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Calcium in PDB 3onr: Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site

Protein crystallography data

The structure of Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site, PDB code: 3onr was solved by A.Arulandu, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.88 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.193, 78.446, 152.489, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.9

Other elements in 3onr:

The structure of Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site also contains other interesting chemical elements:

Platinum (Pt) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site (pdb code 3onr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site, PDB code: 3onr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3onr

Go back to Calcium Binding Sites List in 3onr
Calcium binding site 1 out of 4 in the Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site


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 the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca72

b:26.2
occ:1.00
O B:HOH200 2.3 7.9 1.0
O A:HOH200 2.4 2.2 1.0
OE1 A:GLU18 2.4 24.4 1.0
OE2 C:GLU18 2.5 27.6 1.0
OE1 B:GLU18 2.5 26.4 1.0
OE2 A:GLU18 2.6 20.4 1.0
OE2 B:GLU18 2.7 23.2 1.0
OE1 C:GLU18 2.7 24.6 1.0
CD A:GLU18 2.9 24.2 1.0
CD C:GLU18 2.9 24.4 1.0
CD B:GLU18 3.0 24.5 1.0
CG A:GLU18 4.4 23.7 1.0
CG B:GLU18 4.4 22.9 1.0
CG C:GLU18 4.5 24.8 1.0
O A:HOH232 4.6 27.6 1.0
O A:HOH231 4.6 21.7 1.0
CB C:SER16 4.7 23.6 1.0
CB B:SER16 4.8 26.4 1.0
CB A:SER16 4.8 26.4 1.0
N A:GLU18 4.9 20.2 1.0
N C:GLU18 5.0 21.0 1.0
N A:TRP17 5.0 20.3 1.0
N C:TRP17 5.0 19.6 1.0
N B:GLU18 5.0 21.1 1.0

Calcium binding site 2 out of 4 in 3onr

Go back to Calcium Binding Sites List in 3onr
Calcium binding site 2 out of 4 in the Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site


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 the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca72

b:30.2
occ:1.00
OE2 E:GLU18 2.3 32.5 1.0
OE2 F:GLU18 2.3 22.2 1.0
O E:HOH200 2.4 2.0 1.0
O D:HOH200 2.4 6.9 1.0
OE2 D:GLU18 2.5 25.5 1.0
OE1 F:GLU18 2.6 20.7 1.0
OE1 E:GLU18 2.6 26.6 1.0
OE1 D:GLU18 2.7 25.1 1.0
CD F:GLU18 2.9 23.0 1.0
CD E:GLU18 2.9 27.5 1.0
CD D:GLU18 3.0 27.0 1.0
CG E:GLU18 4.4 29.1 1.0
CG F:GLU18 4.4 22.4 1.0
CG D:GLU18 4.5 27.5 1.0
CB D:SER16 4.7 29.4 1.0
CB E:SER16 4.8 26.9 1.0
N D:TRP17 4.9 22.8 1.0
CB F:SER16 4.9 24.5 1.0
N D:GLU18 4.9 24.8 1.0
N E:GLU18 4.9 22.9 1.0
N F:GLU18 4.9 23.7 1.0
O F:HOH200 5.0 5.3 1.0
N E:TRP17 5.0 22.2 1.0
CE3 D:TRP17 5.0 19.8 1.0

Calcium binding site 3 out of 4 in 3onr

Go back to Calcium Binding Sites List in 3onr
Calcium binding site 3 out of 4 in the Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site


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 the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca72

b:18.2
occ:1.00
O G:HOH200 2.3 3.3 1.0
OE1 H:GLU18 2.4 13.4 1.0
OE1 I:GLU18 2.4 14.8 1.0
OE1 G:GLU18 2.5 13.1 1.0
OE2 H:GLU18 2.5 13.1 1.0
OE2 I:GLU18 2.6 11.3 1.0
OE2 G:GLU18 2.7 13.4 1.0
CD H:GLU18 2.8 12.9 1.0
CD I:GLU18 2.9 14.6 1.0
CD G:GLU18 2.9 16.0 1.0
CG H:GLU18 4.3 13.8 1.0
CG G:GLU18 4.4 16.8 1.0
CG I:GLU18 4.4 11.8 1.0
O G:HOH211 4.5 13.6 1.0
O G:HOH201 4.8 5.3 1.0
N G:TRP17 4.8 12.3 1.0
CE3 G:TRP17 4.8 15.5 1.0
N G:GLU18 4.8 12.9 1.0
CB G:SER16 4.9 13.8 1.0
N I:GLU18 4.9 12.4 1.0
CB H:SER16 4.9 14.6 1.0
N H:GLU18 5.0 10.9 1.0
CB G:TRP17 5.0 13.8 1.0
CB I:SER16 5.0 14.5 1.0

Calcium binding site 4 out of 4 in 3onr

Go back to Calcium Binding Sites List in 3onr
Calcium binding site 4 out of 4 in the Crystal Structure of the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site


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 the Calcium Chelating Immunodominant Antigen, Calcium Dodecin (RV0379),From Mycobacterium Tuberculosis with A Novel Calcium-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca72

b:23.0
occ:1.00
O K:HOH200 2.4 7.5 1.0
OE2 J:GLU18 2.4 18.7 1.0
O L:HOH200 2.4 7.5 1.0
OE1 L:GLU18 2.5 20.2 1.0
OE2 K:GLU18 2.5 21.2 1.0
OE2 L:GLU18 2.6 17.8 1.0
OE1 K:GLU18 2.6 21.3 1.0
OE1 J:GLU18 2.7 19.9 1.0
CD K:GLU18 2.9 21.5 1.0
CD J:GLU18 2.9 21.0 1.0
CD L:GLU18 2.9 22.2 1.0
CG K:GLU18 4.4 26.1 1.0
CG J:GLU18 4.4 21.2 1.0
CG L:GLU18 4.4 22.0 1.0
CB K:SER16 4.7 21.9 1.0
CB J:SER16 4.8 24.4 1.0
CB L:SER16 4.9 19.2 1.0
N K:TRP17 4.9 17.8 1.0
O L:HOH201 4.9 4.7 1.0
O J:HOH222 4.9 31.6 1.0
N L:GLU18 4.9 17.8 1.0
N K:GLU18 4.9 19.0 1.0
N J:TRP17 5.0 15.9 1.0
N J:GLU18 5.0 17.9 1.0

Reference:

A.Arockiasamy, A.Aggarwal, C.G.Savva, A.Holzenburg, J.C.Sacchettini. Crystal Structure of Calcium Dodecin (RV0379), From Mycobacterium Tuberculosis with A Unique Calcium-Binding Site. Protein Sci. V. 20 827 2011.
ISSN: ISSN 0961-8368
PubMed: 21370306
DOI: 10.1002/PRO.607
Page generated: Wed Oct 28 08:19:00 2020

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