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Calcium in PDB 1cq1: Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose

Enzymatic activity of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose

All present enzymatic activity of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose:
1.1.99.17;

Protein crystallography data

The structure of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose, PDB code: 1cq1 was solved by A.Oubrie, H.J.Rozeboom, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.899, 91.972, 85.747, 90.00, 104.62, 90.00
R / Rfree (%) 19 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose (pdb code 1cq1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose, PDB code: 1cq1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1cq1

Go back to Calcium Binding Sites List in 1cq1
Calcium binding site 1 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:10.1
occ:1.00
 O A:TYR271 2.3 6.7 1.0
O A:HOH545 2.4 7.4 1.0
O A:ALA269 2.4 10.4 1.0
O A:HOH520 2.4 4.6 1.0
OE2 A:GLU309 2.4 14.6 1.0
OD1 A:ASP273 2.4 14.0 1.0
OE1 A:GLU309 2.5 11.2 1.0
CD A:GLU309 2.8 11.9 1.0
CG A:ASP273 3.3 12.3 1.0
C A:TYR271 3.5 6.6 1.0
C A:ALA269 3.5 8.3 1.0
OD2 A:ASP273 3.7 7.4 1.0
N A:TYR271 3.8 5.9 1.0
N A:ASP273 3.9 9.5 1.0
C A:GLY270 4.1 4.9 1.0
CA A:TYR271 4.2 4.1 1.0
N A:ALA269 4.3 7.6 1.0
OD2 A:ASP251 4.3 9.6 1.0
CG A:GLU309 4.3 11.0 1.0
O A:SER275 4.3 13.0 1.0
CA A:ALA269 4.4 8.1 1.0
N A:GLY270 4.4 5.5 1.0
CA A:GLY270 4.5 5.0 1.0
N A:ASP274 4.5 11.3 1.0
OD1 A:ASP251 4.5 7.4 1.0
CB A:ASP273 4.5 8.4 1.0
CG1 A:VAL268 4.5 7.9 1.0
CG A:ASP251 4.6 10.9 1.0
N A:LYS272 4.6 7.6 1.0
CB A:ALA269 4.6 8.0 1.0
N A:SER275 4.6 12.0 1.0
CA A:ASP273 4.7 11.2 1.0
O A:GLY270 4.7 7.1 1.0
CA A:LYS272 4.7 9.0 1.0
CB A:TYR271 4.7 2.0 1.0
C A:LYS272 4.9 10.2 1.0
C A:ASP273 4.9 11.7 1.0

Calcium binding site 2 out of 6 in 1cq1

Go back to Calcium Binding Sites List in 1cq1
Calcium binding site 2 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:8.4
occ:1.00
 O A:TYR263 2.3 4.6 1.0
OE2 A:GLU253 2.3 10.9 1.0
O A:HOH518 2.4 7.2 1.0
OE1 A:GLU253 2.4 5.9 1.0
O A:HOH534 2.4 7.2 1.0
O A:HOH526 2.5 6.9 1.0
O A:HOH505 2.6 3.2 1.0
CD A:GLU253 2.7 6.5 1.0
C A:TYR263 3.4 6.2 1.0
CB A:TYR263 4.0 4.2 1.0
CA A:TYR263 4.1 5.7 1.0
O A:VAL268 4.2 8.5 1.0
CG A:GLU253 4.2 7.3 1.0
N A:GLY270 4.4 5.5 1.0
O A:GLY226 4.5 7.3 1.0
N A:GLY264 4.5 7.4 1.0
OE2 A:GLU245 4.5 7.5 1.0
O A:GLY270 4.5 7.1 1.0
O A:HOH670 4.5 21.8 1.0
O A:HOH567 4.6 9.0 1.0
OD1 A:ASN255 4.6 5.5 1.0
N A:TRP265 4.8 10.8 1.0
ND2 A:ASN255 4.8 6.4 1.0
CE1 A:PHE317 4.8 7.4 1.0
CA A:GLY264 4.9 8.7 1.0
O A:VAL318 4.9 5.2 1.0
CA A:GLY270 4.9 5.0 1.0
CD A:PRO320 5.0 4.6 1.0

Calcium binding site 3 out of 6 in 1cq1

Go back to Calcium Binding Sites List in 1cq1
Calcium binding site 3 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:12.7
occ:1.00
 O7A A:PQQ504 2.3 14.4 1.0
O A:GLY247 2.4 9.3 1.0
O A:HOH529 2.4 6.8 1.0
O5 A:PQQ504 2.4 13.8 1.0
N6 A:PQQ504 2.4 15.3 1.0
O A:PRO248 2.4 7.3 1.0
O A:HOH543 2.5 13.3 1.0
C7X A:PQQ504 3.2 14.9 1.0
C5 A:PQQ504 3.2 13.9 1.0
C7 A:PQQ504 3.3 10.9 1.0
C6A A:PQQ504 3.3 15.2 1.0
C A:PRO248 3.4 9.2 1.0
C A:GLY247 3.5 9.3 1.0
CA A:PRO248 3.8 9.5 1.0
NH2 A:ARG228 4.0 8.9 1.0
N A:PRO248 4.1 9.2 1.0
NH1 A:ARG228 4.1 10.7 1.0
CG2 A:THR348 4.2 9.3 1.0
CZ A:ARG228 4.3 11.8 1.0
NE2 A:GLN246 4.4 11.1 1.0
O7B A:PQQ504 4.4 12.8 1.0
OD1 A:ASP252 4.4 7.1 1.0
OG1 A:THR348 4.5 12.7 1.0
N A:GLY247 4.5 7.0 1.0
C4 A:PQQ504 4.5 12.8 1.0
O A:HOH564 4.6 10.9 1.0
O5 A:BGC455 4.6 21.2 1.0
N A:ASN249 4.6 8.4 1.0
C8 A:PQQ504 4.6 13.6 1.0
CB A:THR348 4.6 11.3 1.0
O1 A:BGC455 4.6 18.2 1.0
CA A:GLY247 4.7 8.0 1.0
C1 A:BGC455 4.7 19.4 1.0
C9A A:PQQ504 4.7 14.5 1.0

Calcium binding site 4 out of 6 in 1cq1

Go back to Calcium Binding Sites List in 1cq1
Calcium binding site 4 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:11.6
occ:1.00
 O B:TYR263 2.3 5.9 1.0
OE2 B:GLU253 2.3 3.4 1.0
O B:HOH511 2.4 5.1 1.0
OE1 B:GLU253 2.4 4.5 1.0
O B:HOH506 2.5 4.2 1.0
O B:HOH547 2.5 7.1 1.0
O B:HOH505 2.5 2.9 1.0
CD B:GLU253 2.7 4.5 1.0
C B:TYR263 3.5 3.4 1.0
CB B:TYR263 4.0 2.0 1.0
CA B:TYR263 4.1 3.6 1.0
O B:VAL268 4.2 4.9 1.0
CG B:GLU253 4.2 2.0 1.0
N B:GLY270 4.3 5.0 1.0
O B:GLY226 4.5 5.7 1.0
O B:GLY270 4.5 4.7 1.0
O B:HOH540 4.5 6.8 1.0
N B:GLY264 4.5 3.9 1.0
OE2 B:GLU245 4.6 6.9 1.0
OD1 B:ASN255 4.6 3.0 1.0
N B:TRP265 4.7 4.4 1.0
ND2 B:ASN255 4.8 2.9 1.0
CA B:GLY264 4.8 3.9 1.0
CA B:GLY270 4.9 4.7 1.0
O B:VAL318 4.9 3.2 1.0
CE1 B:PHE317 4.9 5.7 1.0
CD B:PRO320 4.9 3.4 1.0

Calcium binding site 5 out of 6 in 1cq1

Go back to Calcium Binding Sites List in 1cq1
Calcium binding site 5 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:6.4
occ:1.00
 O B:TYR271 2.3 7.3 1.0
OE2 B:GLU309 2.4 6.9 1.0
O B:ALA269 2.4 3.1 1.0
O B:HOH513 2.4 3.6 1.0
O B:HOH510 2.4 5.3 1.0
OD1 B:ASP273 2.5 7.7 1.0
OE1 B:GLU309 2.6 8.9 1.0
CD B:GLU309 2.8 4.4 1.0
CG B:ASP273 3.4 6.1 1.0
C B:TYR271 3.5 6.8 1.0
C B:ALA269 3.5 4.5 1.0
N B:TYR271 3.8 4.3 1.0
OD2 B:ASP273 3.8 6.1 1.0
N B:ASP273 4.0 6.8 1.0
C B:GLY270 4.1 4.2 1.0
CA B:TYR271 4.2 4.8 1.0
N B:ALA269 4.2 5.2 1.0
O B:SER275 4.3 9.9 1.0
OD2 B:ASP251 4.3 9.7 1.0
CG B:GLU309 4.3 5.7 1.0
CA B:ALA269 4.4 2.5 1.0
N B:GLY270 4.4 5.0 1.0
CA B:GLY270 4.4 4.7 1.0
CG1 B:VAL268 4.4 5.7 1.0
OD1 B:ASP251 4.5 7.7 1.0
N B:LYS272 4.5 5.5 1.0
CG B:ASP251 4.6 8.9 1.0
N B:ASP274 4.6 9.3 1.0
CB B:ASP273 4.6 5.9 1.0
CB B:ALA269 4.6 6.3 1.0
N B:SER275 4.7 9.9 1.0
O B:GLY270 4.7 4.7 1.0
CA B:ASP273 4.7 7.8 1.0
CA B:LYS272 4.7 5.7 1.0
CB B:TYR271 4.8 5.5 1.0
C B:LYS272 4.9 7.3 1.0
C B:ASP273 5.0 9.7 1.0
CB B:TYR277 5.0 8.2 1.0

Calcium binding site 6 out of 6 in 1cq1

Go back to Calcium Binding Sites List in 1cq1
Calcium binding site 6 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:6.8
occ:1.00
 O5 B:PQQ504 2.3 7.1 1.0
O7A B:PQQ504 2.4 11.0 1.0
O B:HOH550 2.4 7.1 1.0
O B:GLY247 2.4 8.7 1.0
N6 B:PQQ504 2.4 10.7 1.0
O B:HOH521 2.4 6.9 1.0
O B:PRO248 2.5 8.6 1.0
C7X B:PQQ504 3.2 12.3 1.0
C5 B:PQQ504 3.2 7.8 1.0
C7 B:PQQ504 3.3 10.8 1.0
C6A B:PQQ504 3.3 10.6 1.0
C B:PRO248 3.5 7.9 1.0
C B:GLY247 3.5 7.7 1.0
CA B:PRO248 3.9 6.7 1.0
NH2 B:ARG228 4.1 5.8 1.0
NH1 B:ARG228 4.1 6.0 1.0
N B:PRO248 4.1 7.1 1.0
CG2 B:THR348 4.3 7.9 1.0
NE2 B:GLN246 4.4 5.3 1.0
CZ B:ARG228 4.4 6.0 1.0
O7B B:PQQ504 4.4 13.5 1.0
OG1 B:THR348 4.4 6.6 1.0
OD1 B:ASP252 4.5 5.5 1.0
C4 B:PQQ504 4.5 10.5 1.0
O5 B:BGC455 4.6 14.4 1.0
C8 B:PQQ504 4.6 12.3 1.0
N B:GLY247 4.6 5.1 1.0
CB B:THR348 4.6 8.8 1.0
N B:ASN249 4.7 7.6 1.0
O1 B:BGC455 4.7 14.7 1.0
O B:HOH558 4.7 8.8 1.0
C9A B:PQQ504 4.7 11.7 1.0
CA B:GLY247 4.7 3.0 1.0
C1 B:BGC455 4.7 13.6 1.0
CB B:GLN246 4.9 4.4 1.0
O4 B:PQQ504 5.0 7.1 1.0

Reference:

A.Oubrie, H.J.Rozeboom, K.H.Kalk, A.J.Olsthoorn, J.A.Duine, B.W.Dijkstra. Structure and Mechanism of Soluble Quinoprotein Glucose Dehydrogenase. Embo J. V. 18 5187 1999.
ISSN: ISSN 0261-4189
PubMed: 10508152
DOI: 10.1093/EMBOJ/18.19.5187
Page generated: Thu Jul 11 07:07:20 2024

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