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Potassium in PDB 5g17: Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.

Enzymatic activity of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.

All present enzymatic activity of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.:
3.5.1.4;

Protein crystallography data

The structure of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide., PDB code: 5g17 was solved by A.Kraemer, F.J.Meyer-Almes, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.68 / 1.51
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.270, 101.270, 175.220, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 15.8

Other elements in 5g17:

The structure of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. (pdb code 5g17). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide., PDB code: 5g17:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5g17

Go back to Potassium Binding Sites List in 5g17
Potassium binding site 1 out of 4 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K371

b:10.0
occ:1.00
 O A:ASP180 2.6 7.7 1.0
O A:LEU202 2.7 10.4 1.0
OG A:SER201 2.7 9.3 1.0
O A:HIS182 2.7 8.6 1.0
OD1 A:ASP178 2.7 10.4 1.0
O A:ASP178 2.8 10.2 1.0
CG A:ASP178 3.1 10.4 1.0
OD2 A:ASP178 3.4 11.2 1.0
C A:ASP178 3.6 9.2 1.0
C A:ASP180 3.6 7.5 1.0
C A:LEU202 3.7 9.2 1.0
C A:HIS182 3.8 7.2 1.0
CB A:SER201 3.8 9.9 1.0
N A:LEU202 3.9 8.7 1.0
CB A:ASP178 3.9 10.0 1.0
N A:ASP180 4.0 7.5 1.0
N A:GLY184 4.0 9.1 1.0
CB A:HIS203 4.0 8.6 1.0
CA A:SER201 4.1 8.9 1.0
CA A:ASP180 4.2 7.2 1.0
N A:TRP179 4.2 8.3 1.0
C A:SER201 4.2 9.3 1.0
C A:TRP179 4.3 8.3 1.0
CA A:HIS183 4.3 8.3 1.0
CA A:ASP178 4.4 9.5 1.0
CA A:TRP179 4.4 8.2 1.0
CB A:ASP180 4.4 7.6 1.0
ND1 A:HIS203 4.4 10.3 1.0
CA A:LEU202 4.5 9.7 1.0
CE1 A:HIS142 4.5 8.9 1.0
N A:HIS182 4.5 7.1 1.0
ND1 A:HIS142 4.5 8.7 1.0
N A:HIS183 4.5 7.9 1.0
C A:HIS183 4.5 9.0 1.0
N A:HIS203 4.6 8.8 1.0
CA A:HIS203 4.6 8.6 1.0
CG A:HIS203 4.7 9.5 1.0
N A:VAL181 4.7 7.2 1.0
O A:HOH2291 4.7 9.7 1.0
C A:VAL181 4.8 7.2 1.0
CA A:HIS182 4.8 6.9 1.0
CA A:GLY184 4.9 9.3 1.0

Potassium binding site 2 out of 4 in 5g17

Go back to Potassium Binding Sites List in 5g17
Potassium binding site 2 out of 4 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K372

b:16.8
occ:1.00
 O A:HOH2303 2.6 15.4 1.0
O A:VAL197 2.6 13.1 1.0
O A:TRP191 2.6 12.5 1.0
O A:HOH2296 2.7 17.0 1.0
O A:ASP194 2.7 16.4 1.0
O A:TYR226 2.8 13.7 1.0
C A:TRP191 3.5 11.1 1.0
CB A:TRP191 3.6 10.6 1.0
C A:TYR226 3.7 11.7 1.0
OG1 A:THR199 3.8 13.4 1.0
C A:VAL197 3.8 11.7 1.0
C A:ASP194 3.9 14.8 1.0
CB A:TYR226 4.0 13.2 1.0
CA A:TRP191 4.2 10.8 1.0
N A:THR199 4.3 10.4 1.0
CG2 A:THR199 4.4 11.9 1.0
N A:ASN227 4.5 11.7 1.0
CA A:TYR226 4.5 12.4 1.0
N A:TRP192 4.5 10.4 1.0
N A:ASP194 4.6 13.8 1.0
CA A:LEU198 4.6 11.4 1.0
N A:LEU198 4.6 11.4 1.0
CB A:THR199 4.7 12.1 1.0
CA A:ASP194 4.7 13.8 1.0
CA A:TRP192 4.8 12.5 1.0
O A:TRP192 4.8 12.6 1.0
C A:TRP192 4.8 13.6 1.0
CA A:VAL197 4.8 12.1 1.0
N A:PRO195 4.9 13.7 1.0
C A:LEU198 4.9 10.9 1.0
CB A:ASN227 4.9 11.2 1.0
CA A:ASN227 4.9 10.8 1.0
CG A:TRP191 4.9 11.8 1.0
O A:GLY223 4.9 13.6 1.0
CA A:PRO195 5.0 14.2 1.0
N A:VAL197 5.0 12.0 1.0

Potassium binding site 3 out of 4 in 5g17

Go back to Potassium Binding Sites List in 5g17
Potassium binding site 3 out of 4 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K371

b:10.1
occ:1.00
 O B:ASP180 2.6 7.8 1.0
O B:LEU202 2.7 10.6 1.0
OG B:SER201 2.7 9.9 1.0
O B:HIS182 2.7 8.6 1.0
OD1 B:ASP178 2.7 10.1 1.0
O B:ASP178 2.8 9.7 1.0
CG B:ASP178 3.1 8.8 1.0
OD2 B:ASP178 3.5 9.5 1.0
C B:ASP178 3.6 8.6 1.0
C B:ASP180 3.6 8.3 1.0
C B:LEU202 3.7 9.6 1.0
C B:HIS182 3.8 7.7 1.0
CB B:SER201 3.8 9.9 1.0
N B:LEU202 3.9 9.0 1.0
CB B:ASP178 3.9 9.0 1.0
N B:ASP180 4.0 8.1 1.0
N B:GLY184 4.0 8.3 1.0
CB B:HIS203 4.0 9.1 1.0
CA B:SER201 4.1 9.0 1.0
CA B:ASP180 4.2 7.9 1.0
C B:SER201 4.3 9.5 1.0
N B:TRP179 4.3 8.2 1.0
C B:TRP179 4.3 8.3 1.0
CA B:HIS183 4.3 8.0 1.0
CA B:TRP179 4.4 8.8 1.0
CA B:ASP178 4.4 8.6 1.0
CB B:ASP180 4.4 7.7 1.0
ND1 B:HIS203 4.4 10.3 1.0
CE1 B:HIS142 4.5 9.6 1.0
CA B:LEU202 4.5 10.2 1.0
N B:HIS182 4.5 7.2 1.0
N B:HIS183 4.5 8.0 1.0
ND1 B:HIS142 4.5 8.8 1.0
C B:HIS183 4.5 8.6 1.0
CA B:HIS203 4.5 9.1 1.0
N B:HIS203 4.6 9.1 1.0
CG B:HIS203 4.7 9.9 1.0
O B:HOH2291 4.7 9.5 1.0
N B:VAL181 4.7 7.3 1.0
C B:VAL181 4.7 7.3 1.0
CA B:HIS182 4.8 7.2 1.0
CA B:GLY184 4.9 8.6 1.0
O B:TRP179 5.0 8.6 1.0

Potassium binding site 4 out of 4 in 5g17

Go back to Potassium Binding Sites List in 5g17
Potassium binding site 4 out of 4 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K372

b:10.0
occ:0.70
 O B:HOH2306 2.6 12.9 1.0
O B:VAL197 2.6 10.9 1.0
O B:TRP191 2.7 10.5 1.0
O B:HOH2297 2.8 12.9 1.0
O B:ASP194 2.8 14.1 1.0
O B:TYR226 2.8 10.6 1.0
C B:TRP191 3.5 9.4 1.0
CB B:TRP191 3.6 9.6 1.0
C B:TYR226 3.7 9.5 1.0
OG1 B:THR199 3.8 11.4 1.0
C B:VAL197 3.8 9.4 1.0
C B:ASP194 3.9 11.4 1.0
CB B:TYR226 4.0 11.5 1.0
CA B:TRP191 4.2 9.8 1.0
N B:THR199 4.4 9.8 1.0
CG2 B:THR199 4.4 11.2 1.0
N B:ASN227 4.5 9.8 1.0
CA B:TYR226 4.5 10.3 1.0
N B:TRP192 4.5 10.0 1.0
N B:ASP194 4.6 12.1 1.0
CA B:LEU198 4.6 10.4 1.0
N B:LEU198 4.7 9.7 1.0
CB B:THR199 4.7 10.3 1.0
CA B:ASP194 4.7 11.8 1.0
O B:TRP192 4.8 10.2 1.0
CA B:TRP192 4.8 10.1 1.0
CA B:VAL197 4.8 10.7 1.0
C B:TRP192 4.8 11.4 1.0
CB B:ASN227 4.9 9.9 1.0
CA B:ASN227 4.9 9.0 1.0
C B:LEU198 4.9 10.2 1.0
CG B:TRP191 4.9 10.2 1.0
N B:PRO195 4.9 10.8 1.0
O B:GLY223 4.9 11.7 1.0
N B:VAL197 4.9 10.9 1.0
CA B:PRO195 4.9 11.7 1.0

Reference:

C.Meyners, A.Kramer, O.Yildiz, F.J.Meyer-Almes. The Thermodynamic Signature of Ligand Binding to Histone Deacetylase-Like Amidohydrolases Is Most Sensitive to the Flexibility in the L2-Loop Lining the Active Site Pocket. Biochim. Biophys. Acta V.1861 1855 2017.
ISSN: ISSN 0006-3002
PubMed: 28389333
DOI: 10.1016/J.BBAGEN.2017.04.001
Page generated: Mon Aug 12 13:45:34 2024

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