Atomistry » Zinc » PDB 1qm6-1r1v » 1qm6
Atomistry »
  Zinc »
    PDB 1qm6-1r1v »
      1qm6 »

Zinc in PDB 1qm6: Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237

Enzymatic activity of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237

All present enzymatic activity of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237:
3.1.4.3;

Protein crystallography data

The structure of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237, PDB code: 1qm6 was solved by C.E.Naylor, J.Miller, R.W.Titball, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 149.540, 149.540, 193.830, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 (pdb code 1qm6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237, PDB code: 1qm6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1qm6

Go back to Zinc Binding Sites List in 1qm6
Zinc binding site 1 out of 4 in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:13.3
occ:1.00
OD1 A:ASP130 2.3 12.7 1.0
O A:TRP1 2.3 8.1 1.0
NE2 A:HIS11 2.3 9.6 1.0
N A:TRP1 2.4 6.4 1.0
C A:TRP1 3.1 8.5 1.0
CA A:TRP1 3.1 7.9 1.0
CD2 A:HIS11 3.2 8.7 1.0
ZN A:ZN401 3.2 15.9 1.0
CE1 A:HIS11 3.4 9.7 1.0
CG A:ASP130 3.4 12.2 1.0
CB A:TRP1 3.7 7.2 1.0
OE2 A:GLU152 3.8 8.6 1.0
CE1 A:HIS126 3.9 9.9 1.0
OD2 A:ASP130 3.9 14.3 1.0
OD2 A:ASP56 4.0 11.1 1.0
NE2 A:HIS126 4.2 10.5 1.0
N A:ASP2 4.3 9.6 1.0
CG A:HIS11 4.4 9.5 1.0
ND1 A:HIS11 4.5 9.2 1.0
CG A:TRP1 4.6 7.7 1.0
ND1 A:HIS126 4.6 10.9 1.0
CB A:ASP130 4.6 12.4 1.0
CA A:ASP130 4.7 11.3 1.0
CD A:GLU152 4.8 9.8 1.0
OD1 A:ASP56 4.8 12.2 1.0
CG A:ASP56 4.8 11.7 1.0
O A:HIS126 4.9 10.9 1.0
CE1 A:HIS148 4.9 9.6 1.0
N A:ASP130 4.9 11.6 1.0
OG1 A:THR133 4.9 11.1 1.0
CD1 A:TRP1 5.0 7.9 1.0

Zinc binding site 2 out of 4 in 1qm6

Go back to Zinc Binding Sites List in 1qm6
Zinc binding site 2 out of 4 in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:15.9
occ:1.00
ND1 A:HIS68 2.3 15.6 1.0
NE2 A:HIS126 2.3 10.5 1.0
OD2 A:ASP130 2.4 14.3 1.0
OD1 A:ASP56 2.5 12.2 1.0
CE1 A:HIS126 3.0 9.9 1.0
OD1 A:ASP130 3.1 12.7 1.0
CG A:ASP130 3.1 12.2 1.0
CE1 A:HIS68 3.2 15.9 1.0
ZN A:ZN400 3.2 13.3 1.0
CG A:HIS68 3.3 15.8 1.0
CG A:ASP56 3.3 11.7 1.0
OD2 A:ASP56 3.4 11.1 1.0
CD2 A:HIS126 3.5 10.5 1.0
CB A:HIS68 3.6 16.1 1.0
ND1 A:HIS126 4.2 10.9 1.0
NE2 A:HIS11 4.3 9.6 1.0
NE2 A:HIS68 4.3 17.2 1.0
CD2 A:HIS68 4.4 16.7 1.0
CG A:HIS126 4.4 9.9 1.0
CB A:ASP130 4.5 12.4 1.0
CB A:ASP56 4.8 11.2 1.0
O A:TRP1 4.8 8.1 1.0
O A:HIS126 5.0 10.9 1.0

Zinc binding site 3 out of 4 in 1qm6

Go back to Zinc Binding Sites List in 1qm6
Zinc binding site 3 out of 4 in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:21.6
occ:1.00
OD1 B:ASP130 2.3 9.5 1.0
NE2 B:HIS11 2.3 8.6 1.0
O B:TRP1 2.4 6.4 1.0
N B:TRP1 2.4 6.8 1.0
C B:TRP1 3.0 7.6 1.0
CA B:TRP1 3.1 7.6 1.0
CD2 B:HIS11 3.1 8.9 1.0
ZN B:ZN401 3.3 22.7 1.0
CE1 B:HIS11 3.4 9.1 1.0
CG B:ASP130 3.4 11.3 1.0
CB B:TRP1 3.6 7.1 1.0
OE2 B:GLU152 3.7 8.0 1.0
OD2 B:ASP130 3.9 12.4 1.0
CE1 B:HIS126 3.9 8.5 1.0
OD2 B:ASP56 4.0 10.7 1.0
NE2 B:HIS126 4.2 9.8 1.0
N B:ASP2 4.3 8.4 1.0
CG B:HIS11 4.4 9.5 1.0
ND1 B:HIS11 4.5 9.2 1.0
CG B:TRP1 4.6 8.2 1.0
CB B:ASP130 4.7 11.7 1.0
ND1 B:HIS126 4.7 9.0 1.0
CA B:ASP130 4.7 11.6 1.0
CD B:GLU152 4.8 9.8 1.0
OD1 B:ASP56 4.8 13.8 1.0
CG B:ASP56 4.9 11.7 1.0
OG1 B:THR133 4.9 10.1 1.0
O B:HIS126 4.9 10.8 1.0
CE1 B:HIS148 4.9 10.8 1.0
N B:ASP130 4.9 12.2 1.0
CD1 B:TRP1 4.9 7.4 1.0

Zinc binding site 4 out of 4 in 1qm6

Go back to Zinc Binding Sites List in 1qm6
Zinc binding site 4 out of 4 in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:22.7
occ:1.00
ND1 B:HIS68 2.3 14.6 1.0
NE2 B:HIS126 2.3 9.8 1.0
OD2 B:ASP130 2.4 12.4 1.0
OD1 B:ASP56 2.5 13.8 1.0
CE1 B:HIS126 3.0 8.5 1.0
OD1 B:ASP130 3.1 9.5 1.0
CG B:ASP130 3.1 11.3 1.0
CE1 B:HIS68 3.2 16.2 1.0
CG B:HIS68 3.3 14.4 1.0
ZN B:ZN400 3.3 21.6 1.0
CG B:ASP56 3.3 11.7 1.0
OD2 B:ASP56 3.4 10.7 1.0
CD2 B:HIS126 3.4 9.7 1.0
CB B:HIS68 3.6 14.8 1.0
ND1 B:HIS126 4.1 9.0 1.0
NE2 B:HIS68 4.3 14.7 1.0
NE2 B:HIS11 4.3 8.6 1.0
CD2 B:HIS68 4.4 15.4 1.0
CG B:HIS126 4.4 9.5 1.0
CB B:ASP130 4.6 11.7 1.0
CB B:ASP56 4.7 12.3 1.0
O B:TRP1 4.9 6.4 1.0
O B:HIS126 4.9 10.8 1.0

Reference:

C.E.Naylor, M.Jepson, D.T.Crane, R.W.Titball, J.Miller, A.K.Basak, B.Bolgiano. Characterisation of the Calcium-Binding C-Terminal Domain of Clostridium Perfringens Alpha-Toxin J.Mol.Biol. V. 294 757 1999.
ISSN: ISSN 0022-2836
PubMed: 10610794
DOI: 10.1006/JMBI.1999.3279
Page generated: Wed Dec 16 03:02:03 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy