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Cadmium in PDB 2a97: Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F

Enzymatic activity of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F

All present enzymatic activity of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F:
3.4.24.69;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F, PDB code: 2a97 was solved by R.Agarwal, T.Binz, S.Swaminathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.05 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.400, 53.240, 113.870, 90.00, 119.17, 90.00
R / Rfree (%) 24.1 / 26.9

Other elements in 2a97:

The structure of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F (pdb code 2a97). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F, PDB code: 2a97:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 2a97

Go back to Cadmium Binding Sites List in 2a97
Cadmium binding site 1 out of 7 in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5500

b:21.7
occ:1.00
 OD1 A:ASP383 2.2 25.2 1.0
OD2 B:ASP383 2.2 24.4 1.0
OD2 A:ASP383 2.4 25.3 1.0
OD1 B:ASP383 2.5 26.9 1.0
O B:HOH5621 2.5 5.4 1.0
CG A:ASP383 2.6 25.8 1.0
O A:HOH5510 2.7 9.8 1.0
CG B:ASP383 2.7 26.5 1.0
NZ B:LYS93 3.9 18.1 1.0
NZ A:LYS93 4.0 16.9 1.0
CB A:ASP383 4.1 25.1 1.0
CE B:LYS93 4.1 14.2 1.0
CB B:ASP383 4.2 23.1 1.0
CE A:LYS93 4.3 16.6 1.0
O A:HOH5609 4.4 29.6 1.0
O B:LEU381 4.9 21.4 1.0
O A:LEU381 4.9 24.0 1.0
CA A:ASP383 5.0 24.1 1.0

Cadmium binding site 2 out of 7 in 2a97

Go back to Cadmium Binding Sites List in 2a97
Cadmium binding site 2 out of 7 in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5502

b:32.9
occ:1.00
 O A:HOH5574 2.4 14.8 1.0
OD2 A:ASP121 2.6 23.8 1.0
O A:HOH5596 2.6 10.5 1.0
OD1 A:ASP121 3.2 29.8 1.0
CG A:ASP121 3.2 27.1 1.0
CD A:LYS296 4.2 34.4 1.0
NH2 A:ARG300 4.3 33.3 1.0
CG A:LYS296 4.4 31.3 1.0
CB A:ASP121 4.6 22.1 1.0

Cadmium binding site 3 out of 7 in 2a97

Go back to Cadmium Binding Sites List in 2a97
Cadmium binding site 3 out of 7 in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5504

b:45.5
occ:1.00
 OE2 A:GLU127 2.5 25.8 1.0
OE1 A:GLU127 2.6 28.4 1.0
CD A:GLU127 2.9 29.4 1.0
CG A:GLU127 4.4 27.1 1.0
CG A:PRO124 4.7 24.6 1.0

Cadmium binding site 4 out of 7 in 2a97

Go back to Cadmium Binding Sites List in 2a97
Cadmium binding site 4 out of 7 in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5506

b:39.1
occ:1.00
 OE1 A:GLU246 2.4 36.3 1.0
OE2 A:GLU246 2.6 37.3 1.0
CD A:GLU246 2.8 34.2 1.0
O A:HOH5580 3.3 43.2 1.0
CG A:GLU246 4.3 34.8 1.0
CE A:MET282 4.9 44.5 1.0

Cadmium binding site 5 out of 7 in 2a97

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Cadmium binding site 5 out of 7 in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5507

b:29.4
occ:1.00
 ND1 A:HIS122 2.3 25.6 1.0
CE1 A:HIS122 3.2 25.3 1.0
CG A:HIS122 3.3 22.7 1.0
CB A:HIS122 3.6 23.9 1.0
O A:HOH5509 3.8 6.1 1.0
CA A:HIS122 4.2 21.9 1.0
NE2 A:HIS122 4.3 17.7 1.0
O A:HOH5599 4.3 39.0 1.0
CD2 A:HIS122 4.4 25.9 1.0
O A:HIS122 4.7 25.8 1.0
C A:HIS122 4.9 22.8 1.0

Cadmium binding site 6 out of 7 in 2a97

Go back to Cadmium Binding Sites List in 2a97
Cadmium binding site 6 out of 7 in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd5503

b:46.1
occ:1.00
 O B:HOH5550 2.3 34.0 1.0
O B:HOH5582 2.5 16.2 1.0
OE2 B:GLU338 4.2 38.2 1.0
O B:VAL336 4.3 22.3 1.0
OD2 B:ASP327 4.6 29.1 1.0
N B:GLU338 4.6 24.7 1.0
CG B:GLU338 4.6 34.5 1.0
CA B:ASN337 4.8 22.4 1.0
CD B:GLU338 4.8 35.7 1.0

Cadmium binding site 7 out of 7 in 2a97

Go back to Cadmium Binding Sites List in 2a97
Cadmium binding site 7 out of 7 in the Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Catalytic Domain of Clostridium Botulinum Neurotoxin Serotype F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd5505

b:53.5
occ:1.00
 O B:HOH5632 2.3 25.8 1.0
O B:HOH5622 2.5 14.6 1.0
O B:HOH5624 2.5 15.5 1.0
OD2 B:ASP121 2.5 23.2 1.0
O B:HOH5623 2.6 13.0 1.0
OD1 B:ASP121 3.1 31.1 1.0
CG B:ASP121 3.2 27.6 1.0
CD B:LYS296 4.1 31.0 1.0
CG B:LYS296 4.3 27.0 1.0
NH1 B:ARG300 4.5 24.5 1.0
CB B:ASP121 4.6 24.1 1.0
CA B:ASP121 4.9 23.5 1.0

Reference:

R.Agarwal, T.Binz, S.Swaminathan. Structural Analysis of Botulinum Neurotoxin Serotype F Light Chain: Implications on Substrate Binding and Inhibitor Design Biochemistry V. 44 11758 2005.
ISSN: ISSN 0006-2960
PubMed: 16128577
DOI: 10.1021/BI0510072
Page generated: Sat Dec 12 08:16:39 2020

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