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Calcium in PDB 9dr6: Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc Bound)

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

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

Protein crystallography data

The structure of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc Bound), PDB code: 9dr6 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) 60.26 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.247, 52.271, 120.634, 90, 92.5, 90
R / Rfree (%) 15.3 / 19.2

Other elements in 9dr6:

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

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc Bound) (pdb code 9dr6). 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 (Zinc Bound), PDB code: 9dr6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 9dr6

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Calcium binding site 1 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc 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 (Zinc Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:54.7
occ:1.00
 O A:HOH839 2.3 57.9 1.0
O A:HOH710 2.4 40.6 1.0
O A:HOH940 2.4 52.9 1.0
O A:HOH529 2.4 21.1 1.0
O A:LEU125 2.5 23.6 1.0
O A:HOH569 2.9 43.4 1.0
C A:LEU125 3.5 20.4 1.0
CA A:LEU125 4.0 20.5 1.0
O A:HOH753 4.1 27.1 1.0
O A:HOH702 4.3 29.7 1.0
O A:HOH791 4.4 44.4 1.0
O A:HOH922 4.5 47.4 1.0
N A:ASP126 4.5 17.5 1.0
O A:HOH534 4.6 30.9 1.0
OD1 A:ASP127 4.6 39.4 1.0
O A:ASP124 4.8 19.8 1.0
CB A:LEU125 4.9 19.9 1.0
CA A:ASP126 4.9 20.2 1.0

Calcium binding site 2 out of 7 in 9dr6

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Calcium binding site 2 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc 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 (Zinc Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:29.9
occ:1.00
 O A:HOH744 2.3 29.7 1.0
O A:HOH636 2.4 23.8 1.0
O A:HOH700 2.4 30.4 1.0
O A:HOH887 2.5 26.0 1.0
O A:HOH612 4.2 23.8 1.0
O A:HOH562 4.5 20.4 1.0
O A:HOH934 4.6 38.1 1.0
O A:GLY171 4.6 23.8 1.0
O A:HOH568 4.7 30.3 1.0
O A:HOH754 4.7 25.7 1.0
OG1 A:THR170 4.8 29.9 1.0
OD2 A:ASP168 4.9 20.6 1.0
O A:ALA172 4.9 23.1 1.0

Calcium binding site 3 out of 7 in 9dr6

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Calcium binding site 3 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc 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 (Zinc Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:51.0
occ:1.00
 OD1 A:ASP98 2.3 37.5 1.0
O A:HOH713 2.3 26.6 1.0
O A:HOH812 2.9 30.1 1.0
CG A:ASP98 3.4 32.5 1.0
OD2 A:ASP98 3.8 34.4 1.0
O A:ASP98 4.2 38.9 1.0
N A:ASP98 4.6 22.4 1.0
C A:ASP98 4.6 24.3 1.0
CB A:ASP98 4.6 38.1 1.0
O A:HOH689 4.7 24.6 1.0
CA A:ASP98 4.8 21.7 1.0
O A:HOH845 4.9 39.2 1.0
O A:GLY96 5.0 31.2 1.0

Calcium binding site 4 out of 7 in 9dr6

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Calcium binding site 4 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc 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 (Zinc Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:54.2
occ:1.00
 OD2 A:ASP24 3.2 63.4 1.0
O A:HOH788 4.3 39.6 1.0
CG A:ASP24 4.3 86.6 1.0
O A:HOH815 4.5 39.5 1.0
CB A:ASP24 4.7 64.5 1.0
O B:GLY216 4.7 20.9 1.0

Calcium binding site 5 out of 7 in 9dr6

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Calcium binding site 5 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc 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 (Zinc Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:30.6
occ:1.00
 OD1 B:ASP127 2.3 26.9 1.0
O B:HOH665 2.4 29.4 1.0
O B:HOH625 2.4 30.6 1.0
O B:HOH720 2.4 28.1 1.0
O B:HOH813 2.5 36.5 1.0
CG B:ASP127 3.5 24.8 1.0
N B:ASP127 4.2 24.1 1.0
OD2 B:ASP127 4.2 26.6 1.0
O B:HOH552 4.2 36.8 1.0
CA B:ASP127 4.4 24.1 1.0
O B:LEU125 4.4 25.4 1.0
O B:ASP124 4.4 20.6 1.0
C B:ASP126 4.4 20.2 1.0
NZ B:LYS122 4.5 18.4 0.3
CB B:ASP127 4.5 26.4 1.0
OD2 B:ASP124 4.7 32.4 1.0
O B:ASP126 4.7 24.3 1.0
C B:LEU125 4.8 27.4 1.0
O B:HOH761 4.8 39.2 1.0

Calcium binding site 6 out of 7 in 9dr6

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Calcium binding site 6 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc 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 (Zinc Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:39.6
occ:1.00
 O B:HOH922 2.3 42.0 1.0
O A:HOH724 2.4 29.5 1.0
O B:HOH684 2.4 26.3 1.0
O B:HOH670 2.6 28.5 1.0
O A:HOH665 2.7 26.8 1.0
OD1 B:ASP40 4.3 25.7 1.0
OD1 A:ASP40 4.3 27.2 1.0
O B:HOH520 4.4 22.8 1.0
CE B:LYS43 4.5 19.9 0.5
O B:HOH833 4.5 37.4 1.0
O A:HOH525 4.6 19.8 1.0
CD B:LYS43 4.7 18.4 0.5
O A:HOH854 4.8 51.0 1.0
CD A:LYS43 4.9 56.3 1.0
O B:HOH894 4.9 51.2 1.0

Calcium binding site 7 out of 7 in 9dr6

Go back to Calcium Binding Sites List in 9dr6
Calcium binding site 7 out of 7 in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc 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 (Zinc Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:52.3
occ:1.00
 O B:HOH902 2.6 30.5 1.0
O B:HOH853 4.3 40.0 1.0
O B:HOH544 4.5 23.3 1.0
CD B:LYS122 4.6 25.3 0.7
CD B:LYS122 4.6 22.5 0.3
O B:HOH825 4.9 41.4 1.0

Reference:

L.Liu, P.Enayati, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Multivorans (Zinc Bound) To Be Published.
Page generated: Thu Jul 10 09:23:17 2025

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