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Calcium in PDB 5min: Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus

Enzymatic activity of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus

All present enzymatic activity of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus:
1.1.5.2;

Protein crystallography data

The structure of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus, PDB code: 5min was solved by C.Stines-Chaumeil, F.Mavre, B.Limoges, B.Kauffmann, N.Mano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.73 / 1.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.407, 54.898, 85.474, 88.04, 81.58, 69.62
R / Rfree (%) 17.8 / 21.4

Other elements in 5min:

The structure of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus (pdb code 5min). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus, PDB code: 5min:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5min

Go back to Calcium Binding Sites List in 5min
Calcium binding site 1 out of 6 in the Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:8.9
occ:1.00
 O A:TYR263 2.4 7.2 1.0
OE2 A:GLU253 2.4 16.1 1.0
O A:HOH758 2.4 9.6 1.0
O A:HOH871 2.5 8.7 1.0
O A:HOH651 2.5 11.8 1.0
O A:HOH613 2.5 8.2 1.0
OE1 A:GLU253 2.5 7.8 1.0
CD A:GLU253 2.8 16.4 1.0
C A:TYR263 3.5 8.5 1.0
CB A:TYR263 4.0 7.4 1.0
CA A:TYR263 4.2 7.8 1.0
CG A:GLU253 4.3 9.7 1.0
O A:VAL268 4.3 9.6 1.0
N A:GLY270 4.3 7.4 1.0
O A:HOH900 4.5 23.2 1.0
O A:GLY270 4.5 10.0 1.0
O A:GLY226 4.5 7.8 1.0
ND2 A:ASN255 4.6 7.6 1.0
OE2 A:GLU245 4.6 11.2 1.0
N A:GLY264 4.6 6.9 1.0
O A:HOH851 4.7 10.7 1.0
N A:TRP265 4.7 6.9 1.0
OD1 A:ASN255 4.7 14.6 1.0
CA A:GLY270 4.9 7.7 1.0
O A:VAL318 4.9 10.9 1.0
CE1 A:PHE317 4.9 11.2 1.0
CA A:GLY264 5.0 6.8 1.0

Calcium binding site 2 out of 6 in 5min

Go back to Calcium Binding Sites List in 5min
Calcium binding site 2 out of 6 in the Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:11.1
occ:1.00
 O A:ALA269 2.3 7.2 1.0
O A:HOH753 2.4 11.2 1.0
O A:TYR271 2.4 10.6 1.0
OD1 A:ASP273 2.4 9.9 1.0
OE2 A:GLU309 2.5 9.4 1.0
OE1 A:GLU309 2.5 9.7 1.0
O A:HOH688 2.6 6.8 1.0
CD A:GLU309 2.8 10.7 1.0
CG A:ASP273 3.4 12.7 1.0
C A:ALA269 3.5 10.7 1.0
C A:TYR271 3.6 11.6 1.0
OD2 A:ASP273 3.8 10.8 1.0
N A:TYR271 3.9 8.6 1.0
N A:ASP273 4.0 10.6 1.0
C A:GLY270 4.2 10.3 1.0
CG A:GLU309 4.3 9.8 1.0
N A:ALA269 4.3 8.8 1.0
CA A:TYR271 4.3 8.5 1.0
OD2 A:ASP251 4.3 10.3 1.0
O A:SER275 4.4 11.6 1.0
CA A:ALA269 4.4 8.9 1.0
CA A:GLY270 4.4 7.7 1.0
N A:GLY270 4.5 7.4 1.0
OD1 A:ASP251 4.5 12.9 1.0
CB A:ASP273 4.5 11.0 1.0
N A:ASP274 4.5 9.3 1.0
N A:SER275 4.6 9.9 1.0
CG A:ASP251 4.6 12.8 1.0
CG1 A:VAL268 4.6 11.7 1.0
N A:LYS272 4.6 8.1 1.0
CB A:ALA269 4.7 10.6 1.0
CA A:ASP273 4.7 9.8 1.0
O A:GLY270 4.8 10.0 1.0
CA A:LYS272 4.8 8.6 1.0
CB A:TYR277 4.9 8.3 1.0
CB A:TYR271 4.9 9.5 1.0
C A:LYS272 4.9 13.2 1.0
C A:ASP273 5.0 11.2 1.0

Calcium binding site 3 out of 6 in 5min

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Calcium binding site 3 out of 6 in the Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:27.1
occ:1.00
 O A:HOH930 3.0 26.1 1.0
O A:HOH684 3.0 23.1 1.0
NH1 A:ARG406 3.3 16.5 1.0
O A:HOH969 3.4 18.4 1.0
NH2 A:ARG406 3.5 18.4 1.0
CZ A:ARG406 3.9 25.1 1.0
CB A:ALA350 3.9 11.9 1.0
CB A:LEU376 4.1 9.1 1.0
CE2 A:TYR343 4.1 20.2 1.0
CB A:LYS377 4.3 18.3 1.0
CD1 A:LEU376 4.4 10.9 1.0
N A:LYS377 4.6 13.8 1.0
CA A:LYS377 4.8 15.1 1.0
OH A:TYR343 4.9 21.8 1.0
CG A:LEU376 4.9 11.6 1.0
CD2 A:TYR343 4.9 19.5 1.0
C A:LEU376 4.9 16.8 1.0
O A:HOH1073 5.0 51.8 1.0
OE1 A:GLN246 5.0 18.4 1.0
CZ A:TYR343 5.0 26.3 1.0

Calcium binding site 4 out of 6 in 5min

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Calcium binding site 4 out of 6 in the Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:10.6
occ:1.00
 O B:TYR263 2.4 5.8 1.0
O B:HOH723 2.4 8.0 1.0
OE2 B:GLU253 2.4 11.7 1.0
O B:HOH634 2.4 10.2 1.0
OE1 B:GLU253 2.5 8.4 1.0
O B:HOH880 2.5 10.1 1.0
O B:HOH629 2.5 10.9 1.0
CD B:GLU253 2.8 14.7 1.0
C B:TYR263 3.5 9.3 1.0
CB B:TYR263 4.1 6.3 1.0
CA B:TYR263 4.2 6.2 1.0
O B:VAL268 4.3 7.7 1.0
CG B:GLU253 4.3 10.1 1.0
N B:GLY270 4.4 8.8 1.0
O B:GLY270 4.5 9.6 1.0
O B:GLY226 4.6 9.7 1.0
OE2 B:GLU245 4.6 13.1 1.0
N B:GLY264 4.6 7.2 1.0
OD1 B:ASN255 4.6 11.5 1.0
O B:HOH805 4.6 11.4 1.0
N B:TRP265 4.7 9.7 1.0
ND2 B:ASN255 4.8 8.5 1.0
O B:HOH795 4.8 31.9 1.0
CA B:GLY264 4.9 7.6 1.0
CA B:GLY270 4.9 8.9 1.0
O B:VAL318 4.9 9.7 1.0
CE1 B:PHE317 5.0 12.2 1.0
CD B:PRO320 5.0 8.1 1.0

Calcium binding site 5 out of 6 in 5min

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Calcium binding site 5 out of 6 in the Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:11.4
occ:1.00
 O B:HOH707 2.3 10.0 1.0
O B:ALA269 2.4 10.9 1.0
O B:TYR271 2.4 8.8 1.0
OD1 B:ASP273 2.5 10.7 1.0
OE2 B:GLU309 2.5 10.5 1.0
OE1 B:GLU309 2.5 10.2 1.0
O B:HOH638 2.5 8.8 1.0
CD B:GLU309 2.8 11.7 1.0
CG B:ASP273 3.4 13.0 1.0
C B:TYR271 3.6 10.8 1.0
C B:ALA269 3.6 12.0 1.0
OD2 B:ASP273 3.9 11.7 1.0
N B:TYR271 3.9 8.3 1.0
N B:ASP273 4.0 10.0 1.0
C B:GLY270 4.2 11.1 1.0
N B:ALA269 4.3 8.5 1.0
CA B:TYR271 4.3 7.1 1.0
CG B:GLU309 4.3 10.2 1.0
O B:SER275 4.3 10.0 1.0
OD2 B:ASP251 4.4 13.5 1.0
CA B:ALA269 4.5 8.5 1.0
CA B:GLY270 4.5 8.9 1.0
N B:GLY270 4.5 8.8 1.0
OD1 B:ASP251 4.5 12.8 1.0
N B:ASP274 4.6 9.2 1.0
CG1 B:VAL268 4.6 12.3 1.0
CB B:ASP273 4.6 8.9 1.0
N B:LYS272 4.6 8.3 1.0
N B:SER275 4.6 9.8 1.0
CG B:ASP251 4.6 13.0 1.0
CA B:ASP273 4.7 8.9 1.0
CB B:ALA269 4.7 10.5 1.0
CA B:LYS272 4.8 8.7 1.0
O B:GLY270 4.8 9.6 1.0
CB B:TYR277 4.9 10.3 1.0
CB B:TYR271 4.9 8.4 1.0
C B:LYS272 4.9 13.5 1.0

Calcium binding site 6 out of 6 in 5min

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Calcium binding site 6 out of 6 in the Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:41.9
occ:1.00
 O B:HOH759 2.3 20.0 1.0
O B:HOH952 2.3 27.4 1.0
O B:HOH810 2.4 12.1 1.0
O B:HOH662 2.4 15.2 1.0
O B:HOH1057 2.5 35.9 1.0
NE2 B:HIS193 3.9 17.7 1.0
CG2 B:THR194 4.0 8.6 1.0
ND1 B:HIS180 4.2 17.7 1.0
OE2 B:GLU186 4.3 14.1 1.0
O B:THR181 4.6 13.8 1.0
CE1 B:HIS193 4.7 17.6 1.0
OE1 B:GLU186 4.7 17.6 1.0
NE2 B:GLN177 4.8 10.9 1.0
CD2 B:HIS193 4.9 17.4 1.0
CB B:HIS180 4.9 11.0 1.0
CD B:GLU186 5.0 19.2 1.0

Reference:

C.Stines-Chaumeil, F.Mavre, B.Limoges, B.Kauffmann, N.Mano. Apo Form of the Soluble Pqq-Dependent Glucose Dehydrogenase From Acinetobacter Calcoaceticus To Be Published.
Page generated: Wed Jul 9 08:24:39 2025

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