Calcium in PDB 1qbi: Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus
Enzymatic activity of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus
All present enzymatic activity of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus:
1.1.99.17;
Protein crystallography data
The structure of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus, PDB code: 1qbi
was solved by
A.Oubrie,
H.J.Rozeboom,
K.H.Kalk,
J.A.Duine,
B.W.Dijkstra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.72
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.148,
92.100,
84.910,
90.00,
105.17,
90.00
|
R / Rfree (%)
|
16.5 /
20.8
|
Other elements in 1qbi:
The structure of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus
(pdb code 1qbi). 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, PDB code: 1qbi:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1qbi
Go back to
Calcium Binding Sites List in 1qbi
Calcium binding site 1 out
of 6 in the Soluble Quinoprotein 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 Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca465
b:8.4
occ:1.00
|
O
|
A:TYR271
|
2.3
|
8.2
|
1.0
|
OD1
|
A:ASP273
|
2.3
|
6.1
|
1.0
|
O
|
A:ALA269
|
2.3
|
7.5
|
1.0
|
O
|
A:HOH486
|
2.3
|
5.3
|
1.0
|
O
|
A:HOH875
|
2.5
|
7.7
|
1.0
|
OE1
|
A:GLU309
|
2.5
|
11.7
|
1.0
|
OE2
|
A:GLU309
|
2.5
|
7.8
|
1.0
|
CD
|
A:GLU309
|
2.9
|
11.9
|
1.0
|
CG
|
A:ASP273
|
3.3
|
8.9
|
1.0
|
C
|
A:TYR271
|
3.5
|
8.8
|
1.0
|
C
|
A:ALA269
|
3.5
|
8.3
|
1.0
|
OD2
|
A:ASP273
|
3.7
|
7.9
|
1.0
|
N
|
A:TYR271
|
3.8
|
8.7
|
1.0
|
N
|
A:ASP273
|
3.9
|
7.8
|
1.0
|
C
|
A:GLY270
|
4.1
|
7.0
|
1.0
|
CA
|
A:TYR271
|
4.2
|
7.6
|
1.0
|
N
|
A:ALA269
|
4.2
|
8.7
|
1.0
|
O
|
A:SER275
|
4.3
|
7.5
|
1.0
|
CG
|
A:GLU309
|
4.4
|
10.2
|
1.0
|
OD2
|
A:ASP251
|
4.4
|
7.1
|
1.0
|
CA
|
A:ALA269
|
4.4
|
6.9
|
1.0
|
OD1
|
A:ASP251
|
4.4
|
9.3
|
1.0
|
CA
|
A:GLY270
|
4.4
|
8.6
|
1.0
|
N
|
A:GLY270
|
4.4
|
7.2
|
1.0
|
CB
|
A:ASP273
|
4.5
|
6.7
|
1.0
|
CG
|
A:ASP251
|
4.5
|
10.4
|
1.0
|
N
|
A:LYS272
|
4.5
|
8.2
|
1.0
|
N
|
A:ASP274
|
4.5
|
8.7
|
1.0
|
CG1
|
A:VAL268
|
4.5
|
7.8
|
1.0
|
N
|
A:SER275
|
4.6
|
7.9
|
1.0
|
CA
|
A:ASP273
|
4.6
|
9.0
|
1.0
|
CB
|
A:ALA269
|
4.7
|
8.8
|
1.0
|
O
|
A:GLY270
|
4.7
|
9.9
|
1.0
|
CA
|
A:LYS272
|
4.7
|
10.2
|
1.0
|
CB
|
A:TYR271
|
4.7
|
8.0
|
1.0
|
C
|
A:LYS272
|
4.8
|
10.7
|
1.0
|
C
|
A:ASP273
|
4.9
|
9.6
|
1.0
|
CB
|
A:TYR277
|
4.9
|
9.6
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1qbi
Go back to
Calcium Binding Sites List in 1qbi
Calcium binding site 2 out
of 6 in the Soluble Quinoprotein 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 Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca466
b:7.3
occ:1.00
|
O
|
A:TYR263
|
2.3
|
8.9
|
1.0
|
O
|
A:HOH504
|
2.3
|
7.5
|
1.0
|
O
|
A:HOH521
|
2.3
|
7.8
|
1.0
|
OE2
|
A:GLU253
|
2.4
|
8.8
|
1.0
|
O
|
A:HOH487
|
2.4
|
8.7
|
1.0
|
O
|
A:HOH500
|
2.4
|
9.1
|
1.0
|
OE1
|
A:GLU253
|
2.5
|
10.3
|
1.0
|
CD
|
A:GLU253
|
2.8
|
11.0
|
1.0
|
C
|
A:TYR263
|
3.5
|
8.6
|
1.0
|
CB
|
A:TYR263
|
4.0
|
7.3
|
1.0
|
CA
|
A:TYR263
|
4.1
|
8.2
|
1.0
|
O
|
A:VAL268
|
4.2
|
10.1
|
1.0
|
N
|
A:GLY270
|
4.3
|
7.2
|
1.0
|
CG
|
A:GLU253
|
4.3
|
11.0
|
1.0
|
O
|
A:GLY226
|
4.4
|
7.9
|
1.0
|
O
|
A:HOH928
|
4.4
|
23.7
|
1.0
|
O
|
A:GLY270
|
4.4
|
9.9
|
1.0
|
OE2
|
A:GLU245
|
4.5
|
11.9
|
1.0
|
O
|
A:HOH499
|
4.5
|
11.2
|
1.0
|
N
|
A:GLY264
|
4.5
|
7.8
|
1.0
|
OD1
|
A:ASN255
|
4.6
|
8.0
|
1.0
|
ND2
|
A:ASN255
|
4.6
|
7.7
|
1.0
|
N
|
A:TRP265
|
4.7
|
7.4
|
1.0
|
O
|
A:VAL318
|
4.8
|
9.1
|
1.0
|
CA
|
A:GLY270
|
4.9
|
8.6
|
1.0
|
CD
|
A:PRO320
|
4.9
|
6.5
|
1.0
|
CA
|
A:GLY264
|
4.9
|
7.5
|
1.0
|
CE1
|
A:PHE317
|
4.9
|
6.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1qbi
Go back to
Calcium Binding Sites List in 1qbi
Calcium binding site 3 out
of 6 in the Soluble Quinoprotein 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 Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca468
b:18.4
occ:1.00
|
O
|
A:HOH664
|
2.3
|
14.5
|
1.0
|
O
|
A:GLY247
|
2.4
|
9.0
|
1.0
|
O
|
A:PRO248
|
2.4
|
7.4
|
1.0
|
O
|
A:HOH672
|
2.4
|
17.7
|
1.0
|
O
|
A:HOH520
|
2.4
|
10.0
|
1.0
|
O
|
A:HOH870
|
2.6
|
26.1
|
1.0
|
C
|
A:PRO248
|
3.4
|
7.9
|
1.0
|
C
|
A:GLY247
|
3.5
|
8.9
|
1.0
|
CA
|
A:PRO248
|
3.8
|
8.6
|
1.0
|
N
|
A:PRO248
|
4.0
|
8.8
|
1.0
|
NH1
|
A:ARG228
|
4.1
|
10.9
|
1.0
|
CG2
|
A:THR348
|
4.2
|
11.7
|
1.0
|
NH2
|
A:ARG228
|
4.2
|
9.6
|
1.0
|
O
|
A:HOH746
|
4.3
|
28.0
|
1.0
|
NE2
|
A:GLN246
|
4.3
|
11.2
|
1.0
|
OD1
|
A:ASP252
|
4.3
|
9.3
|
1.0
|
O
|
A:HOH759
|
4.3
|
33.7
|
1.0
|
CZ
|
A:ARG228
|
4.4
|
9.7
|
1.0
|
O
|
A:HOH659
|
4.5
|
25.4
|
1.0
|
OG1
|
A:THR348
|
4.5
|
16.2
|
1.0
|
N
|
A:GLY247
|
4.5
|
8.5
|
1.0
|
N
|
A:ASN249
|
4.6
|
8.4
|
1.0
|
CB
|
A:THR348
|
4.6
|
11.9
|
1.0
|
CA
|
A:GLY247
|
4.7
|
8.2
|
1.0
|
O
|
A:HOH709
|
4.7
|
22.4
|
1.0
|
CB
|
A:GLN246
|
4.8
|
5.8
|
1.0
|
CE3
|
A:TRP346
|
4.9
|
19.6
|
1.0
|
CA
|
A:ASN249
|
5.0
|
8.2
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1qbi
Go back to
Calcium Binding Sites List in 1qbi
Calcium binding site 4 out
of 6 in the Soluble Quinoprotein 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 Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca463
b:8.0
occ:1.00
|
O
|
B:TYR263
|
2.2
|
6.1
|
1.0
|
O
|
B:HOH470
|
2.3
|
6.4
|
1.0
|
O
|
B:HOH473
|
2.3
|
6.0
|
1.0
|
O
|
B:HOH493
|
2.4
|
4.7
|
1.0
|
O
|
B:HOH483
|
2.4
|
6.0
|
1.0
|
OE2
|
B:GLU253
|
2.4
|
9.5
|
1.0
|
OE1
|
B:GLU253
|
2.5
|
8.1
|
1.0
|
CD
|
B:GLU253
|
2.9
|
8.8
|
1.0
|
C
|
B:TYR263
|
3.4
|
4.3
|
1.0
|
CB
|
B:TYR263
|
4.0
|
5.4
|
1.0
|
CA
|
B:TYR263
|
4.1
|
6.7
|
1.0
|
O
|
B:VAL268
|
4.3
|
9.4
|
1.0
|
N
|
B:GLY270
|
4.3
|
6.8
|
1.0
|
CG
|
B:GLU253
|
4.4
|
5.3
|
1.0
|
O
|
B:GLY226
|
4.4
|
7.5
|
1.0
|
O
|
B:GLY270
|
4.4
|
7.5
|
1.0
|
N
|
B:GLY264
|
4.5
|
6.1
|
1.0
|
O
|
B:HOH600
|
4.5
|
19.9
|
1.0
|
OE2
|
B:GLU245
|
4.6
|
10.9
|
1.0
|
O
|
B:HOH590
|
4.6
|
9.4
|
1.0
|
OD1
|
B:ASN255
|
4.6
|
7.8
|
1.0
|
N
|
B:TRP265
|
4.6
|
6.6
|
1.0
|
ND2
|
B:ASN255
|
4.7
|
9.2
|
1.0
|
O
|
B:VAL318
|
4.8
|
7.0
|
1.0
|
CA
|
B:GLY264
|
4.8
|
6.7
|
1.0
|
CE1
|
B:PHE317
|
4.8
|
6.6
|
1.0
|
CA
|
B:GLY270
|
4.9
|
5.3
|
1.0
|
CD2
|
B:TYR263
|
5.0
|
5.7
|
1.0
|
CD
|
B:PRO320
|
5.0
|
6.8
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1qbi
Go back to
Calcium Binding Sites List in 1qbi
Calcium binding site 5 out
of 6 in the Soluble Quinoprotein 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 Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca464
b:7.9
occ:1.00
|
O
|
B:ALA269
|
2.3
|
5.4
|
1.0
|
O
|
B:HOH999
|
2.3
|
6.2
|
1.0
|
O
|
B:TYR271
|
2.3
|
8.5
|
1.0
|
OD1
|
B:ASP273
|
2.3
|
4.8
|
1.0
|
OE2
|
B:GLU309
|
2.5
|
6.6
|
1.0
|
OE1
|
B:GLU309
|
2.5
|
9.4
|
1.0
|
O
|
B:HOH480
|
2.5
|
5.4
|
1.0
|
CD
|
B:GLU309
|
2.8
|
9.7
|
1.0
|
CG
|
B:ASP273
|
3.3
|
10.4
|
1.0
|
C
|
B:ALA269
|
3.5
|
8.2
|
1.0
|
C
|
B:TYR271
|
3.5
|
6.8
|
1.0
|
OD2
|
B:ASP273
|
3.7
|
7.5
|
1.0
|
N
|
B:TYR271
|
3.9
|
7.0
|
1.0
|
N
|
B:ASP273
|
4.0
|
8.4
|
1.0
|
C
|
B:GLY270
|
4.2
|
5.3
|
1.0
|
N
|
B:ALA269
|
4.2
|
7.0
|
1.0
|
CA
|
B:TYR271
|
4.3
|
6.3
|
1.0
|
O
|
B:SER275
|
4.3
|
9.2
|
1.0
|
CG
|
B:GLU309
|
4.3
|
6.7
|
1.0
|
CA
|
B:ALA269
|
4.3
|
7.3
|
1.0
|
OD2
|
B:ASP251
|
4.3
|
7.0
|
1.0
|
N
|
B:GLY270
|
4.4
|
6.8
|
1.0
|
CA
|
B:GLY270
|
4.4
|
5.3
|
1.0
|
CB
|
B:ASP273
|
4.5
|
9.3
|
1.0
|
N
|
B:ASP274
|
4.5
|
8.0
|
1.0
|
CG1
|
B:VAL268
|
4.5
|
10.2
|
1.0
|
CG
|
B:ASP251
|
4.6
|
8.0
|
1.0
|
N
|
B:SER275
|
4.6
|
6.9
|
1.0
|
OD1
|
B:ASP251
|
4.6
|
7.4
|
1.0
|
N
|
B:LYS272
|
4.6
|
6.8
|
1.0
|
CB
|
B:ALA269
|
4.6
|
6.3
|
1.0
|
CA
|
B:ASP273
|
4.7
|
9.2
|
1.0
|
O
|
B:GLY270
|
4.7
|
7.5
|
1.0
|
CA
|
B:LYS272
|
4.7
|
8.0
|
1.0
|
CB
|
B:TYR271
|
4.8
|
8.1
|
1.0
|
CB
|
B:TYR277
|
4.9
|
10.1
|
1.0
|
C
|
B:LYS272
|
4.9
|
9.0
|
1.0
|
C
|
B:ASP273
|
5.0
|
10.4
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1qbi
Go back to
Calcium Binding Sites List in 1qbi
Calcium binding site 6 out
of 6 in the Soluble Quinoprotein 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 Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca467
b:17.5
occ:1.00
|
O
|
B:HOH592
|
2.3
|
12.6
|
1.0
|
O
|
B:PRO248
|
2.3
|
7.0
|
1.0
|
O
|
B:GLY247
|
2.3
|
8.5
|
1.0
|
O
|
B:HOH572
|
2.4
|
13.2
|
1.0
|
O
|
B:HOH533
|
2.4
|
10.2
|
1.0
|
C
|
B:PRO248
|
3.3
|
5.4
|
1.0
|
C
|
B:GLY247
|
3.5
|
7.6
|
1.0
|
CA
|
B:PRO248
|
3.7
|
6.0
|
1.0
|
O
|
B:HOH634
|
3.9
|
28.1
|
1.0
|
O
|
B:HOH567
|
3.9
|
31.0
|
1.0
|
N
|
B:PRO248
|
4.0
|
7.1
|
1.0
|
NH1
|
B:ARG228
|
4.1
|
8.5
|
1.0
|
O
|
B:HOH729
|
4.1
|
32.5
|
1.0
|
NH2
|
B:ARG228
|
4.1
|
8.6
|
1.0
|
CG2
|
B:THR348
|
4.2
|
11.9
|
1.0
|
NE2
|
B:GLN246
|
4.3
|
9.1
|
1.0
|
OD1
|
B:ASP252
|
4.4
|
7.0
|
1.0
|
CZ
|
B:ARG228
|
4.4
|
8.7
|
1.0
|
OG1
|
B:THR348
|
4.5
|
14.8
|
1.0
|
N
|
B:ASN249
|
4.5
|
6.4
|
1.0
|
CB
|
B:THR348
|
4.6
|
10.4
|
1.0
|
N
|
B:GLY247
|
4.6
|
7.2
|
1.0
|
O
|
B:HOH539
|
4.6
|
14.6
|
1.0
|
CA
|
B:GLY247
|
4.7
|
7.2
|
1.0
|
O
|
B:HOH608
|
4.8
|
18.0
|
1.0
|
CB
|
B:GLN246
|
4.8
|
7.8
|
1.0
|
CA
|
B:ASN249
|
4.9
|
6.5
|
1.0
|
|
Reference:
A.Oubrie,
H.J.Rozeboom,
K.H.Kalk,
J.A.Duine,
B.W.Dijkstra.
The 1.7 A Crystal Structure of the Apo Form of the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus Reveals A Novel Internal Conserved Sequence Repeat. J.Mol.Biol. V. 289 319 1999.
ISSN: ISSN 0022-2836
PubMed: 10366508
DOI: 10.1006/JMBI.1999.2766
Page generated: Thu Jul 11 14:27:00 2024
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