Zinc in PDB 3d3x: Crystal Structure of Botulinum Neurotoxin Serotype E Catalytic Domain in Complex with Snap-25 Substrate Peptide

The structure of Crystal Structure of Botulinum Neurotoxin Serotype E Catalytic Domain in Complex with Snap-25 Substrate Peptide, PDB code: 3d3x was solved by R.Agarwal, S.Swaminathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.48 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.410, 144.738, 83.303, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 28.8

The binding sites of Zinc atom in the Crystal Structure of Botulinum Neurotoxin Serotype E Catalytic Domain in Complex with Snap-25 Substrate Peptide (pdb code 3d3x). 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 Botulinum Neurotoxin Serotype E Catalytic Domain in Complex with Snap-25 Substrate Peptide, PDB code: 3d3x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Botulinum Neurotoxin Serotype E Catalytic Domain in Complex with Snap-25 Substrate Peptide


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 Botulinum Neurotoxin Serotype E Catalytic Domain in Complex with Snap-25 Substrate Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn428 b:50.5 occ:1.00 OE2 A:GLU250 2.1 39.7 1.0 NE2 A:HIS215 2.1 28.8 1.0 O C:ARG180 2.3 49.2 1.0 NE2 A:HIS211 2.3 35.8 1.0 CD A:GLU250 2.8 38.4 1.0 OE1 A:GLU250 2.8 41.5 1.0 CD2 A:HIS215 2.9 29.9 1.0 N C:ARG180 3.0 49.6 1.0 C C:ARG180 3.0 49.1 1.0 CD2 A:HIS211 3.1 34.7 1.0 CE1 A:HIS215 3.3 30.3 1.0 CE1 A:HIS211 3.4 36.1 1.0 CA C:ARG180 3.6 49.1 1.0 OE2 A:GLU212 4.0 35.3 1.0 N C:ILE181 4.0 49.8 1.0 OH A:TYR350 4.1 44.6 1.0 CE1 A:TYR350 4.2 38.2 1.0 CG A:HIS215 4.2 29.0 1.0 CG A:GLU250 4.2 34.4 1.0 ND1 A:HIS215 4.3 31.2 1.0 CZ A:TYR350 4.3 39.6 1.0 CG A:HIS211 4.4 32.7 1.0 CA C:ILE181 4.4 48.6 1.0 ND1 A:HIS211 4.5 34.7 1.0 CB C:ARG180 4.5 47.8 1.0 OE1 A:GLU212 4.6 34.2 1.0 CD A:GLU212 4.7 31.9 1.0 CB A:GLU250 4.8 30.2 1.0 CA A:GLU250 4.8 27.8 1.0 C C:ILE181 5.0 50.1 1.0 CD1 A:TYR350 5.0 34.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Botulinum Neurotoxin Serotype E Catalytic Domain in Complex with Snap-25 Substrate Peptide


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 Botulinum Neurotoxin Serotype E Catalytic Domain in Complex with Snap-25 Substrate Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn822 b:43.8 occ:1.00 NE2 B:HIS215 2.0 46.3 1.0 NE2 B:HIS211 2.0 31.5 1.0 OE1 B:GLU250 2.1 37.3 1.0 OE2 B:GLU250 2.4 36.8 1.0 CD B:GLU250 2.6 35.5 1.0 O D:ARG180 2.7 47.1 1.0 CD2 B:HIS215 2.9 44.2 1.0 CD2 B:HIS211 3.0 31.5 1.0 CE1 B:HIS211 3.1 31.4 1.0 CE1 B:HIS215 3.1 45.9 1.0 C D:ARG180 3.4 45.5 1.0 N D:ARG180 3.6 45.5 1.0 CA D:ARG180 3.9 44.5 1.0 CB D:ARG180 4.0 43.7 1.0 CG B:HIS215 4.1 42.1 1.0 CG B:GLU250 4.1 35.0 1.0 OH B:TYR350 4.1 38.2 1.0 ND1 B:HIS215 4.2 43.8 1.0 CG B:HIS211 4.2 32.2 1.0 ND1 B:HIS211 4.2 32.4 1.0 OE2 B:GLU212 4.2 44.4 1.0 N D:ILE181 4.3 44.5 1.0 O D:HOH230 4.4 42.5 1.0 CE1 B:TYR350 4.4 38.7 1.0 CZ B:TYR350 4.6 38.3 1.0 OE1 B:GLU212 4.7 43.1 1.0 CA D:ILE181 4.7 43.8 1.0 CB B:GLU250 4.8 34.7 1.0 CA B:GLU250 4.8 35.9 1.0 CD B:GLU212 4.9 42.7 1.0

R.Agarwal, S.Swaminathan. Snap-25 Substrate Peptide (Residues 180-183) Binds to But Bypasses Cleavage By Catalytically Active Clostridium Botulinum Neurotoxin E. J.Biol.Chem. V. 283 25944 2008.
ISSN: ISSN 0021-9258
PubMed: 18658150
DOI: 10.1074/JBC.M803756200