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

Go back to Calcium Binding Sites List in 9dr8
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

Go back to Calcium Binding Sites List in 9dr8
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

Go back to Calcium Binding Sites List in 9dr8
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

Go back to Calcium Binding Sites List in 9dr8
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

Go back to Calcium Binding Sites List in 9dr8
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

Go back to Calcium Binding Sites List in 9dr8
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

Go back to Calcium Binding Sites List in 9dr8
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

Last articles

Zn in 9IRQ
Zn in 9IYX
Zn in 9J8P
Zn in 9IUU
Zn in 9GBF
Zn in 9G2V
Zn in 9G2L
Zn in 9G2X
Zn in 9G2Z
Zn in 9G2K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy