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Calcium in PDB 1up8: Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera

Protein crystallography data

The structure of Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera, PDB code: 1up8 was solved by E.Garcia-Rodriguez, M.Isupov, T.Ohshiro, Y.Izumi, J.A.Littlechild, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.0 / 2.20
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 185.948, 185.948, 180.279, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera (pdb code 1up8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera, PDB code: 1up8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1up8

Go back to Calcium Binding Sites List in 1up8
Calcium binding site 1 out of 4 in the Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca599

b:22.9
occ:1.00
 O A:HOH2397 2.3 29.8 1.0
O A:GLN369 2.4 24.3 1.0
O A:GLN362 2.4 24.8 1.0
OD1 A:ASP364 2.4 21.7 1.0
O A:PHE360 2.5 26.6 1.0
OD2 A:ASP367 2.6 24.6 1.0
OD1 A:ASP367 2.6 26.5 1.0
CG A:ASP367 3.0 22.9 1.0
C A:GLN369 3.5 24.4 1.0
C A:PHE360 3.5 26.9 1.0
C A:GLN362 3.6 26.8 1.0
CG A:ASP364 3.6 29.0 1.0
N A:GLN362 3.9 23.7 1.0
CA A:ASP364 4.2 24.1 1.0
CA A:PHE360 4.2 24.1 1.0
N A:ASP364 4.3 22.1 1.0
C A:GLN361 4.3 26.6 1.0
CA A:GLN362 4.3 22.1 1.0
C A:GLU363 4.3 23.5 1.0
N A:ASP370 4.3 24.5 1.0
CA A:ASP370 4.4 24.5 1.0
N A:GLN361 4.4 25.3 1.0
OD2 A:ASP364 4.4 24.1 1.0
CA A:GLN369 4.4 23.5 1.0
N A:GLN369 4.4 22.4 1.0
CB A:PHE360 4.5 22.8 1.0
CB A:ASP364 4.5 23.6 1.0
O A:GLU363 4.5 29.4 1.0
CB A:ASP367 4.6 22.3 1.0
CA A:GLN361 4.6 24.5 1.0
N A:GLU363 4.6 25.3 1.0
O A:HOH2400 4.8 28.6 1.0
CA A:GLU363 4.9 28.0 1.0
O A:GLN361 4.9 24.2 1.0
O A:HOH2405 4.9 43.9 1.0
O A:HOH2406 5.0 29.2 1.0
CB A:GLN362 5.0 25.6 1.0

Calcium binding site 2 out of 4 in 1up8

Go back to Calcium Binding Sites List in 1up8
Calcium binding site 2 out of 4 in the Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca599

b:26.0
occ:1.00
 O B:GLN369 2.4 23.4 1.0
O B:GLN362 2.4 25.9 1.0
OD1 B:ASP364 2.5 27.1 1.0
O B:HOH2431 2.5 30.9 1.0
OD2 B:ASP367 2.5 27.7 1.0
O B:PHE360 2.6 26.2 1.0
OD1 B:ASP367 2.6 25.9 1.0
CG B:ASP367 3.0 32.1 1.0
C B:PHE360 3.5 27.7 1.0
C B:GLN369 3.5 24.4 1.0
C B:GLN362 3.6 30.7 1.0
CG B:ASP364 3.7 32.4 1.0
N B:GLN362 3.9 29.1 1.0
N B:ASP364 4.1 27.4 1.0
CA B:ASP364 4.2 26.9 1.0
CA B:PHE360 4.2 23.6 1.0
C B:GLN361 4.2 28.8 1.0
C B:GLU363 4.3 30.0 1.0
N B:GLN361 4.3 22.3 1.0
N B:ASP370 4.3 24.9 1.0
CA B:ASP370 4.4 25.2 1.0
CA B:GLN362 4.4 29.7 1.0
N B:GLN369 4.4 25.2 1.0
CB B:PHE360 4.4 23.6 1.0
OD2 B:ASP364 4.5 35.1 1.0
CB B:ASP367 4.5 28.3 1.0
CA B:GLN369 4.5 25.9 1.0
O B:GLU363 4.5 27.8 1.0
CA B:GLN361 4.5 25.1 1.0
CB B:ASP364 4.5 28.9 1.0
N B:GLU363 4.6 30.6 1.0
O B:GLN361 4.8 30.5 1.0
CA B:GLU363 4.8 32.6 1.0
O B:HOH2434 4.9 35.8 1.0

Calcium binding site 3 out of 4 in 1up8

Go back to Calcium Binding Sites List in 1up8
Calcium binding site 3 out of 4 in the Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca599

b:27.3
occ:1.00
 O C:HOH2409 2.4 25.7 1.0
O C:GLN369 2.4 27.9 1.0
OD1 C:ASP364 2.4 30.6 1.0
O C:PHE360 2.5 24.4 1.0
OD2 C:ASP367 2.5 26.8 1.0
O C:GLN362 2.5 28.3 1.0
OD1 C:ASP367 2.6 26.0 1.0
CG C:ASP367 2.9 26.5 1.0
C C:PHE360 3.5 24.1 1.0
C C:GLN369 3.5 26.7 1.0
C C:GLN362 3.6 34.0 1.0
CG C:ASP364 3.7 37.2 1.0
N C:GLN362 3.9 30.5 1.0
C C:GLN361 4.2 31.9 1.0
CA C:PHE360 4.2 22.0 1.0
N C:ASP364 4.2 27.2 1.0
CA C:ASP364 4.3 29.6 1.0
C C:GLU363 4.3 29.1 1.0
CA C:GLN362 4.3 32.4 1.0
N C:ASP370 4.3 27.6 1.0
N C:GLN361 4.4 23.9 1.0
CA C:ASP370 4.4 29.5 1.0
CB C:PHE360 4.4 19.6 1.0
OD2 C:ASP364 4.4 34.1 1.0
CB C:ASP367 4.5 27.1 1.0
O C:GLU363 4.5 24.8 1.0
N C:GLN369 4.5 22.1 1.0
CA C:GLN361 4.5 25.8 1.0
CA C:GLN369 4.5 25.5 1.0
CB C:ASP364 4.6 31.2 1.0
N C:GLU363 4.6 34.0 1.0
O C:HOH2416 4.7 34.7 1.0
O C:GLN361 4.8 35.0 1.0
CA C:GLU363 4.9 33.2 1.0
O C:HOH2413 4.9 28.8 1.0
CB C:GLN362 5.0 33.0 1.0

Calcium binding site 4 out of 4 in 1up8

Go back to Calcium Binding Sites List in 1up8
Calcium binding site 4 out of 4 in the Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Recombinant Vanadium-Dependent Bromoperoxidase From Red Algae Corallina Pilulifera within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca599

b:30.4
occ:1.00
 O D:GLN369 2.4 26.4 1.0
O D:GLN362 2.4 27.1 1.0
OD2 D:ASP367 2.5 17.1 1.0
OD1 D:ASP364 2.5 28.5 1.0
OD1 D:ASP367 2.6 23.5 1.0
O D:HOH2424 2.6 29.7 1.0
O D:PHE360 2.7 23.7 1.0
CG D:ASP367 2.9 23.0 1.0
C D:GLN369 3.5 24.7 1.0
C D:PHE360 3.6 27.2 1.0
C D:GLN362 3.6 29.7 1.0
CG D:ASP364 3.7 35.1 1.0
N D:GLN362 3.8 27.6 1.0
CA D:ASP364 4.1 26.2 1.0
N D:ASP364 4.2 25.4 1.0
CA D:GLN362 4.3 27.8 1.0
CA D:PHE360 4.3 24.0 1.0
C D:GLN361 4.3 28.8 1.0
N D:ASP370 4.3 26.5 1.0
C D:GLU363 4.3 26.9 1.0
CA D:ASP370 4.4 26.7 1.0
N D:GLN369 4.4 24.0 1.0
N D:GLN361 4.4 22.1 1.0
CB D:ASP367 4.5 20.7 1.0
CA D:GLN369 4.5 26.2 1.0
O D:GLU363 4.5 28.2 1.0
CB D:PHE360 4.5 24.4 1.0
CB D:ASP364 4.5 26.4 1.0
OD2 D:ASP364 4.5 32.7 1.0
CA D:GLN361 4.6 26.9 1.0
N D:GLU363 4.7 30.6 1.0
CB D:GLN362 4.8 26.5 1.0
CA D:GLU363 4.9 32.1 1.0
O D:GLN361 5.0 29.5 1.0
O D:HOH2427 5.0 30.6 1.0

Reference:

E.Garcia-Rodriguez, T.Ohshiro, T.Aibara, Y.Izumi, J.Littlechild. Enhancing Effect of Calcium and Vanadium Ions on Thermal Stability of Bromoperoxidase From Corallina Pilulifera. J.Biol.Inorg.Chem. V. 10 275 2005.
ISSN: ISSN 0949-8257
PubMed: 15776268
DOI: 10.1007/S00775-005-0639-3
Page generated: Thu Jul 11 23:34:55 2024

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