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Potassium in PDB 5g1b: Bordetella Alcaligenes Hdah Native

Enzymatic activity of Bordetella Alcaligenes Hdah Native

All present enzymatic activity of Bordetella Alcaligenes Hdah Native:
3.5.1.4;

Protein crystallography data

The structure of Bordetella Alcaligenes Hdah Native, PDB code: 5g1b 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) 87.56 / 1.70
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.660, 100.660, 175.110, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 19.1

Other elements in 5g1b:

The structure of Bordetella Alcaligenes Hdah Native also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Bordetella Alcaligenes Hdah Native (pdb code 5g1b). 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 Native, PDB code: 5g1b:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5g1b

Go back to Potassium Binding Sites List in 5g1b
Potassium binding site 1 out of 4 in the Bordetella Alcaligenes Hdah Native


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 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K371

b:20.0
occ:1.00
 O A:ASP180 2.6 12.1 1.0
OG A:SER201 2.8 12.1 1.0
O A:HIS182 2.8 13.1 1.0
O A:LEU202 2.9 17.8 1.0
OD1 A:ASP178 2.9 15.2 1.0
O A:ASP178 3.1 14.7 1.0
CG A:ASP178 3.1 13.6 1.0
OD2 A:ASP178 3.4 15.9 1.0
C A:ASP180 3.6 12.6 1.0
C A:ASP178 3.7 12.4 1.0
C A:LEU202 3.8 14.1 1.0
C A:HIS182 3.8 11.9 1.0
CB A:SER201 3.8 11.9 1.0
CB A:ASP178 3.9 13.5 1.0
N A:ASP180 3.9 12.5 1.0
N A:LEU202 3.9 11.6 1.0
N A:GLY184 4.0 11.2 1.0
CB A:HIS203 4.0 12.1 1.0
CA A:SER201 4.1 10.7 1.0
CA A:ASP180 4.2 12.5 1.0
C A:SER201 4.2 11.5 1.0
CB A:ASP180 4.3 9.1 1.0
N A:TRP179 4.3 10.6 1.0
C A:TRP179 4.3 11.3 1.0
CA A:HIS183 4.4 11.2 1.0
CA A:ASP178 4.4 11.8 1.0
CA A:TRP179 4.4 13.3 1.0
ND1 A:HIS142 4.5 15.2 1.0
C A:HIS183 4.5 11.8 1.0
CE1 A:HIS142 4.5 15.1 1.0
N A:HIS183 4.5 11.6 1.0
CA A:HIS203 4.6 12.7 1.0
N A:HIS203 4.6 12.7 1.0
N A:HIS182 4.6 10.1 1.0
CD2 A:HIS203 4.6 14.0 1.0
CA A:LEU202 4.6 14.4 1.0
CG A:HIS203 4.6 13.3 1.0
N A:VAL181 4.8 11.7 1.0
CA A:GLY184 4.8 12.3 1.0
C A:VAL181 4.8 10.6 1.0
CA A:HIS182 4.9 11.2 1.0
O A:HOH2308 4.9 15.2 1.0

Potassium binding site 2 out of 4 in 5g1b

Go back to Potassium Binding Sites List in 5g1b
Potassium binding site 2 out of 4 in the Bordetella Alcaligenes Hdah Native


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 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K372

b:14.6
occ:1.00
 O A:VAL197 2.6 13.2 1.0
O A:TRP191 2.7 15.0 1.0
O A:HOH2320 2.8 17.9 1.0
O A:ASP194 2.8 18.2 1.0
O A:HOH2314 2.8 14.5 1.0
O A:TYR226 2.9 12.7 1.0
C A:TRP191 3.6 13.5 1.0
CB A:TRP191 3.6 14.9 1.0
OG1 A:THR199 3.7 14.4 1.0
C A:TYR226 3.7 13.2 1.0
C A:VAL197 3.8 13.3 1.0
C A:ASP194 4.0 15.9 1.0
CB A:TYR226 4.1 13.8 1.0
CA A:TRP191 4.2 14.6 1.0
CG2 A:THR199 4.3 12.3 1.0
N A:THR199 4.3 11.9 1.0
N A:ASN227 4.5 13.6 1.0
CA A:TYR226 4.5 13.0 1.0
N A:TRP192 4.5 13.9 1.0
CB A:THR199 4.6 13.5 1.0
CA A:LEU198 4.6 12.7 1.0
N A:ASP194 4.6 15.6 1.0
N A:LEU198 4.7 12.2 1.0
CA A:ASP194 4.7 16.4 1.0
O A:TRP192 4.8 14.3 1.0
CB A:ASN227 4.8 12.3 1.0
CA A:TRP192 4.8 14.9 1.0
CA A:ASN227 4.8 12.2 1.0
CA A:VAL197 4.8 13.2 1.0
C A:LEU198 4.8 12.6 1.0
C A:TRP192 4.9 15.9 1.0
CG A:TRP191 4.9 14.2 1.0
N A:PRO195 4.9 15.2 1.0
O A:GLY223 5.0 15.8 1.0
N A:VAL197 5.0 13.9 1.0
CB A:ASP194 5.0 16.3 1.0
CA A:PRO195 5.0 17.3 1.0

Potassium binding site 3 out of 4 in 5g1b

Go back to Potassium Binding Sites List in 5g1b
Potassium binding site 3 out of 4 in the Bordetella Alcaligenes Hdah Native


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 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K371

b:13.2
occ:0.70
 O B:ASP180 2.6 10.7 1.0
OG B:SER201 2.8 10.9 1.0
O B:HIS182 2.8 11.6 1.0
O B:LEU202 2.9 15.8 1.0
OD1 B:ASP178 3.0 13.1 1.0
O B:ASP178 3.1 13.0 1.0
CG B:ASP178 3.2 13.1 1.0
OD2 B:ASP178 3.4 13.3 1.0
C B:ASP180 3.6 10.4 1.0
C B:ASP178 3.7 11.6 1.0
C B:LEU202 3.8 13.6 1.0
C B:HIS182 3.8 10.8 1.0
N B:ASP180 3.9 10.8 1.0
CB B:SER201 3.9 11.1 1.0
CB B:ASP178 3.9 12.6 1.0
N B:LEU202 3.9 10.1 1.0
CB B:HIS203 4.0 10.3 1.0
N B:GLY184 4.0 11.8 1.0
CA B:SER201 4.1 10.7 1.0
CA B:ASP180 4.2 10.3 1.0
C B:SER201 4.2 11.6 1.0
C B:TRP179 4.3 11.2 1.0
CB B:ASP180 4.3 8.5 1.0
N B:TRP179 4.3 10.9 1.0
CA B:HIS183 4.4 11.3 1.0
CA B:TRP179 4.4 12.0 1.0
CA B:ASP178 4.4 10.9 1.0
ND1 B:HIS142 4.5 13.1 1.0
ND1 B:HIS203 4.5 14.2 1.0
C B:HIS183 4.5 12.1 1.0
N B:HIS183 4.5 10.4 1.0
CE1 B:HIS142 4.5 13.1 1.0
N B:HIS203 4.5 11.8 1.0
CA B:HIS203 4.5 12.1 1.0
N B:HIS182 4.6 9.3 1.0
CA B:LEU202 4.6 13.3 1.0
CG B:HIS203 4.7 10.8 1.0
N B:VAL181 4.7 10.0 1.0
CA B:GLY184 4.8 11.5 1.0
C B:VAL181 4.8 9.4 1.0
CA B:HIS182 4.9 9.0 1.0
O B:HOH2252 4.9 12.8 1.0

Potassium binding site 4 out of 4 in 5g1b

Go back to Potassium Binding Sites List in 5g1b
Potassium binding site 4 out of 4 in the Bordetella Alcaligenes Hdah Native


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 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K372

b:15.1
occ:1.00
 O B:VAL197 2.6 12.0 1.0
O B:HOH2264 2.7 13.7 1.0
O B:TRP191 2.7 14.4 1.0
O B:ASP194 2.8 16.9 1.0
O B:TYR226 2.8 13.9 1.0
O B:HOH2258 2.9 15.4 1.0
C B:TRP191 3.6 14.0 1.0
CB B:TRP191 3.6 14.0 1.0
C B:TYR226 3.7 14.3 1.0
OG1 B:THR199 3.7 13.2 1.0
C B:VAL197 3.8 13.7 1.0
C B:ASP194 4.0 16.6 1.0
CB B:TYR226 4.0 12.2 1.0
CA B:TRP191 4.2 13.1 1.0
N B:THR199 4.3 12.5 1.0
CG2 B:THR199 4.3 14.8 1.0
N B:ASN227 4.4 13.2 1.0
CA B:TYR226 4.5 12.1 1.0
N B:TRP192 4.5 13.1 1.0
CA B:LEU198 4.6 12.5 1.0
CB B:THR199 4.6 13.2 1.0
N B:ASP194 4.6 18.5 1.0
N B:LEU198 4.6 13.5 1.0
CA B:ASP194 4.7 18.1 1.0
O B:TRP192 4.8 13.3 1.0
CB B:ASN227 4.8 10.8 1.0
CA B:ASN227 4.8 12.2 1.0
CA B:TRP192 4.8 14.6 1.0
C B:LEU198 4.8 12.9 1.0
C B:TRP192 4.8 15.5 1.0
CG B:TRP191 4.9 13.6 1.0
CA B:VAL197 4.9 13.1 1.0
N B:PRO195 4.9 15.8 1.0
CA B:PRO195 5.0 15.9 1.0
O B:GLY223 5.0 16.0 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: Sun Dec 13 23:58:45 2020

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