Zinc in PDB 7dvl: Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3

The structure of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3, PDB code: 7dvl was solved by Y.Wu, O.Leka, R.Kammerer, X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.71 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.25, 97.42, 141.25, 90, 90, 90
R / Rfree (%)	20.5 / 23.2

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3 (pdb code 7dvl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3, PDB code: 7dvl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:25.2 occ:1.00 NE2 A:HIS225 2.0 26.6 1.0 OE1 A:GLU264 2.1 41.9 1.0 NE2 A:HIS229 2.1 25.9 1.0 OE2 A:GLU264 2.1 45.0 1.0 O A:HOH805 2.1 16.1 1.0 CD A:GLU264 2.4 44.0 1.0 CD2 A:HIS225 2.9 27.0 1.0 CD2 A:HIS229 3.0 25.4 1.0 HD2 A:HIS225 3.0 32.5 1.0 HD2 A:HIS229 3.1 30.5 1.0 CE1 A:HIS225 3.1 27.8 1.0 CE1 A:HIS229 3.1 25.3 1.0 HE1 A:HIS229 3.4 30.4 1.0 HE1 A:HIS225 3.4 33.4 1.0 CG A:GLU264 3.9 37.3 1.0 HG21 A:THR267 4.1 25.9 1.0 HA A:GLU264 4.1 24.6 1.0 CG A:HIS225 4.1 24.7 1.0 ND1 A:HIS225 4.2 27.2 1.0 CG A:HIS229 4.2 23.0 1.0 ND1 A:HIS229 4.2 24.6 1.0 HG22 A:THR267 4.2 25.9 1.0 HG3 A:GLU264 4.3 44.8 1.0 OE1 A:GLN226 4.3 29.8 1.0 HG2 A:GLU264 4.3 44.8 1.0 HB A:THR267 4.3 25.1 1.0 CG2 A:THR267 4.6 21.6 1.0 HB2 A:GLU264 4.6 29.7 1.0 CB A:GLU264 4.7 24.7 1.0 HE22 A:GLN226 4.8 34.4 1.0 O A:HOH722 4.8 25.7 1.0 CA A:GLU264 4.8 20.6 1.0 CB A:THR267 4.9 20.9 1.0 HD1 A:HIS225 5.0 32.6 1.0 HD1 A:HIS229 5.0 29.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:34.5 occ:1.00 OE1 B:GLU264 2.0 41.4 1.0 NE2 B:HIS225 2.0 34.8 1.0 OE2 B:GLU264 2.1 41.2 1.0 NE2 B:HIS229 2.1 36.2 1.0 O B:HOH817 2.2 13.3 1.0 CD B:GLU264 2.3 45.9 1.0 CD2 B:HIS225 3.0 32.5 1.0 CE1 B:HIS225 3.0 32.4 1.0 CD2 B:HIS229 3.1 32.1 1.0 CE1 B:HIS229 3.1 33.2 1.0 HD2 B:HIS225 3.1 39.0 1.0 HD2 B:HIS229 3.2 38.5 1.0 HE1 B:HIS225 3.3 38.9 1.0 HE1 B:HIS229 3.3 39.9 1.0 CG B:GLU264 3.9 41.4 1.0 HE22 B:GLN226 3.9 36.6 1.0 HA B:GLU264 4.1 27.7 1.0 ND1 B:HIS225 4.1 30.6 1.0 CG B:HIS225 4.1 28.8 1.0 HG21 B:THR267 4.2 28.6 1.0 ND1 B:HIS229 4.2 31.3 1.0 CG B:HIS229 4.2 28.9 1.0 HB B:THR267 4.3 28.7 1.0 HG2 B:GLU264 4.3 49.7 1.0 HG3 B:GLU264 4.3 49.7 1.0 HG22 B:THR267 4.3 28.6 1.0 NE2 B:GLN226 4.5 30.4 1.0 HB2 B:GLU264 4.5 34.6 1.0 CG2 B:THR267 4.6 23.8 1.0 CB B:GLU264 4.6 28.8 1.0 O B:HOH786 4.7 30.1 1.0 CA B:GLU264 4.8 23.0 1.0 HE21 B:GLN226 4.9 36.6 1.0 CB B:THR267 4.9 23.9 1.0 HD1 B:HIS225 4.9 36.8 1.0 HD1 B:HIS229 5.0 37.5 1.0

O.Leka, Y.Wu, X.Li, R.Kammerer. Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3. J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X