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Calcium in PDB 1olp: Alpha Toxin From Clostridium Absonum

Enzymatic activity of Alpha Toxin From Clostridium Absonum

All present enzymatic activity of Alpha Toxin From Clostridium Absonum:
3.1.4.3;

Protein crystallography data

The structure of Alpha Toxin From Clostridium Absonum, PDB code: 1olp was solved by D.C.Briggs, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.75 / 2.5
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.956, 193.592, 92.686, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 23.7

Other elements in 1olp:

The structure of Alpha Toxin From Clostridium Absonum also contains other interesting chemical elements:

Zinc (Zn) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Alpha Toxin From Clostridium Absonum (pdb code 1olp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Alpha Toxin From Clostridium Absonum, PDB code: 1olp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1olp

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Calcium binding site 1 out of 8 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Alpha Toxin From Clostridium Absonum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1371

b:51.7
occ:1.00
 O A:GLY271 2.1 27.6 1.0
O A:GLY337 2.2 35.1 1.0
O A:ASP269 2.4 24.5 1.0
O A:HOH2101 3.0 27.6 1.0
OD1 A:ASP269 3.1 23.5 1.0
C A:GLY271 3.3 27.4 1.0
C A:ASP269 3.4 24.2 1.0
C A:GLY337 3.4 36.1 1.0
CG A:ASP269 3.6 24.0 1.0
N A:GLY271 4.0 25.4 1.0
OD2 A:ASP269 4.0 22.6 1.0
C A:ALA270 4.0 24.8 1.0
CA A:ASP269 4.1 23.9 1.0
O A:ALA270 4.2 24.1 1.0
CA A:GLY271 4.2 26.4 1.0
N A:GLY337 4.2 41.3 1.0
N A:THR272 4.3 28.0 1.0
CA A:GLY337 4.3 38.5 1.0
N A:ALA270 4.3 24.5 1.0
CB A:ASP269 4.3 24.0 1.0
CA A:THR272 4.4 28.2 1.0
N A:TRP338 4.4 33.7 1.0
CA A:TRP338 4.5 31.9 1.0
CB A:THR272 4.6 28.0 1.0
CA A:ALA270 4.6 24.7 1.0
CZ3 A:TRP360 4.7 28.5 1.0
O B:HOH2002 4.8 15.9 1.0
OG1 A:THR272 5.0 28.8 1.0

Calcium binding site 2 out of 8 in 1olp

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Calcium binding site 2 out of 8 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Alpha Toxin From Clostridium Absonum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1372

b:69.2
occ:1.00
 O A:ASN294 2.3 38.1 1.0
O A:GLY296 2.4 35.9 1.0
OD2 A:ASP298 2.6 31.0 1.0
OD1 A:ASP293 2.7 39.0 1.0
CG A:ASP293 3.4 37.4 1.0
C A:ASN294 3.5 37.8 1.0
C A:GLY296 3.6 36.0 1.0
OD2 A:ASP293 3.6 40.9 1.0
CG A:ASP298 3.8 29.2 1.0
N A:GLY296 4.0 37.4 1.0
O A:HOH2108 4.0 41.6 1.0
CA A:PRO295 4.1 38.4 1.0
N A:ASN294 4.1 36.6 1.0
C A:PRO295 4.1 37.9 1.0
N A:PRO295 4.3 38.3 1.0
C A:ASP293 4.4 35.8 1.0
CA A:ASP293 4.4 35.2 1.0
CB A:ASP293 4.4 35.9 1.0
CA A:GLY296 4.5 36.7 1.0
C A:ASN297 4.5 33.3 1.0
CA A:ASN294 4.5 37.4 1.0
N A:ASN297 4.5 35.3 1.0
N A:ASP298 4.5 30.7 1.0
CA A:ASN297 4.6 34.7 1.0
OD1 A:ASP298 4.6 28.6 1.0
CB A:ASP298 4.6 29.3 1.0
O A:PRO295 4.8 38.3 1.0
O A:ASN297 5.0 33.8 1.0

Calcium binding site 3 out of 8 in 1olp

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Calcium binding site 3 out of 8 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Alpha Toxin From Clostridium Absonum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1371

b:67.4
occ:1.00
 OD2 B:ASP298 2.4 34.1 1.0
O B:ASN294 2.5 35.6 1.0
O B:GLY296 2.6 34.7 1.0
OD1 B:ASP293 2.9 41.4 1.0
CG B:ASP293 3.3 37.7 1.0
OD2 B:ASP293 3.3 41.4 1.0
CG B:ASP298 3.5 33.2 1.0
C B:ASN294 3.7 35.8 1.0
C B:GLY296 3.9 35.1 1.0
N B:ASN294 4.0 35.5 1.0
CB B:ASP298 4.1 31.9 1.0
CA B:ASP293 4.2 35.3 1.0
C B:ASP293 4.3 35.4 1.0
CB B:ASP293 4.3 35.6 1.0
N B:ASP298 4.3 32.6 1.0
N B:GLY296 4.5 35.1 1.0
CA B:ASN294 4.5 35.9 1.0
C B:ASN297 4.5 34.4 1.0
OD1 B:ASP298 4.5 35.4 1.0
C B:PRO295 4.6 35.5 1.0
N B:PRO295 4.6 35.6 1.0
CA B:PRO295 4.6 35.7 1.0
CA B:ASN297 4.7 35.4 1.0
N B:ASN297 4.7 35.4 1.0
CA B:GLY296 4.8 35.2 1.0
CA B:ASP298 4.9 31.3 1.0
O B:ASN297 5.0 35.2 1.0

Calcium binding site 4 out of 8 in 1olp

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Calcium binding site 4 out of 8 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Alpha Toxin From Clostridium Absonum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1372

b:52.3
occ:1.00
 O B:GLY271 2.2 23.3 1.0
OD1 B:ASP336 2.4 36.0 1.0
O B:ASP269 2.4 19.9 1.0
O B:GLY337 2.5 29.4 1.0
OD1 B:ASP269 2.7 22.2 1.0
CG B:ASP269 3.2 21.1 1.0
C B:GLY271 3.4 23.4 1.0
O B:HOH2078 3.4 33.0 1.0
C B:ASP269 3.4 19.9 1.0
OD2 B:ASP269 3.4 21.6 1.0
CG B:ASP336 3.6 37.1 1.0
C B:GLY337 3.6 29.9 1.0
C B:ASP336 3.9 34.7 1.0
N B:GLY337 4.0 32.8 1.0
CA B:ASP269 4.0 19.7 1.0
N B:GLY271 4.1 21.6 1.0
O B:ASP336 4.1 33.8 1.0
CB B:ASP269 4.1 19.9 1.0
C B:ALA270 4.2 20.9 1.0
CA B:ASP336 4.2 36.0 1.0
N B:THR272 4.3 25.0 1.0
CA B:THR272 4.3 26.0 1.0
O B:HOH2079 4.3 26.3 1.0
CA B:GLY271 4.3 22.5 1.0
OD2 B:ASP336 4.4 39.6 1.0
CA B:GLY337 4.4 31.4 1.0
N B:ALA270 4.4 20.4 1.0
O B:ALA270 4.5 21.3 1.0
CB B:ASP336 4.5 36.1 1.0
CB B:THR272 4.5 26.3 1.0
N B:TRP338 4.6 28.5 1.0
CA B:ALA270 4.7 20.7 1.0
CZ3 B:TRP360 4.8 24.8 1.0
CA B:TRP338 4.8 27.7 1.0
O A:HOH2003 4.9 17.4 1.0

Calcium binding site 5 out of 8 in 1olp

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Calcium binding site 5 out of 8 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Alpha Toxin From Clostridium Absonum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1371

b:80.5
occ:1.00
 O C:GLY296 2.4 43.9 1.0
O C:ASN294 2.4 46.9 1.0
OD1 C:ASP298 2.5 39.5 1.0
OD1 C:ASP293 3.1 49.5 1.0
CG C:ASP293 3.5 48.1 1.0
C C:GLY296 3.6 44.0 1.0
C C:ASN294 3.6 46.6 1.0
CG C:ASP298 3.7 38.4 1.0
OD2 C:ASP293 3.8 49.5 1.0
C C:ASP293 4.0 46.4 1.0
N C:ASN294 4.1 46.5 1.0
N C:GLY296 4.1 45.3 1.0
CA C:ASP293 4.2 46.3 1.0
N C:ASP298 4.3 39.6 1.0
O C:ASP293 4.3 46.9 1.0
OD2 C:ASP298 4.4 37.5 1.0
CB C:ASP293 4.4 46.5 1.0
C C:PRO295 4.5 46.1 1.0
CA C:ASN294 4.5 46.5 1.0
CA C:GLY296 4.5 44.6 1.0
N C:ASN297 4.5 43.1 1.0
CA C:ASN297 4.6 42.6 1.0
N C:PRO295 4.6 46.6 1.0
CB C:ASP298 4.6 38.6 1.0
CA C:PRO295 4.6 46.6 1.0
C C:ASN297 4.8 41.3 1.0

Calcium binding site 6 out of 8 in 1olp

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Calcium binding site 6 out of 8 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Alpha Toxin From Clostridium Absonum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1372

b:77.4
occ:1.00
 O C:GLY271 2.3 36.2 1.0
O C:GLY337 2.4 36.9 1.0
O C:ASP269 2.5 38.6 1.0
OD1 C:ASP336 3.0 46.2 1.0
C C:ASP269 3.5 39.2 1.0
C C:GLY271 3.5 36.5 1.0
C C:GLY337 3.6 37.0 1.0
C C:ASP336 3.9 41.5 1.0
N C:GLY337 4.0 39.8 1.0
O C:ASP336 4.1 41.5 1.0
CG C:ASP336 4.1 44.6 1.0
CA C:ASP269 4.2 40.1 1.0
C C:ALA270 4.2 37.5 1.0
O C:ALA270 4.2 37.4 1.0
CB C:ASP269 4.2 40.4 1.0
N C:GLY271 4.3 37.0 1.0
CA C:GLY337 4.3 38.4 1.0
CA C:ASP336 4.3 43.0 1.0
N C:THR272 4.3 36.5 1.0
CA C:THR272 4.3 36.2 1.0
N C:ALA270 4.5 38.6 1.0
CA C:GLY271 4.5 36.9 1.0
CB C:THR272 4.5 36.1 1.0
N C:TRP338 4.6 35.5 1.0
CA C:ALA270 4.7 38.0 1.0
CZ3 C:TRP360 4.8 42.3 1.0
CB C:ASP336 4.8 43.1 1.0
CA C:TRP338 4.8 34.6 1.0
OG1 C:THR272 4.9 35.1 1.0

Calcium binding site 7 out of 8 in 1olp

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Calcium binding site 7 out of 8 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Alpha Toxin From Clostridium Absonum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1371

b:69.7
occ:1.00
 O D:GLY271 2.3 33.1 1.0
O D:ASP269 2.5 34.9 1.0
O D:GLY337 2.6 36.4 1.0
C D:ASP269 3.4 35.2 1.0
O D:ASP336 3.5 41.0 1.0
O D:THR335 3.5 41.2 1.0
C D:GLY271 3.5 32.8 1.0
C D:GLY337 3.8 36.5 1.0
C D:THR335 3.8 41.0 1.0
CA D:ASP269 3.9 36.1 1.0
CB D:ASP269 4.0 36.4 1.0
CA D:THR335 4.0 41.4 1.0
O D:HOH2050 4.0 33.1 1.0
N D:GLY271 4.2 32.9 1.0
C D:ASP336 4.2 40.0 1.0
C D:ALA270 4.3 33.4 1.0
N D:ALA270 4.4 34.6 1.0
CA D:GLY271 4.4 32.9 1.0
N D:THR272 4.4 32.5 1.0
CB D:THR335 4.5 41.3 1.0
O D:HOH2049 4.5 34.3 1.0
CA D:GLY337 4.5 37.7 1.0
CA D:THR272 4.5 32.0 1.0
O D:ALA270 4.6 33.2 1.0
CZ3 D:TRP360 4.6 28.8 1.0
N D:ASP336 4.7 40.6 1.0
N D:GLY337 4.7 38.9 1.0
CA D:ALA270 4.8 33.9 1.0
N D:TRP338 4.8 35.5 1.0
CB D:THR272 4.8 31.9 1.0

Calcium binding site 8 out of 8 in 1olp

Go back to Calcium Binding Sites List in 1olp
Calcium binding site 8 out of 8 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Alpha Toxin From Clostridium Absonum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1372

b:83.7
occ:1.00
 O D:ASP293 2.7 44.3 1.0
OH C:TYR219 3.0 37.6 1.0
O D:ASN294 3.1 47.0 1.0
O D:GLY296 3.1 46.6 1.0
OD2 D:ASP298 3.4 46.1 1.0
C D:ASP293 3.5 44.2 1.0
C D:ASN294 3.6 46.6 1.0
N D:GLY296 3.7 47.0 1.0
CG D:ASP298 3.7 45.3 1.0
CA D:PRO295 3.9 46.8 1.0
N D:PRO295 4.0 46.8 1.0
CZ C:TYR219 4.0 36.0 1.0
C D:GLY296 4.0 47.3 1.0
C D:PRO295 4.0 46.9 1.0
CE2 C:TYR219 4.1 35.2 1.0
OD1 D:ASP298 4.2 45.7 1.0
CA D:ASP293 4.3 43.5 1.0
CB D:ASP298 4.3 43.5 1.0
N D:ASN294 4.4 45.1 1.0
CA D:GLY296 4.5 47.1 1.0
CA D:ASN294 4.6 46.0 1.0
N D:ASP298 4.6 44.4 1.0
O D:HOH2058 4.8 37.2 1.0
O D:PRO295 4.9 46.9 1.0

Reference:

G.Clark, D.C.Briggs, T.Karasawa, X.Wang, A.Cole, T.Maegawa, P.Jayasekera, C.Naylor, J.Miller, D.Moss, S.Nakamura, A.K.Basak, R.Titball. Clostridium Absonum Alpha-Toxin: New Insights Into Clostridial Phospholipase C Substrate Binding and Specificity J.Mol.Biol. V. 333 759 2003.
ISSN: ISSN 0022-2836
PubMed: 14568535
DOI: 10.1016/J.JMB.2003.07.016
Page generated: Thu Jul 11 13:23:11 2024

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