Zinc in PDB 5v8p: Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain

All present enzymatic activity of Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain:
3.4.24.69;

The structure of Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain, PDB code: 5v8p was solved by K.N.Allen, N.R.Silvaggi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.33 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.172, 67.327, 98.140, 90.00, 105.60, 90.00
R / Rfree (%)	20.2 / 25.2

The structure of Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain (pdb code 5v8p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain, PDB code: 5v8p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:49.1 occ:1.00 NE2 A:HIS223 2.0 61.7 1.0 OE1 A:GLU262 2.1 70.1 1.0 NE2 A:HIS227 2.2 41.0 1.0 S17 A:90G502 2.3 75.6 1.0 CD A:GLU262 2.8 69.7 1.0 CD2 A:HIS223 2.8 61.8 1.0 HD2 A:HIS223 2.8 74.2 1.0 OE2 A:GLU262 2.9 71.0 1.0 C16 A:90G502 3.0 78.3 1.0 CD2 A:HIS227 3.0 40.8 1.0 HD2 A:HIS227 3.0 48.9 1.0 CE1 A:HIS223 3.2 62.8 1.0 CE1 A:HIS227 3.3 41.8 1.0 HE1 A:HIS223 3.5 75.3 1.0 HH A:TYR366 3.6 71.6 1.0 HE1 A:HIS227 3.6 50.2 1.0 HE1 A:TYR366 3.8 69.8 1.0 C14 A:90G502 3.9 80.3 1.0 O15 A:90G502 3.9 79.0 1.0 CG A:HIS223 4.0 59.1 1.0 HA A:GLU262 4.0 68.8 1.0 HG21 A:THR265 4.1 43.8 1.0 ND1 A:HIS223 4.2 61.9 1.0 CG A:HIS227 4.2 39.6 1.0 CG A:GLU262 4.3 67.0 1.0 OH A:TYR366 4.3 59.7 1.0 OE2 A:GLU224 4.3 44.5 1.0 ND1 A:HIS227 4.3 41.2 1.0 HB A:THR265 4.5 46.1 1.0 CE1 A:TYR366 4.6 58.2 1.0 HB3 A:GLU262 4.6 75.5 1.0 HG3 A:GLU262 4.7 80.5 1.0 OE1 A:GLU224 4.7 42.6 1.0 HG2 A:GLU262 4.8 80.5 1.0 CB A:GLU262 4.8 62.9 1.0 CD A:GLU224 4.8 43.4 1.0 CA A:GLU262 4.9 57.3 1.0 CG2 A:THR265 4.9 36.5 1.0 CZ A:TYR366 4.9 59.6 1.0 HG22 A:THR265 5.0 43.8 1.0

Zinc binding site 2 out of 2 in the Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:46.6 occ:1.00 OE1 B:GLU262 2.1 76.6 1.0 NE2 B:HIS227 2.1 53.4 1.0 S17 B:90G501 2.2 56.0 1.0 NE2 B:HIS223 2.4 37.9 1.0 OE2 B:GLU262 2.5 79.4 1.0 CD B:GLU262 2.6 76.0 1.0 CD2 B:HIS227 3.0 51.4 1.0 C16 B:90G501 3.1 57.4 1.0 CD2 B:HIS223 3.1 36.6 1.0 HD2 B:HIS223 3.1 43.9 1.0 HD2 B:HIS227 3.1 61.7 1.0 CE1 B:HIS227 3.2 53.3 1.0 HE1 B:HIS227 3.4 64.0 1.0 CE1 B:HIS223 3.5 39.0 1.0 HE1 B:HIS223 3.7 46.9 1.0 O15 B:90G501 3.8 58.2 1.0 C14 B:90G501 3.8 57.5 1.0 HE1 B:TYR366 3.9 67.5 1.0 HH B:TYR366 3.9 68.1 1.0 HG21 B:THR265 4.0 53.0 1.0 CG B:GLU262 4.0 71.8 1.0 HA B:GLU262 4.1 73.8 1.0 CG B:HIS227 4.2 51.3 1.0 ND1 B:HIS227 4.3 52.4 1.0 CG B:HIS223 4.3 36.5 1.0 HG2 B:GLU262 4.4 86.2 1.0 HB3 B:GLU262 4.5 80.8 1.0 HB B:THR265 4.5 55.8 1.0 ND1 B:HIS223 4.5 38.1 1.0 CE1 B:TYR366 4.5 56.2 1.0 HG3 B:GLU262 4.6 86.2 1.0 OH B:TYR366 4.6 56.7 1.0 OE1 B:GLU224 4.6 44.6 1.0 OE2 B:GLU224 4.6 44.6 1.0 CB B:GLU262 4.7 67.3 1.0 CG2 B:THR265 4.8 44.1 1.0 CA B:GLU262 4.8 61.5 1.0 CD B:GLU224 4.9 43.8 1.0 N13 B:90G501 4.9 56.8 1.0 CZ B:TYR366 5.0 57.5 1.0 HG22 B:THR265 5.0 53.0 1.0

A.R.Jacobson, M.Adler, N.R.Silvaggi, K.N.Allen, G.M.Smith, R.A.Fredenburg, R.L.Stein, J.B.Park, X.Feng, C.B.Shoemaker, S.S.Deshpande, M.C.Goodnough, C.J.Malizio, E.A.Johnson, S.Pellett, W.H.Tepp, S.Tzipori. Small Molecule Metalloprotease Inhibitor with in Vitro, Ex Vivo and in Vivo Efficacy Against Botulinum Neurotoxin Serotype A. Toxicon V. 137 36 2017.
ISSN: ISSN 1879-3150
PubMed: 28698055
DOI: 10.1016/J.TOXICON.2017.06.016