Calcium in PDB 1qhb: Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
Enzymatic activity of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
All present enzymatic activity of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis:
1.11.1.10;
Protein crystallography data
The structure of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis, PDB code: 1qhb
was solved by
M.N.Isupov,
A.R.Dalby,
A.A.Brindley,
J.A.Littlechild,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.30
|
Space group
|
P 42 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
201.915,
201.915,
178.109,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
22.7
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
(pdb code 1qhb). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Vanadium Bromoperoxidase From Red Alga Corallina Officinalis, PDB code: 1qhb:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1qhb
Go back to
Calcium Binding Sites List in 1qhb
Calcium binding site 1 out
of 6 in the Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca3001
b:46.8
occ:1.00
|
O
|
A:GLN361
|
2.8
|
33.9
|
1.0
|
OD1
|
A:ASP363
|
2.9
|
29.1
|
1.0
|
O
|
A:GLN368
|
2.9
|
34.6
|
1.0
|
O
|
A:PHE359
|
3.0
|
28.4
|
1.0
|
OD1
|
A:ASP366
|
3.0
|
31.9
|
1.0
|
OD2
|
A:ASP366
|
3.1
|
36.5
|
1.0
|
CG
|
A:ASP366
|
3.4
|
40.2
|
1.0
|
C
|
A:GLN368
|
3.8
|
36.6
|
1.0
|
C
|
A:PHE359
|
3.9
|
30.9
|
1.0
|
C
|
A:GLN361
|
3.9
|
39.0
|
1.0
|
N
|
A:ASP363
|
4.0
|
38.8
|
1.0
|
CG
|
A:ASP363
|
4.1
|
47.7
|
1.0
|
C
|
A:GLU362
|
4.1
|
38.8
|
1.0
|
CA
|
A:ASP363
|
4.1
|
37.3
|
1.0
|
N
|
A:GLN361
|
4.1
|
37.5
|
1.0
|
C
|
A:GLN360
|
4.3
|
35.3
|
1.0
|
O
|
A:GLU362
|
4.3
|
34.7
|
1.0
|
CA
|
A:ASP369
|
4.4
|
32.6
|
1.0
|
N
|
A:ASP369
|
4.5
|
35.8
|
1.0
|
CB
|
A:PHE359
|
4.5
|
27.4
|
1.0
|
N
|
A:GLN368
|
4.5
|
32.4
|
1.0
|
CA
|
A:PHE359
|
4.5
|
27.1
|
1.0
|
CA
|
A:GLN361
|
4.6
|
38.7
|
1.0
|
N
|
A:GLN360
|
4.6
|
30.9
|
1.0
|
CA
|
A:GLN360
|
4.6
|
32.1
|
1.0
|
CB
|
A:ASP363
|
4.7
|
41.9
|
1.0
|
CA
|
A:GLN368
|
4.7
|
34.2
|
1.0
|
CA
|
A:GLU362
|
4.7
|
41.5
|
1.0
|
O
|
A:GLN360
|
4.7
|
39.6
|
1.0
|
N
|
A:GLU362
|
4.8
|
41.3
|
1.0
|
CB
|
A:ASP366
|
4.9
|
34.5
|
1.0
|
OD2
|
A:ASP363
|
5.0
|
45.4
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1qhb
Go back to
Calcium Binding Sites List in 1qhb
Calcium binding site 2 out
of 6 in the Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca3003
b:44.8
occ:1.00
|
O
|
B:GLN361
|
2.8
|
33.4
|
1.0
|
O
|
B:GLN368
|
2.8
|
34.3
|
1.0
|
OD1
|
B:ASP363
|
2.9
|
27.7
|
1.0
|
O
|
B:PHE359
|
3.0
|
27.7
|
1.0
|
OD2
|
B:ASP366
|
3.0
|
35.8
|
1.0
|
OD1
|
B:ASP366
|
3.1
|
31.2
|
1.0
|
CG
|
B:ASP366
|
3.4
|
39.9
|
1.0
|
C
|
B:GLN368
|
3.8
|
36.4
|
1.0
|
C
|
B:PHE359
|
3.8
|
30.7
|
1.0
|
C
|
B:GLN361
|
3.9
|
38.8
|
1.0
|
CG
|
B:ASP363
|
4.1
|
47.3
|
1.0
|
N
|
B:ASP363
|
4.1
|
38.6
|
1.0
|
N
|
B:GLN361
|
4.1
|
37.2
|
1.0
|
C
|
B:GLU362
|
4.2
|
38.5
|
1.0
|
CA
|
B:ASP363
|
4.2
|
37.1
|
1.0
|
C
|
B:GLN360
|
4.3
|
34.8
|
1.0
|
CA
|
B:ASP369
|
4.3
|
32.5
|
1.0
|
O
|
B:GLU362
|
4.4
|
34.6
|
1.0
|
CB
|
B:PHE359
|
4.4
|
27.3
|
1.0
|
N
|
B:ASP369
|
4.4
|
35.5
|
1.0
|
CA
|
B:PHE359
|
4.5
|
26.9
|
1.0
|
CA
|
B:GLN361
|
4.5
|
38.6
|
1.0
|
N
|
B:GLN360
|
4.6
|
30.5
|
1.0
|
CA
|
B:GLN360
|
4.6
|
32.1
|
1.0
|
N
|
B:GLN368
|
4.6
|
32.0
|
1.0
|
O
|
B:GLN360
|
4.7
|
38.7
|
1.0
|
CA
|
B:GLN368
|
4.7
|
34.1
|
1.0
|
CB
|
B:ASP363
|
4.7
|
41.8
|
1.0
|
CA
|
B:GLU362
|
4.8
|
41.7
|
1.0
|
N
|
B:GLU362
|
4.8
|
41.1
|
1.0
|
CB
|
B:ASP366
|
4.9
|
34.3
|
1.0
|
OD2
|
B:ASP363
|
4.9
|
45.4
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1qhb
Go back to
Calcium Binding Sites List in 1qhb
Calcium binding site 3 out
of 6 in the Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca3005
b:45.9
occ:1.00
|
O
|
C:GLN361
|
2.8
|
33.5
|
1.0
|
O
|
C:GLN368
|
2.8
|
35.0
|
1.0
|
OD1
|
C:ASP363
|
2.8
|
28.6
|
1.0
|
O
|
C:PHE359
|
3.0
|
28.1
|
1.0
|
OD1
|
C:ASP366
|
3.0
|
31.0
|
1.0
|
OD2
|
C:ASP366
|
3.0
|
36.0
|
1.0
|
CG
|
C:ASP366
|
3.4
|
39.8
|
1.0
|
C
|
C:GLN368
|
3.8
|
36.5
|
1.0
|
C
|
C:PHE359
|
3.8
|
30.5
|
1.0
|
C
|
C:GLN361
|
3.9
|
38.9
|
1.0
|
N
|
C:ASP363
|
3.9
|
38.2
|
1.0
|
CG
|
C:ASP363
|
4.0
|
47.5
|
1.0
|
N
|
C:GLN361
|
4.1
|
37.3
|
1.0
|
CA
|
C:ASP363
|
4.1
|
36.8
|
1.0
|
C
|
C:GLU362
|
4.1
|
38.4
|
1.0
|
C
|
C:GLN360
|
4.3
|
34.9
|
1.0
|
CA
|
C:ASP369
|
4.4
|
32.4
|
1.0
|
O
|
C:GLU362
|
4.4
|
34.5
|
1.0
|
CB
|
C:PHE359
|
4.4
|
27.3
|
1.0
|
CA
|
C:PHE359
|
4.5
|
27.1
|
1.0
|
N
|
C:ASP369
|
4.5
|
35.8
|
1.0
|
N
|
C:GLN360
|
4.5
|
30.4
|
1.0
|
N
|
C:GLN368
|
4.5
|
32.1
|
1.0
|
CA
|
C:GLN361
|
4.6
|
38.9
|
1.0
|
CA
|
C:GLN360
|
4.6
|
32.0
|
1.0
|
CB
|
C:ASP363
|
4.7
|
41.8
|
1.0
|
CA
|
C:GLN368
|
4.7
|
33.8
|
1.0
|
CA
|
C:GLU362
|
4.7
|
41.7
|
1.0
|
N
|
C:GLU362
|
4.8
|
41.2
|
1.0
|
O
|
C:GLN360
|
4.8
|
39.3
|
1.0
|
O
|
C:HOH3351
|
4.9
|
44.0
|
1.0
|
CB
|
C:ASP366
|
4.9
|
34.2
|
1.0
|
OD2
|
C:ASP363
|
4.9
|
45.1
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1qhb
Go back to
Calcium Binding Sites List in 1qhb
Calcium binding site 4 out
of 6 in the Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca3007
b:45.8
occ:1.00
|
O
|
D:GLN361
|
2.8
|
33.7
|
1.0
|
OD1
|
D:ASP363
|
2.8
|
28.9
|
1.0
|
O
|
D:GLN368
|
2.8
|
34.8
|
1.0
|
OD2
|
D:ASP366
|
3.0
|
36.2
|
1.0
|
O
|
D:PHE359
|
3.0
|
28.1
|
1.0
|
OD1
|
D:ASP366
|
3.1
|
31.8
|
1.0
|
CG
|
D:ASP366
|
3.4
|
39.9
|
1.0
|
C
|
D:GLN368
|
3.8
|
36.6
|
1.0
|
C
|
D:PHE359
|
3.9
|
30.9
|
1.0
|
C
|
D:GLN361
|
3.9
|
39.1
|
1.0
|
N
|
D:ASP363
|
4.0
|
38.8
|
1.0
|
CG
|
D:ASP363
|
4.0
|
47.6
|
1.0
|
N
|
D:GLN361
|
4.1
|
37.0
|
1.0
|
CA
|
D:ASP363
|
4.1
|
37.2
|
1.0
|
C
|
D:GLU362
|
4.1
|
38.6
|
1.0
|
C
|
D:GLN360
|
4.3
|
35.0
|
1.0
|
CA
|
D:ASP369
|
4.3
|
32.6
|
1.0
|
O
|
D:GLU362
|
4.4
|
34.4
|
1.0
|
N
|
D:ASP369
|
4.4
|
35.8
|
1.0
|
CB
|
D:PHE359
|
4.4
|
27.6
|
1.0
|
CA
|
D:PHE359
|
4.5
|
27.1
|
1.0
|
N
|
D:GLN368
|
4.5
|
32.4
|
1.0
|
CA
|
D:GLN361
|
4.6
|
38.8
|
1.0
|
CA
|
D:GLN360
|
4.6
|
32.2
|
1.0
|
N
|
D:GLN360
|
4.6
|
30.7
|
1.0
|
CB
|
D:ASP363
|
4.7
|
41.8
|
1.0
|
CA
|
D:GLN368
|
4.7
|
34.0
|
1.0
|
CA
|
D:GLU362
|
4.8
|
41.7
|
1.0
|
O
|
D:GLN360
|
4.8
|
39.5
|
1.0
|
N
|
D:GLU362
|
4.8
|
41.2
|
1.0
|
OD2
|
D:ASP363
|
4.9
|
45.1
|
1.0
|
CB
|
D:ASP366
|
4.9
|
34.5
|
1.0
|
O
|
D:HOH3308
|
5.0
|
34.7
|
1.0
|
O
|
D:HOH3264
|
5.0
|
29.4
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1qhb
Go back to
Calcium Binding Sites List in 1qhb
Calcium binding site 5 out
of 6 in the Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca3009
b:45.6
occ:1.00
|
O
|
E:GLN361
|
2.8
|
33.3
|
1.0
|
OD1
|
E:ASP363
|
2.9
|
28.5
|
1.0
|
O
|
E:GLN368
|
2.9
|
34.8
|
1.0
|
O
|
E:PHE359
|
3.0
|
28.1
|
1.0
|
OD2
|
E:ASP366
|
3.0
|
36.1
|
1.0
|
OD1
|
E:ASP366
|
3.1
|
32.0
|
1.0
|
CG
|
E:ASP366
|
3.4
|
40.1
|
1.0
|
C
|
E:GLN368
|
3.8
|
36.6
|
1.0
|
C
|
E:PHE359
|
3.9
|
30.8
|
1.0
|
C
|
E:GLN361
|
3.9
|
38.7
|
1.0
|
N
|
E:ASP363
|
4.0
|
38.6
|
1.0
|
CG
|
E:ASP363
|
4.1
|
47.5
|
1.0
|
N
|
E:GLN361
|
4.1
|
37.3
|
1.0
|
C
|
E:GLU362
|
4.1
|
38.6
|
1.0
|
CA
|
E:ASP363
|
4.1
|
36.9
|
1.0
|
C
|
E:GLN360
|
4.3
|
34.8
|
1.0
|
CA
|
E:ASP369
|
4.3
|
32.6
|
1.0
|
O
|
E:GLU362
|
4.3
|
34.6
|
1.0
|
N
|
E:ASP369
|
4.4
|
35.3
|
1.0
|
CB
|
E:PHE359
|
4.5
|
27.4
|
1.0
|
CA
|
E:PHE359
|
4.5
|
26.7
|
1.0
|
CA
|
E:GLN361
|
4.6
|
39.1
|
1.0
|
N
|
E:GLN368
|
4.6
|
32.4
|
1.0
|
CA
|
E:GLN360
|
4.6
|
32.0
|
1.0
|
N
|
E:GLN360
|
4.6
|
30.8
|
1.0
|
CB
|
E:ASP363
|
4.7
|
41.8
|
1.0
|
CA
|
E:GLN368
|
4.7
|
34.2
|
1.0
|
CA
|
E:GLU362
|
4.7
|
41.4
|
1.0
|
O
|
E:GLN360
|
4.8
|
39.2
|
1.0
|
N
|
E:GLU362
|
4.8
|
41.1
|
1.0
|
OD2
|
E:ASP363
|
4.9
|
45.5
|
1.0
|
CB
|
E:ASP366
|
4.9
|
34.3
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1qhb
Go back to
Calcium Binding Sites List in 1qhb
Calcium binding site 6 out
of 6 in the Vanadium Bromoperoxidase From Red Alga Corallina Officinalis
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Vanadium Bromoperoxidase From Red Alga Corallina Officinalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca3011
b:45.5
occ:1.00
|
O
|
F:GLN368
|
2.8
|
34.6
|
1.0
|
O
|
F:GLN361
|
2.8
|
33.8
|
1.0
|
OD1
|
F:ASP363
|
2.9
|
28.4
|
1.0
|
O
|
F:PHE359
|
3.0
|
27.8
|
1.0
|
OD1
|
F:ASP366
|
3.1
|
31.9
|
1.0
|
OD2
|
F:ASP366
|
3.1
|
36.1
|
1.0
|
CG
|
F:ASP366
|
3.4
|
40.1
|
1.0
|
C
|
F:GLN368
|
3.8
|
36.2
|
1.0
|
C
|
F:PHE359
|
3.8
|
30.7
|
1.0
|
C
|
F:GLN361
|
3.9
|
39.0
|
1.0
|
N
|
F:ASP363
|
4.1
|
38.4
|
1.0
|
CG
|
F:ASP363
|
4.1
|
47.6
|
1.0
|
N
|
F:GLN361
|
4.1
|
37.4
|
1.0
|
CA
|
F:ASP363
|
4.2
|
37.0
|
1.0
|
C
|
F:GLU362
|
4.2
|
38.7
|
1.0
|
CA
|
F:ASP369
|
4.3
|
32.1
|
1.0
|
C
|
F:GLN360
|
4.3
|
35.1
|
1.0
|
N
|
F:ASP369
|
4.4
|
35.3
|
1.0
|
CB
|
F:PHE359
|
4.4
|
27.3
|
1.0
|
CA
|
F:PHE359
|
4.5
|
26.8
|
1.0
|
O
|
F:GLU362
|
4.5
|
34.7
|
1.0
|
N
|
F:GLN360
|
4.6
|
30.5
|
1.0
|
N
|
F:GLN368
|
4.6
|
32.4
|
1.0
|
CA
|
F:GLN360
|
4.6
|
32.2
|
1.0
|
CA
|
F:GLN361
|
4.6
|
38.8
|
1.0
|
O
|
F:HOH3223
|
4.6
|
29.2
|
1.0
|
CA
|
F:GLN368
|
4.7
|
34.1
|
1.0
|
CB
|
F:ASP363
|
4.7
|
41.7
|
1.0
|
O
|
F:GLN360
|
4.8
|
39.6
|
1.0
|
CA
|
F:GLU362
|
4.8
|
41.6
|
1.0
|
N
|
F:GLU362
|
4.9
|
40.9
|
1.0
|
CB
|
F:ASP366
|
4.9
|
34.3
|
1.0
|
OD2
|
F:ASP363
|
4.9
|
45.7
|
1.0
|
|
Reference:
M.N.Isupov,
A.R.Dalby,
A.A.Brindley,
Y.Izumi,
T.Tanabe,
G.N.Murshudov,
J.A.Littlechild.
Crystal Structure of Dodecameric Vanadium-Dependent Bromoperoxidase From the Red Algae Corallina Officinalis. J.Mol.Biol. V. 299 1035 2000.
ISSN: ISSN 0022-2836
PubMed: 10843856
DOI: 10.1006/JMBI.2000.3806
Page generated: Thu Jul 11 21:45:26 2024
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