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Calcium in PDB 9dr8: Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)

Enzymatic activity of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)

All present enzymatic activity of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound):
1.13.11.1;

Protein crystallography data

The structure of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound), PDB code: 9dr8 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.68 / 1.42
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.467, 52.327, 120.396, 90, 92.5, 90
R / Rfree (%) 14.4 / 17.3

Other elements in 9dr8:

The structure of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) (pdb code 9dr8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound), PDB code: 9dr8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 9dr8

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Calcium binding site 1 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:43.5
occ:1.00
 O A:HOH753 2.3 32.3 1.0
O A:HOH860 2.4 42.9 1.0
O A:LEU125 2.4 20.0 1.0
O A:HOH528 2.5 20.4 1.0
O A:HOH953 2.5 50.0 1.0
O A:HOH672 2.6 36.4 1.0
C A:LEU125 3.4 18.8 1.0
CA A:LEU125 4.0 17.7 1.0
O A:HOH781 4.2 40.2 1.0
O A:HOH770 4.2 25.7 1.0
O A:HOH757 4.2 28.2 1.0
N A:ASP126 4.5 18.4 1.0
O A:HOH560 4.5 23.1 1.0
O A:HOH938 4.5 35.5 1.0
OD1 A:ASP127 4.7 32.0 1.0
O A:ASP124 4.7 20.0 1.0
CB A:LEU125 4.8 18.3 1.0
CA A:ASP126 4.8 18.5 1.0

Calcium binding site 2 out of 7 in 9dr8

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Calcium binding site 2 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:27.0
occ:1.00
 O A:HOH745 2.3 27.0 1.0
O A:HOH743 2.4 29.6 1.0
O A:HOH654 2.4 22.2 1.0
O A:HOH897 2.4 23.0 1.0
O A:HOH592 4.2 20.3 1.0
O A:HOH580 4.4 18.1 1.0
O A:HOH944 4.6 37.6 1.0
O A:GLY171 4.7 24.3 1.0
O A:HOH539 4.7 32.0 1.0
OG1 A:THR170 4.8 24.9 1.0
O A:HOH752 4.8 20.7 1.0
OD2 A:ASP168 4.9 19.4 1.0
O A:ALA172 4.9 22.3 1.0

Calcium binding site 3 out of 7 in 9dr8

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Calcium binding site 3 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:55.2
occ:1.00
 OD1 A:ASP98 2.2 26.9 1.0
O A:HOH617 2.3 39.3 1.0
O A:HOH673 2.4 28.9 1.0
O A:HOH811 3.0 29.2 1.0
CG A:ASP98 3.3 24.7 1.0
OD2 A:ASP98 3.7 25.5 1.0
O A:ASP98 4.2 24.7 1.0
C A:ASP98 4.6 23.1 1.0
CB A:ASP98 4.6 24.7 1.0
N A:ASP98 4.6 23.0 1.0
O A:HOH718 4.6 24.4 1.0
CA A:ASP98 4.8 22.3 1.0

Calcium binding site 4 out of 7 in 9dr8

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Calcium binding site 4 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:47.8
occ:1.00
 OD2 A:ASP24 3.2 66.1 1.0
O A:HOH823 4.1 44.6 1.0
O A:HOH836 4.3 39.7 1.0
CG A:ASP24 4.3 65.6 1.0
O B:HOH853 4.5 49.1 1.0
O B:GLY216 4.7 20.6 1.0
CB A:ASP24 4.7 62.5 1.0

Calcium binding site 5 out of 7 in 9dr8

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Calcium binding site 5 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:24.1
occ:1.00
 OD1 B:ASP127 2.2 21.8 1.0
O B:HOH640 2.3 25.3 1.0
O B:HOH734 2.3 22.2 1.0
O B:HOH685 2.4 24.2 1.0
O B:HOH813 2.5 30.2 1.0
CG B:ASP127 3.5 21.0 1.0
N B:ASP127 4.2 20.2 1.0
O B:HOH622 4.2 32.0 1.0
OD2 B:ASP127 4.2 22.8 1.0
CA B:ASP127 4.3 18.6 1.0
O B:ASP124 4.4 19.6 1.0
C B:ASP126 4.4 17.9 1.0
O B:LEU125 4.5 20.5 1.0
CB B:ASP127 4.5 20.2 1.0
NZ B:LYS122 4.6 19.2 0.4
OD2 B:ASP124 4.6 24.4 1.0
O B:HOH910 4.6 24.6 1.0
O B:ASP126 4.8 18.9 1.0
C B:LEU125 4.8 18.2 1.0
O B:HOH774 4.9 34.2 1.0
O B:HOH784 5.0 16.7 1.0

Calcium binding site 6 out of 7 in 9dr8

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Calcium binding site 6 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:31.5
occ:1.00
 O B:HOH939 2.2 40.7 1.0
O B:HOH718 2.3 24.3 1.0
O A:HOH663 2.4 23.5 1.0
O B:HOH679 2.5 24.3 1.0
O A:HOH676 2.5 24.7 1.0
OD1 B:ASP40 4.3 22.7 1.0
OD1 A:ASP40 4.4 21.9 1.0
O A:HOH883 4.4 38.5 1.0
O B:HOH525 4.4 19.1 1.0
CE B:LYS43 4.5 22.6 0.5
O A:HOH516 4.5 19.2 1.0
O B:HOH868 4.7 33.1 1.0
CE A:LYS43 4.7 34.2 1.0
CD B:LYS43 4.8 20.4 0.5
O B:HOH913 4.9 46.0 1.0

Calcium binding site 7 out of 7 in 9dr8

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Calcium binding site 7 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:28.3
occ:1.00
 O B:HOH931 2.3 25.4 1.0
CD B:LYS122 4.3 17.8 0.4
CD B:LYS122 4.3 21.7 0.6
O B:HOH873 4.4 33.5 1.0
O B:HOH859 4.7 40.2 1.0
CE B:LYS122 4.9 18.5 0.4

Reference:

L.Liu, P.Enayati, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Iron Bound) To Be Published.
Page generated: Thu Oct 31 17:22:57 2024

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