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Calcium in PDB 1qmd: Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens

Enzymatic activity of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens

All present enzymatic activity of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens:
3.1.4.3;

Protein crystallography data

The structure of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens, PDB code: 1qmd was solved by C.E.Naylor, J.Miller, R.W.Titball, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 149.890, 149.890, 192.930, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 23.5

Other elements in 1qmd:

The structure of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens (pdb code 1qmd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens, PDB code: 1qmd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1qmd

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Calcium binding site 1 out of 6 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:27.4
occ:1.00
 O A:ALA337 2.4 21.9 1.0
O A:ASP269 2.4 28.1 1.0
OD1 A:ASP336 2.4 26.4 1.0
O A:GLY271 2.5 23.8 1.0
C A:ASP269 3.5 27.6 1.0
C A:ALA337 3.5 24.0 1.0
CG A:ASP336 3.6 28.9 1.0
C A:GLY271 3.7 23.9 1.0
N A:ALA337 3.7 27.1 1.0
C A:ASP336 3.8 28.3 1.0
CB A:ASP269 4.0 36.2 1.0
CA A:ASP336 4.0 28.4 1.0
CA A:ASP269 4.1 31.0 1.0
CA A:ALA337 4.2 24.6 1.0
O A:ASP336 4.2 27.9 1.0
C A:ALA270 4.3 23.1 1.0
N A:GLY271 4.4 22.1 1.0
CA A:THR272 4.4 22.4 1.0
CB A:ASP336 4.5 28.2 1.0
O A:ALA270 4.5 21.9 1.0
OD2 A:ASP336 4.5 28.5 1.0
N A:THR272 4.5 21.9 1.0
N A:ALA270 4.5 24.9 1.0
N A:TYR338 4.6 22.6 1.0
CA A:GLY271 4.6 23.4 1.0
CZ3 A:TRP360 4.6 30.3 1.0
CB A:THR272 4.7 21.8 1.0
CA A:ALA270 4.8 24.1 1.0
OG1 A:THR272 4.8 20.1 1.0
CB A:ALA337 4.9 24.5 1.0
CA A:TYR338 4.9 23.0 1.0

Calcium binding site 2 out of 6 in 1qmd

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Calcium binding site 2 out of 6 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:30.4
occ:1.00
 OD2 A:ASP298 2.3 24.0 1.0
OD1 A:ASP293 2.3 35.6 1.0
O A:ASN294 2.3 28.8 1.0
O A:GLY296 2.5 23.3 1.0
CG A:ASP298 3.5 26.3 1.0
CG A:ASP293 3.5 36.3 1.0
C A:ASN294 3.6 28.4 1.0
C A:GLY296 3.7 27.4 1.0
N A:ASN294 3.9 30.8 1.0
C A:PRO295 4.2 27.1 1.0
OD1 A:ASP298 4.2 25.1 1.0
N A:ASP298 4.2 24.8 1.0
O A:PRO295 4.3 29.7 1.0
N A:GLY296 4.3 25.7 1.0
OD2 A:ASP293 4.3 39.7 1.0
CA A:ASN294 4.4 30.4 1.0
CB A:ASP298 4.4 24.4 1.0
C A:ASP293 4.5 30.9 1.0
CB A:ASP293 4.5 34.4 1.0
N A:PRO295 4.5 27.5 1.0
CA A:ASP293 4.5 31.4 1.0
CA A:GLY296 4.6 26.4 1.0
CA A:PRO295 4.7 27.4 1.0
N A:ASN297 4.7 27.4 1.0
CA A:ASN297 4.8 28.3 1.0
CA A:ASP298 4.9 24.9 1.0
C A:ASN297 5.0 27.4 1.0

Calcium binding site 3 out of 6 in 1qmd

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Calcium binding site 3 out of 6 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:42.6
occ:1.00
 O A:ASP298 2.3 23.3 1.0
OD1 A:ASN297 2.4 35.9 1.0
OD1 A:ASP273 2.6 26.6 1.0
O A:THR272 2.7 21.1 1.0
O A:HOH2141 2.8 42.1 1.0
C A:ASP298 3.4 24.2 1.0
C A:THR272 3.6 21.6 1.0
CG A:ASN297 3.6 33.4 1.0
CA A:ASP273 3.7 22.8 1.0
N A:ASP298 3.7 24.8 1.0
CG A:ASP273 3.7 26.8 1.0
N A:ASP273 4.0 22.5 1.0
CA A:ASP298 4.1 24.9 1.0
O A:HOH2131 4.1 30.7 1.0
C A:ASN297 4.1 27.4 1.0
O A:PHE299 4.2 25.4 1.0
CB A:ASP273 4.3 24.7 1.0
ND2 A:ASN297 4.3 34.3 1.0
C A:PHE299 4.4 23.4 1.0
CA A:ASN297 4.5 28.3 1.0
N A:PHE299 4.5 23.2 1.0
CB A:ASN297 4.6 30.9 1.0
CB A:ASP298 4.7 24.4 1.0
O A:ASN297 4.8 27.2 1.0
CA A:THR272 4.8 22.4 1.0
OD2 A:ASP273 4.8 29.2 1.0
N A:THR272 4.8 21.9 1.0
CA A:PHE299 4.8 23.3 1.0
N A:MET300 4.8 24.5 1.0
CG A:MET300 4.9 28.2 1.0
C A:ASP273 4.9 21.4 1.0
CB A:PHE299 5.0 20.7 1.0

Calcium binding site 4 out of 6 in 1qmd

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Calcium binding site 4 out of 6 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:31.6
occ:1.00
 OD2 B:ASP298 2.2 25.5 1.0
O B:ASN294 2.3 25.2 1.0
OD1 B:ASP293 2.4 33.4 1.0
O B:GLY296 2.5 24.6 1.0
CG B:ASP298 3.4 26.8 1.0
CG B:ASP293 3.5 35.3 1.0
C B:ASN294 3.6 25.9 1.0
C B:GLY296 3.7 26.5 1.0
N B:ASN294 3.9 28.8 1.0
O B:PRO295 4.0 28.8 1.0
C B:PRO295 4.0 25.6 1.0
OD1 B:ASP298 4.1 25.6 1.0
OD2 B:ASP293 4.3 36.7 1.0
N B:ASP298 4.3 23.0 1.0
N B:GLY296 4.3 24.8 1.0
CA B:ASN294 4.5 27.8 1.0
N B:PRO295 4.5 24.9 1.0
CB B:ASP298 4.5 24.6 1.0
CA B:PRO295 4.5 25.3 1.0
CA B:GLY296 4.6 26.8 1.0
C B:ASP293 4.6 29.8 1.0
CB B:ASP293 4.6 32.4 1.0
CA B:ASP293 4.6 29.7 1.0
N B:ASN297 4.7 24.9 1.0
CA B:ASN297 4.8 25.1 1.0
C B:ASN297 4.9 24.4 1.0
CA B:ASP298 5.0 25.1 1.0

Calcium binding site 5 out of 6 in 1qmd

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Calcium binding site 5 out of 6 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:29.7
occ:1.00
 O B:GLY271 2.4 23.1 1.0
O B:ASP269 2.4 32.8 1.0
O B:ALA337 2.4 23.9 1.0
OD1 B:ASP336 2.4 30.8 1.0
C B:ASP269 3.4 32.7 1.0
C B:ALA337 3.6 26.6 1.0
C B:GLY271 3.6 25.2 1.0
CG B:ASP336 3.7 31.8 1.0
N B:ALA337 3.8 27.3 1.0
C B:ASP336 3.9 28.7 1.0
CA B:ASP269 4.0 35.9 1.0
CB B:ASP269 4.2 38.1 1.0
CA B:ASP336 4.2 29.1 1.0
C B:ALA270 4.3 25.4 1.0
CA B:ALA337 4.3 27.6 1.0
N B:GLY271 4.3 25.6 1.0
O B:ASP336 4.3 26.3 1.0
CA B:THR272 4.4 24.3 1.0
O B:ALA270 4.4 25.5 1.0
N B:ALA270 4.4 28.5 1.0
N B:THR272 4.4 23.3 1.0
OD2 B:ASP336 4.5 32.0 1.0
CA B:GLY271 4.5 26.1 1.0
CB B:ASP336 4.6 30.7 1.0
CZ3 B:TRP360 4.6 30.0 1.0
N B:TYR338 4.6 27.7 1.0
CB B:THR272 4.6 24.6 1.0
CA B:ALA270 4.7 26.5 1.0
CA B:TYR338 4.9 26.7 1.0
OG1 B:THR272 4.9 23.4 1.0
CB B:ALA337 5.0 27.2 1.0

Calcium binding site 6 out of 6 in 1qmd

Go back to Calcium Binding Sites List in 1qmd
Calcium binding site 6 out of 6 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:51.7
occ:1.00
 O B:ASP298 2.2 22.8 1.0
OD1 B:ASN297 2.4 28.7 1.0
OD1 B:ASP273 2.5 26.7 1.0
O B:THR272 2.6 23.4 1.0
C B:ASP298 3.4 25.2 1.0
C B:THR272 3.5 24.6 1.0
CG B:ASN297 3.5 27.1 1.0
CG B:ASP273 3.8 27.8 1.0
N B:ASP298 3.9 23.0 1.0
CA B:ASP273 4.0 25.9 1.0
O B:PHE299 4.0 25.1 1.0
N B:ASP273 4.1 25.6 1.0
C B:PHE299 4.1 25.2 1.0
ND2 B:ASN297 4.2 25.4 1.0
CA B:ASP298 4.2 25.1 1.0
C B:ASN297 4.2 24.4 1.0
N B:PHE299 4.4 25.5 1.0
CG B:MET300 4.4 29.6 1.0
N B:MET300 4.4 27.0 1.0
N B:THR272 4.4 23.3 1.0
CB B:ASP273 4.5 25.8 1.0
CA B:THR272 4.5 24.3 1.0
CA B:PHE299 4.6 25.6 1.0
CB B:ASN297 4.6 25.4 1.0
OD2 B:ASP273 4.7 28.4 1.0
CA B:ASN297 4.7 25.1 1.0
CA B:MET300 4.7 26.9 1.0
CB B:PHE299 4.7 24.7 1.0
O B:ASN297 4.8 22.9 1.0
CB B:ASP298 4.9 24.6 1.0

Reference:

C.E.Naylor, M.Jepson, D.T.Crane, R.W.Titball, J.Miller, A.K.Basak, B.Bolgiano. Characterisation of the Calcium-Binding C-Terminal Domain of Clostridium Perfringens Alpha-Toxin J.Mol.Biol. V. 294 757 1999.
ISSN: ISSN 0022-2836
PubMed: 10610794
DOI: 10.1006/JMBI.1999.3279
Page generated: Thu Jul 11 21:54:57 2024

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