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Potassium in PDB 5g1a: Bordetella Alcaligenes Hdah Bound to Pfsaha

Enzymatic activity of Bordetella Alcaligenes Hdah Bound to Pfsaha

All present enzymatic activity of Bordetella Alcaligenes Hdah Bound to Pfsaha:
3.5.1.4;

Protein crystallography data

The structure of Bordetella Alcaligenes Hdah Bound to Pfsaha, PDB code: 5g1a 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) 87.96 / 1.42
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.440, 101.440, 175.930, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17

Other elements in 5g1a:

The structure of Bordetella Alcaligenes Hdah Bound to Pfsaha also contains other interesting chemical elements:

Fluorine (F) 24 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Bordetella Alcaligenes Hdah Bound to Pfsaha (pdb code 5g1a). 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 Bound to Pfsaha, PDB code: 5g1a:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5g1a

Go back to Potassium Binding Sites List in 5g1a
Potassium binding site 1 out of 4 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


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 Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K371

b:17.9
occ:1.00
 O A:ASP180 2.6 9.2 1.0
OG A:SER201 2.7 10.8 1.0
O A:HIS182 2.8 10.9 1.0
OD1 A:ASP178 3.0 13.6 1.0
O A:LEU202 3.0 15.5 1.0
CG A:ASP178 3.2 10.9 1.0
O A:ASP178 3.2 12.3 1.0
OD2 A:ASP178 3.4 12.5 1.0
C A:ASP180 3.6 8.8 1.0
C A:ASP178 3.7 9.5 1.0
CB A:SER201 3.8 9.7 1.0
C A:HIS182 3.8 8.8 1.0
CB A:ASP178 3.8 11.0 1.0
C A:LEU202 3.9 10.4 1.0
N A:ASP180 3.9 9.0 1.0
CB A:HIS203 3.9 9.8 1.0
N A:GLY184 3.9 9.6 1.0
N A:LEU202 3.9 9.9 1.0
CA A:SER201 4.0 8.7 1.0
CA A:ASP180 4.2 8.6 1.0
C A:SER201 4.2 9.2 1.0
CA A:HIS183 4.2 8.7 1.0
C A:TRP179 4.3 8.5 1.0
N A:TRP179 4.3 8.9 1.0
CB A:ASP180 4.3 8.9 1.0
CA A:ASP178 4.4 9.5 1.0
CA A:TRP179 4.4 9.3 1.0
C A:HIS183 4.4 9.5 1.0
N A:HIS183 4.4 8.4 1.0
ND1 A:HIS142 4.5 11.8 1.0
CE1 A:HIS142 4.6 11.4 1.0
CA A:HIS203 4.6 9.0 1.0
ND1 A:HIS203 4.6 13.0 1.0
N A:HIS182 4.6 7.6 1.0
N A:HIS203 4.6 9.3 1.0
CA A:LEU202 4.6 10.1 1.0
CG A:HIS203 4.7 10.1 1.0
N A:VAL181 4.7 7.9 1.0
CA A:GLY184 4.8 9.7 1.0
C A:VAL181 4.8 7.9 1.0
CA A:HIS182 4.9 8.2 1.0

Potassium binding site 2 out of 4 in 5g1a

Go back to Potassium Binding Sites List in 5g1a
Potassium binding site 2 out of 4 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


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 Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K372

b:12.7
occ:1.00
 O A:VAL197 2.6 11.9 1.0
O A:HOH2306 2.7 13.5 1.0
O A:TRP191 2.7 12.4 1.0
O A:TYR226 2.9 12.5 1.0
O A:HOH2300 2.9 13.1 1.0
O A:ASP194 2.9 15.7 1.0
CB A:TRP191 3.6 11.9 1.0
C A:TRP191 3.6 12.7 1.0
OG1 A:THR199 3.6 11.5 1.0
C A:TYR226 3.7 11.3 1.0
C A:VAL197 3.9 11.7 1.0
C A:ASP194 4.0 14.8 1.0
CB A:TYR226 4.1 12.2 1.0
CA A:TRP191 4.2 12.4 1.0
N A:THR199 4.3 10.0 1.0
CG2 A:THR199 4.3 10.7 1.0
N A:ASN227 4.5 11.7 1.0
CA A:TYR226 4.5 11.1 1.0
N A:TRP192 4.5 12.3 1.0
CB A:THR199 4.6 11.1 1.0
CA A:LEU198 4.6 11.3 1.0
N A:ASP194 4.6 16.2 1.0
N A:LEU198 4.7 10.8 1.0
CA A:ASP194 4.8 16.9 1.0
CA A:ASN227 4.8 11.2 1.0
O A:TRP192 4.8 14.1 1.0
CA A:TRP192 4.8 12.2 1.0
CB A:ASN227 4.8 11.7 1.0
C A:LEU198 4.8 10.1 1.0
CG A:TRP191 4.8 11.2 1.0
C A:TRP192 4.9 13.2 1.0
CA A:VAL197 4.9 10.8 1.0
N A:PRO195 4.9 14.0 1.0
CA A:PRO195 5.0 15.7 1.0
O A:GLY223 5.0 14.3 1.0
N A:VAL197 5.0 11.8 1.0

Potassium binding site 3 out of 4 in 5g1a

Go back to Potassium Binding Sites List in 5g1a
Potassium binding site 3 out of 4 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


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 Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K371

b:15.6
occ:0.80
 O B:ASP180 2.6 9.5 1.0
OG B:SER201 2.7 11.7 1.0
O B:HIS182 2.8 11.5 1.0
O B:LEU202 3.1 16.0 1.0
OD1 B:ASP178 3.1 13.6 1.0
CG B:ASP178 3.2 11.2 1.0
O B:ASP178 3.2 12.8 1.0
OD2 B:ASP178 3.4 12.5 1.0
C B:ASP180 3.6 9.2 1.0
C B:ASP178 3.7 9.7 1.0
C B:HIS182 3.8 9.7 1.0
CB B:SER201 3.8 10.7 1.0
CB B:ASP178 3.8 11.4 1.0
C B:LEU202 3.9 11.0 1.0
CB B:HIS203 3.9 9.8 1.0
N B:LEU202 3.9 10.1 1.0
N B:GLY184 3.9 9.4 1.0
N B:ASP180 3.9 9.4 1.0
CA B:SER201 4.0 9.4 1.0
CA B:ASP180 4.2 9.2 1.0
C B:SER201 4.2 9.5 1.0
CA B:HIS183 4.2 9.1 1.0
N B:TRP179 4.3 9.4 1.0
CB B:ASP180 4.3 9.6 1.0
C B:TRP179 4.3 9.1 1.0
C B:HIS183 4.4 10.4 1.0
CA B:ASP178 4.4 9.7 1.0
CA B:TRP179 4.4 10.2 1.0
N B:HIS183 4.4 9.2 1.0
ND1 B:HIS142 4.5 12.9 1.0
CE1 B:HIS142 4.5 13.9 1.0
CA B:HIS203 4.6 9.8 1.0
N B:HIS182 4.6 8.6 1.0
ND1 B:HIS203 4.6 13.3 1.0
N B:HIS203 4.6 9.5 1.0
CA B:LEU202 4.6 10.8 1.0
CG B:HIS203 4.7 10.8 1.0
CA B:GLY184 4.7 10.2 1.0
N B:VAL181 4.7 9.1 1.0
C B:VAL181 4.8 8.7 1.0
CA B:HIS182 4.8 8.6 1.0

Potassium binding site 4 out of 4 in 5g1a

Go back to Potassium Binding Sites List in 5g1a
Potassium binding site 4 out of 4 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


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 Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K372

b:12.1
occ:1.00
 O B:VAL197 2.6 12.5 1.0
O B:HOH2290 2.7 13.2 1.0
O B:TRP191 2.7 12.5 1.0
O B:HOH2282 2.9 11.8 1.0
O B:TYR226 2.9 11.5 1.0
O B:ASP194 2.9 14.4 1.0
C B:TRP191 3.6 12.3 1.0
CB B:TRP191 3.6 11.6 1.0
OG1 B:THR199 3.7 11.2 1.0
C B:TYR226 3.7 10.9 1.0
C B:VAL197 3.8 11.2 1.0
C B:ASP194 4.0 13.0 1.0
CB B:TYR226 4.0 12.1 1.0
CA B:TRP191 4.2 12.0 1.0
N B:THR199 4.3 9.7 1.0
CG2 B:THR199 4.3 10.2 1.0
N B:ASN227 4.5 10.6 1.0
CA B:TYR226 4.5 10.9 1.0
N B:TRP192 4.5 12.1 1.0
CB B:THR199 4.6 10.0 1.0
CA B:LEU198 4.6 10.5 1.0
N B:ASP194 4.6 13.5 1.0
N B:LEU198 4.7 10.2 1.0
CA B:ASP194 4.8 13.8 1.0
O B:TRP192 4.8 12.8 1.0
CA B:ASN227 4.8 10.2 1.0
CB B:ASN227 4.8 11.4 1.0
CA B:TRP192 4.8 12.2 1.0
C B:LEU198 4.8 10.4 1.0
CA B:VAL197 4.8 10.5 1.0
C B:TRP192 4.8 12.3 1.0
CG B:TRP191 4.9 10.9 1.0
N B:PRO195 4.9 13.0 1.0
N B:VAL197 5.0 11.4 1.0
O B:GLY223 5.0 13.4 1.0
CA B:PRO195 5.0 14.9 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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