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Cadmium in PDB 1ca1: Alpha-Toxin From Clostridium Perfringens

Enzymatic activity of Alpha-Toxin From Clostridium Perfringens

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

Protein crystallography data

The structure of Alpha-Toxin From Clostridium Perfringens, PDB code: 1ca1 was solved by C.E.Naylor, A.K.Basak, R.W.Titball, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 61.300, 177.300, 79.100, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.4

Other elements in 1ca1:

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

Zinc (Zn) 1 atom

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the Alpha-Toxin From Clostridium Perfringens (pdb code 1ca1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Alpha-Toxin From Clostridium Perfringens, PDB code: 1ca1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 1ca1

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Cadmium binding site 1 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd372

b:22.6
occ:1.00
 O A:HOH483 2.4 30.1 1.0
O A:HOH573 2.4 32.9 1.0
OE2 A:GLU152 2.5 22.5 1.0
NE2 A:HIS136 2.6 19.4 1.0
NE2 A:HIS148 2.6 20.4 1.0
OE1 A:GLU152 2.7 28.1 1.0
CD A:GLU152 2.9 22.9 1.0
CD2 A:HIS136 3.4 20.1 1.0
CD2 A:HIS148 3.5 22.0 1.0
CE1 A:HIS136 3.7 20.4 1.0
CE1 A:HIS148 3.7 21.8 1.0
O A:HOH572 3.8 38.1 1.0
CG A:GLU152 4.3 18.4 1.0
N A:TRP1 4.6 23.4 1.0
O A:HOH497 4.6 22.5 1.0
CG A:HIS136 4.6 21.2 1.0
CG A:HIS148 4.7 22.6 1.0
ND1 A:HIS136 4.7 19.6 1.0
ND1 A:HIS148 4.7 23.1 1.0
ZN A:ZN371 4.8 17.5 1.0

Cadmium binding site 2 out of 12 in 1ca1

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Cadmium binding site 2 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd373

b:19.6
occ:1.00
 O A:HOH572 2.3 38.1 1.0
OD2 A:ASP130 2.4 20.5 1.0
ND1 A:HIS68 2.5 22.8 1.0
OD1 A:ASP56 2.5 16.5 1.0
NE2 A:HIS126 2.6 11.5 1.0
CE1 A:HIS68 3.2 23.2 1.0
CG A:ASP130 3.3 18.9 1.0
CG A:ASP56 3.4 20.4 1.0
CE1 A:HIS126 3.4 11.1 1.0
OD2 A:ASP56 3.5 20.8 1.0
ZN A:ZN371 3.5 17.5 1.0
OD1 A:ASP130 3.5 15.5 1.0
CG A:HIS68 3.6 20.7 1.0
CD2 A:HIS126 3.6 10.6 1.0
O A:HOH573 4.0 32.9 1.0
CB A:HIS68 4.0 17.6 1.0
NE2 A:HIS68 4.4 20.3 1.0
ND1 A:HIS126 4.5 10.0 1.0
CE1 A:HIS136 4.5 20.4 1.0
NE2 A:HIS11 4.6 17.5 1.0
CD2 A:HIS68 4.6 18.5 1.0
CG A:HIS126 4.7 14.1 1.0
CB A:ASP130 4.7 16.3 1.0
CB A:ASP56 4.8 20.1 1.0
O A:HOH483 4.9 30.1 1.0
NE2 A:HIS136 5.0 19.4 1.0

Cadmium binding site 3 out of 12 in 1ca1

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Cadmium binding site 3 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd374

b:28.5
occ:1.00
 O A:HOH492 2.4 35.4 1.0
O A:HOH477 2.5 37.7 1.0
SG A:CYS169 2.6 27.7 1.0
O A:GLY168 2.7 27.8 1.0
C A:GLY168 3.4 26.4 1.0
CB A:CYS169 3.6 27.0 1.0
N A:CYS169 4.0 25.3 1.0
CA A:CYS169 4.2 25.4 1.0
O A:HOH482 4.2 32.9 1.0
CA A:GLY168 4.2 26.7 1.0
CD A:CD375 4.3 26.9 1.0
O A:HOH569 4.3 40.7 1.0
O A:HOH471 4.6 31.6 1.0
O A:HOH494 4.9 27.6 1.0
O A:VAL167 4.9 23.2 1.0

Cadmium binding site 4 out of 12 in 1ca1

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Cadmium binding site 4 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd375

b:26.9
occ:1.00
 OE1 A:GLU173 2.3 24.2 1.0
O A:HOH480 2.3 25.5 1.0
O A:HOH482 2.3 32.9 1.0
OE2 A:GLU173 2.7 21.2 1.0
SG A:CYS169 2.8 27.7 1.0
CD A:GLU173 2.8 23.2 1.0
CB A:CYS169 3.9 27.0 1.0
CA A:CYS169 4.0 25.4 1.0
CD A:CD376 4.0 34.4 1.0
O A:GLY168 4.1 27.8 1.0
O A:HOH494 4.2 27.6 1.0
CG A:GLU173 4.3 24.0 1.0
CD A:CD374 4.3 28.5 1.0
N A:LYS170 4.8 25.9 1.0
CB A:GLU173 4.9 25.8 1.0
C A:GLY168 5.0 26.4 1.0
C A:CYS169 5.0 25.5 1.0
N A:CYS169 5.0 25.3 1.0

Cadmium binding site 5 out of 12 in 1ca1

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Cadmium binding site 5 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd376

b:34.4
occ:1.00
 OE1 A:GLU173 2.4 24.2 1.0
O A:HOH496 2.5 27.8 1.0
O A:HOH494 2.7 27.6 1.0
CD A:GLU173 3.5 23.2 1.0
CG A:GLU173 3.9 24.0 1.0
CD A:CD375 4.0 26.9 1.0
CB A:GLU173 4.2 25.8 1.0
OE2 A:GLU173 4.6 21.2 1.0
O A:HOH480 4.7 25.5 1.0
SG A:CYS169 4.8 27.7 1.0

Cadmium binding site 6 out of 12 in 1ca1

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Cadmium binding site 6 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd377

b:43.1
occ:1.00
 O A:HOH455 2.2 50.5 1.0
O A:HOH409 2.5 43.0 1.0
OD2 A:ASP174 2.5 34.7 1.0
OD2 A:ASP178 2.6 25.6 1.0
OD1 A:ASP174 2.6 37.0 1.0
OD1 A:ASP178 2.8 20.6 1.0
CG A:ASP174 2.9 33.9 1.0
O A:HOH527 2.9 38.1 1.0
CG A:ASP178 3.0 23.5 1.0
CB A:ASP174 4.3 29.7 1.0
O A:ASP174 4.3 23.8 1.0
CB A:ASP178 4.5 21.5 1.0
O A:HOH478 4.6 31.4 1.0
O A:HOH523 4.7 37.9 1.0
CA A:ASP174 4.8 26.5 1.0
C A:ASP174 4.8 24.2 1.0

Cadmium binding site 7 out of 12 in 1ca1

Go back to Cadmium Binding Sites List in 1ca1
Cadmium binding site 7 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd378

b:47.4
occ:1.00
 O A:HOH475 2.3 27.7 1.0
ND1 A:HIS241 2.5 24.3 1.0
OE1 A:GLU245 2.5 43.3 1.0
OE2 A:GLU245 2.6 43.0 1.0
CD A:GLU245 2.9 43.1 1.0
CE1 A:HIS241 3.4 22.0 1.0
CG A:HIS241 3.4 22.5 1.0
CB A:HIS241 3.7 21.4 1.0
CG A:GLU245 4.4 42.6 1.0
NE2 A:HIS241 4.5 23.0 1.0
CA A:HIS241 4.5 23.4 1.0
CD2 A:HIS241 4.6 23.5 1.0
ND2 A:ASN247 4.7 44.5 1.0
O A:HIS241 4.7 27.5 1.0
CD1 A:LEU180 4.8 23.5 1.0
CD2 A:LEU180 4.9 20.8 1.0
C A:HIS241 4.9 25.3 1.0

Cadmium binding site 8 out of 12 in 1ca1

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Cadmium binding site 8 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd379

b:58.0
occ:1.00
 OD1 A:ASP293 2.5 38.5 1.0
O A:HOH555 2.8 48.3 1.0
OD2 A:ASP293 3.0 41.7 1.0
CG A:ASP293 3.1 41.3 1.0
CG A:PRO295 3.9 54.5 1.0
CB A:PRO295 4.0 55.5 1.0
CD A:PRO295 4.2 56.6 1.0
O A:HOH544 4.4 35.3 1.0
CB A:ASP293 4.6 42.8 1.0
O A:ASP293 4.7 44.8 1.0

Cadmium binding site 9 out of 12 in 1ca1

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Cadmium binding site 9 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd380

b:41.6
occ:1.00
 O A:HOH545 2.2 18.6 1.0
O A:HOH525 2.4 36.0 1.0
ND1 A:HIS46 2.6 27.6 1.0
CE1 A:HIS46 3.4 27.9 1.0
CG A:HIS46 3.5 28.2 1.0
CB A:HIS46 3.7 26.1 1.0
O A:HOH415 3.9 56.3 1.0
OE2 A:GLU47 4.4 39.3 1.0
NE2 A:HIS46 4.5 30.0 1.0
CD2 A:HIS46 4.5 29.0 1.0
CD1 A:LEU50 4.6 22.8 1.0
C A:HIS46 4.9 16.9 1.0
CA A:HIS46 5.0 23.1 1.0

Cadmium binding site 10 out of 12 in 1ca1

Go back to Cadmium Binding Sites List in 1ca1
Cadmium binding site 10 out of 12 in the Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Alpha-Toxin From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd381

b:35.7
occ:0.50
 O A:HOH516 2.3 31.4 1.0
OE1 A:GLU157 2.6 35.1 1.0
OE2 A:GLU157 2.7 38.7 1.0
O A:HOH407 2.8 55.9 0.5
CD A:GLU157 3.0 36.3 1.0
O A:HOH416 4.3 42.2 1.0
O A:HOH567 4.4 34.1 1.0
CG A:GLU157 4.4 34.3 1.0
CG2 A:THR153 4.8 17.5 1.0

Reference:

C.E.Naylor, J.T.Eaton, A.Howells, N.Justin, D.S.Moss, R.W.Titball, A.K.Basak. Structure of the Key Toxin in Gas Gangrene. Nat.Struct.Biol. V. 5 738 1998.
ISSN: ISSN 1072-8368
PubMed: 9699639
DOI: 10.1038/1447
Page generated: Fri Jul 19 13:06:03 2024

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