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

Go back to Calcium Binding Sites List in 9dr6
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

Go back to Calcium Binding Sites List in 9dr6
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

Go back to Calcium Binding Sites List in 9dr6
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

Go back to Calcium Binding Sites List in 9dr6
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

Go back to Calcium Binding Sites List in 9dr6
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

Go back to Calcium Binding Sites List in 9dr6
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 Oct 31 17:22:56 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy