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Calcium in PDB 2wxu: Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I

Enzymatic activity of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I

All present enzymatic activity of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I:
3.1.4.3;

Protein crystallography data

The structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I, PDB code: 2wxu was solved by S.G.Vachieri, C.E.Naylor, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.64 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 59.861, 173.643, 78.564, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.6

Other elements in 2wxu:

The structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I also contains other interesting chemical elements:

Cadmium (Cd) 7 atoms
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I (pdb code 2wxu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I, PDB code: 2wxu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2wxu

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Calcium binding site 1 out of 5 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1377

b:13.4
occ:1.00
 OD1 A:ASN297 2.3 27.6 1.0
O A:HOH2339 2.5 30.5 1.0
O A:HOH2307 2.6 26.4 1.0
OD1 A:ASP273 2.8 23.6 1.0
CG A:ASN297 3.3 35.2 1.0
OD2 A:ASP273 3.4 46.0 1.0
CG A:ASP273 3.5 31.2 1.0
ND2 A:ASN297 3.6 32.0 1.0
O A:ASP298 4.1 19.6 1.0
CG A:MET300 4.2 31.6 1.0
O A:THR272 4.6 19.0 1.0
O A:HOH2341 4.6 23.0 1.0
CB A:ASN297 4.6 38.0 1.0
O A:HOH2336 4.8 23.9 1.0
CB A:ASP273 4.9 22.3 1.0
C A:ASN297 5.0 29.7 1.0
O A:HOH2343 5.0 31.2 1.0

Calcium binding site 2 out of 5 in 2wxu

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Calcium binding site 2 out of 5 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1380

b:25.9
occ:0.80
 O A:ALA337 2.4 21.2 1.0
O A:GLY271 2.4 18.9 1.0
O A:ASP269 2.4 19.0 1.0
O A:HOH2305 2.5 34.5 1.0
OD1 A:ASP336 2.5 29.5 1.0
O A:HOH2370 2.8 35.7 1.0
C A:ASP269 3.4 24.6 1.0
C A:ALA337 3.5 24.0 1.0
C A:GLY271 3.6 17.0 1.0
CG A:ASP336 3.7 32.6 1.0
C A:ASP336 4.0 35.9 1.0
N A:ALA337 4.0 28.5 1.0
CA A:ASP269 4.0 26.6 1.0
CB A:ASP269 4.1 34.2 1.0
O A:ASP336 4.2 29.8 1.0
C A:ALA270 4.2 18.1 1.0
N A:GLY271 4.2 15.2 1.0
OD1 A:ASP269 4.3 48.3 1.0
CA A:ALA337 4.3 23.9 1.0
O A:HOH2369 4.3 32.2 1.0
CA A:THR272 4.4 16.9 1.0
N A:ALA270 4.4 22.6 1.0
O A:ALA270 4.4 18.4 1.0
OD2 A:ASP336 4.5 30.8 1.0
N A:THR272 4.5 17.7 1.0
N A:TYR338 4.5 18.9 1.0
CA A:GLY271 4.6 14.6 1.0
CA A:ASP336 4.6 40.0 1.0
CG A:ASP269 4.6 44.8 1.0
CA A:ALA270 4.6 19.7 1.0
CB A:THR272 4.7 14.3 1.0
CA A:TYR338 4.7 15.6 1.0
CB A:ASP336 4.8 35.1 1.0
CZ3 A:TRP360 4.8 18.8 1.0
CB A:ALA337 5.0 23.1 1.0

Calcium binding site 3 out of 5 in 2wxu

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Calcium binding site 3 out of 5 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1381

b:40.8
occ:0.94
 OD1 A:ASP298 2.4 22.9 1.0
O A:ASN294 2.4 26.7 1.0
O A:GLY296 2.5 32.2 1.0
O A:HOH2329 2.6 36.7 1.0
OD2 A:ASP293 2.7 36.6 1.0
O A:HOH2331 2.8 50.6 1.0
CG A:ASP298 3.4 28.3 1.0
C A:ASN294 3.6 33.2 1.0
O A:HOH2330 3.7 8.6 1.0
C A:GLY296 3.7 31.7 1.0
N A:ASN294 3.7 21.1 1.0
N A:GLY296 3.8 26.6 1.0
CG A:ASP293 3.8 37.8 1.0
OD2 A:ASP298 4.0 35.3 1.0
CA A:ASN294 4.2 25.9 1.0
C A:ASP293 4.3 21.0 1.0
N A:ASP298 4.3 28.8 1.0
CA A:GLY296 4.4 19.4 1.0
O A:HOH2340 4.4 31.2 1.0
CA A:ASP293 4.5 22.3 1.0
CB A:ASP298 4.5 23.4 1.0
OD1 A:ASP293 4.6 46.4 1.0
N A:PRO295 4.7 40.3 1.0
N A:ASN297 4.7 33.9 1.0
CB A:ASP293 4.8 27.2 1.0
C A:PRO295 4.8 30.0 1.0
CA A:PRO295 4.9 41.7 1.0
CA A:ASN297 4.9 31.4 1.0
CB A:ASN294 5.0 27.6 1.0

Calcium binding site 4 out of 5 in 2wxu

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Calcium binding site 4 out of 5 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1382

b:21.2
occ:1.00
 OE2 A:GLU291 2.4 27.4 1.0
O A:HOH2326 2.5 35.8 1.0
OD1 A:ASP293 2.7 46.4 1.0
O A:HOH2324 2.7 43.8 1.0
O A:HOH2327 3.2 43.1 1.0
CD A:GLU291 3.3 29.2 1.0
CG A:ASP293 3.7 37.8 1.0
OE1 A:GLU291 3.7 30.9 1.0
O A:HOH2331 3.9 50.6 1.0
O A:HOH2330 4.0 8.6 1.0
O A:HOH2152 4.1 47.0 1.0
O A:HOH2310 4.2 22.4 1.0
CD1 A:TYR275 4.2 35.3 1.0
CE1 A:TYR275 4.3 35.7 1.0
CB A:ASP293 4.3 27.2 1.0
CG A:GLU291 4.4 21.1 1.0
O A:HOH2308 4.4 29.5 1.0
O A:HOH2340 4.5 31.2 1.0
O A:HOH2151 4.5 49.1 1.0
OD2 A:ASP293 4.5 36.6 1.0

Calcium binding site 5 out of 5 in 2wxu

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Calcium binding site 5 out of 5 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1383

b:22.8
occ:1.00
 OD1 A:ASP269 2.5 48.3 1.0
CG A:ASP269 3.2 44.8 1.0
OD2 A:ASP269 3.2 48.5 1.0
O A:HOH2305 4.2 34.5 1.0
NZ A:LYS268 4.4 38.2 1.0
CB A:ASP269 4.6 34.2 1.0
O A:HOH2342 4.9 33.9 1.0

Reference:

S.G.Vachieri, G.C.Clark, A.Alape-Giron, M.Flores-Diaz, N.Justin, C.E.Naylor, R.W.Titball, A.K.Basak. Comparison of A Nontoxic Variant of Clostridium Perfringens [Alpha]-Toxin with the Toxic Wild-Type Strain Acta Crystallogr.,Sect.D V. 66 1067 2010.
ISSN: ISSN 0907-4449
PubMed: 20944240
DOI: 10.1107/S090744491003369X
Page generated: Sat Dec 12 03:57:16 2020

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