8.1 1.0
C B:VAL203 3.5 8.2 1.0
O B:HOH2275 3.6 25.9 1.0
CB B:TYR232 3.9 9.6 1.0
CA B:TRP197 4.0 7.9 1.0
C B:TYR232 4.1 9.7 1.0
N B:ASP200 4.2 12.1 1.0
CA B:ASP200 4.3 11.8 1.0
N B:VAL203 4.3 9.4 1.0
CA B:VAL203 4.4 8.5 1.0
N B:PRO201 4.4 11.5 1.0
N B:LEU204 4.5 8.1 1.0
OG1 B:THR205 4.5 10.9 1.0
CA B:PRO201 4.5 10.9 1.0
CA B:LEU204 4.5 8.3 1.0
N B:TRP198 4.5 8.2 1.0
CB B:ASP200 4.6 11.9 1.0
CA B:TYR232 4.6 9.6 1.0
CB B:VAL203 4.6 7.6 1.0
N B:THR205 4.6 7.8 1.0
O B:TRP198 4.7 8.9 1.0
CG B:TRP197 4.7 9.1 1.0
C B:TRP198 4.8 9.6 1.0
CG2 B:THR205 4.8 8.8 1.0
O B:GLY229 4.8 8.8 1.0
C B:PRO201 4.8 10.5 1.0
CA B:TRP198 4.9 9.2 1.0
C B:LEU204 5.0 7.9 1.0
N B:ASN233 5.0 9.8 1.0

Potassium binding site 5 out of 8 in 2vcg

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Potassium binding site 5 out of 8 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1378

b:9.1
occ:1.00
 O C:ASP186 2.5 6.5 1.0
O C:LEU208 2.6 9.3 1.0
O C:HIS188 2.6 7.3 1.0
OD2 C:ASP184 2.7 6.9 1.0
OG C:SER207 2.7 6.8 1.0
O C:ASP184 3.0 7.3 1.0
CG C:ASP184 3.1 7.8 1.0
OD1 C:ASP184 3.5 9.9 1.0
C C:ASP184 3.6 7.9 1.0
C C:LEU208 3.6 9.2 1.0
C C:ASP186 3.6 7.2 1.0
C C:HIS188 3.7 7.3 1.0
N C:LEU208 3.8 8.2 1.0
CB C:SER207 3.9 7.3 1.0
N C:GLY190 3.9 8.8 1.0
N C:ASP186 3.9 8.0 1.0
CB C:ASP184 3.9 7.0 1.0
CB C:HIS209 4.1 8.8 1.0
CA C:SER207 4.1 7.6 1.0
N C:TRP185 4.2 7.1 1.0
CA C:ASP186 4.2 7.3 1.0
C C:SER207 4.3 8.4 1.0
C C:TRP185 4.3 7.7 1.0
CA C:HIS189 4.3 8.5 1.0
CD2 C:HIS209 4.3 8.9 1.0
CA C:TRP185 4.3 7.9 1.0
CB C:ASP186 4.4 6.9 1.0
CA C:ASP184 4.4 7.3 1.0
CA C:LEU208 4.4 9.3 1.0
N C:HIS188 4.4 6.6 1.0
ND1 C:HIS148 4.4 6.7 1.0
N C:HIS189 4.5 6.6 1.0
C C:HIS189 4.5 8.3 1.0
N C:HIS209 4.5 8.3 1.0
CE1 C:HIS148 4.5 7.6 1.0
CA C:HIS209 4.5 8.2 1.0
O C:HOH2293 4.5 8.1 1.0
CG C:HIS209 4.6 9.2 1.0
C C:VAL187 4.6 7.0 1.0
N C:VAL187 4.7 6.9 1.0
CA C:HIS188 4.7 7.2 1.0
CA C:GLY190 4.9 8.2 1.0
OD1 C:ASP186 4.9 6.4 1.0
CA C:VAL187 5.0 6.6 1.0

Potassium binding site 6 out of 8 in 2vcg

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Potassium binding site 6 out of 8 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1379

b:25.9
occ:1.00
 O C:ASP200 2.4 9.5 1.0
O C:HOH2281 2.4 12.2 1.0
O C:VAL203 2.4 8.0 1.0
O C:TRP197 2.4 7.9 1.0
O C:HOH2258 3.1 26.8 1.0
O C:TYR232 3.4 10.6 1.0
C C:TRP197 3.4 7.7 1.0
CB C:TRP197 3.5 7.2 1.0
C C:ASP200 3.5 10.4 1.0
C C:VAL203 3.6 7.8 1.0
CB C:TYR232 3.9 10.0 1.0
CA C:TRP197 4.0 8.1 1.0
C C:TYR232 4.0 10.2 1.0
N C:ASP200 4.1 11.1 1.0
CA C:ASP200 4.2 10.6 1.0
OG1 C:THR205 4.4 10.8 1.0
N C:TRP198 4.4 9.2 1.0
CA C:VAL203 4.4 7.8 1.0
CB C:ASP200 4.5 10.0 1.0
N C:VAL203 4.5 8.7 1.0
N C:PRO201 4.5 9.8 1.0
N C:LEU204 4.5 8.2 1.0
CA C:TYR232 4.6 10.4 1.0
O C:TRP198 4.6 9.3 1.0
CA C:PRO201 4.6 9.2 1.0
CA C:LEU204 4.7 8.9 1.0
C C:TRP198 4.7 9.6 1.0
CB C:VAL203 4.7 8.1 1.0
CG C:TRP197 4.7 8.3 1.0
N C:THR205 4.7 9.0 1.0
CA C:TRP198 4.8 9.1 1.0
O C:GLY229 4.8 11.5 1.0
N C:ASN233 4.9 10.1 1.0
CG2 C:THR205 4.9 8.3 1.0
C C:PRO201 4.9 9.0 1.0

Potassium binding site 7 out of 8 in 2vcg

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Potassium binding site 7 out of 8 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1379

b:11.3
occ:1.00
 O D:ASP186 2.5 9.7 1.0
O D:HIS188 2.6 10.2 1.0
O D:LEU208 2.7 11.7 1.0
OG D:SER207 2.7 11.8 1.0
OD1 D:ASP184 2.7 9.9 1.0
O D:ASP184 2.9 11.0 1.0
CG D:ASP184 3.1 10.6 1.0
OD2 D:ASP184 3.3 7.6 1.0
C D:ASP186 3.6 9.7 1.0
C D:ASP184 3.6 10.5 1.0
C D:LEU208 3.7 11.7 1.0
C D:HIS188 3.7 10.0 1.0
N D:LEU208 3.9 11.4 1.0
CB D:SER207 3.9 10.3 1.0
CB D:ASP184 3.9 10.4 1.0
N D:ASP186 4.0 9.3 1.0
N D:GLY190 4.0 10.6 1.0
CB D:HIS209 4.1 10.3 1.0
CA D:SER207 4.2 11.1 1.0
N D:TRP185 4.2 9.3 1.0
CA D:ASP186 4.2 9.6 1.0
C D:TRP185 4.3 9.6 1.0
ND1 D:HIS209 4.3 11.5 1.0
C D:SER207 4.3 11.3 1.0
CA D:TRP185 4.3 9.6 1.0
CA D:HIS189 4.3 10.4 1.0
ND1 D:HIS148 4.3 9.1 1.0
N D:HIS188 4.4 9.6 1.0
CA D:ASP184 4.4 10.8 1.0
CE1 D:HIS148 4.4 12.0 1.0
CB D:ASP186 4.4 9.6 1.0
C D:HIS189 4.4 10.1 1.0
N D:HIS189 4.4 9.8 1.0
CA D:LEU208 4.5 11.7 1.0
N D:HIS209 4.5 11.1 1.0
CA D:HIS209 4.5 11.2 1.0
O D:HOH2315 4.6 9.6 1.0
C D:VAL187 4.7 9.6 1.0
CG D:HIS209 4.7 12.0 1.0
N D:VAL187 4.7 9.5 1.0
CA D:HIS188 4.7 9.7 1.0
CA D:GLY190 4.9 10.0 1.0
OD1 D:ASP186 5.0 8.9 1.0
CA D:VAL187 5.0 9.6 1.0

Potassium binding site 8 out of 8 in 2vcg

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Potassium binding site 8 out of 8 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1380

b:27.2
occ:1.00
 O D:HOH2279 2.3 21.1 1.0
O D:HOH2304 2.4 12.9 1.0
O D:ASP200 2.4 13.7 1.0
O D:TRP197 2.4 13.1 1.0
O D:VAL203 2.4 11.4 1.0
O D:TYR232 3.4 13.7 1.0
C D:TRP197 3.4 12.8 1.0
CB D:TRP197 3.5 11.9 1.0
C D:ASP200 3.5 14.1 1.0
C D:VAL203 3.7 11.7 1.0
CB D:TYR232 3.9 13.9 1.0
O D:HOH2262 3.9 27.1 1.0
C D:TYR232 4.0 13.7 1.0
CA D:TRP197 4.0 12.0 1.0
N D:ASP200 4.2 14.3 1.0
CA D:ASP200 4.3 14.4 1.0
N D:TRP198 4.4 13.0 1.0
OG1 D:THR205 4.4 14.8 1.0
N D:PRO201 4.4 13.7 1.0
CA D:PRO201 4.5 13.6 1.0
CB D:ASP200 4.5 14.3 1.0
N D:VAL203 4.5 12.4 1.0
CA D:VAL203 4.5 12.1 1.0
CA D:TYR232 4.6 13.7 1.0
N D:LEU204 4.6 11.4 1.0
N D:THR205 4.6 12.0 1.0
CA D:LEU204 4.6 11.6 1.0
O D:TRP198 4.6 12.1 1.0
CB D:VAL203 4.7 11.7 1.0
O D:GLY229 4.7 15.3 1.0
C D:TRP198 4.7 12.8 1.0
CG D:TRP197 4.7 12.2 1.0
N D:ASN233 4.8 13.5 1.0
CA D:TRP198 4.8 13.1 1.0
C D:PRO201 4.9 13.5 1.0
CG2 D:THR205 4.9 13.8 1.0
CA D:GLY229 5.0 15.7 1.0

Reference:

S.Schaefer, L.Saunders, E.Eliseeva, A.Velena, M.Jung, A.Schwienhorst, A.Strasser, A.Dickmanns, R.Ficner, S.Schlimme, W.Sippl, E.Verdin, M.Jung. Phenylalanine-Containing Hydroxamic Acids As Selective Inhibitors of Class Iib Histone Deacetylases (Hdacs). Bioorg.Med.Chem. V. 16 2011 2008.
ISSN: ISSN 0968-0896
PubMed: 18054239
DOI: 10.1016/J.BMC.2007.10.092
Page generated: Mon Aug 12 07:09:43 2024

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