Atomistry » Calcium » PDB 1of3-1oux » 1olp
Atomistry »
  Calcium »
    PDB 1of3-1oux »
      1olp »

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

Go back to Calcium Binding Sites List in 1olp
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

Go back to Calcium Binding Sites List in 1olp
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

Go back to Calcium Binding Sites List in 1olp
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

Go back to Calcium Binding Sites List in 1olp
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

Go back to Calcium Binding Sites List in 1olp
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

Go back to Calcium Binding Sites List in 1olp
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

Go back to Calcium Binding Sites List in 1olp
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy