Atomistry » Cadmium » PDB 1ykq-2eik » 2a97
Atomistry »
  Cadmium »
    PDB 1ykq-2eik »
      2a97 »

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

Go back to Cadmium Binding Sites List in 2a97
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy