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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

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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

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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: Sat Dec 12 03:16:29 2020

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