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Zinc in PDB 5v8r: Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain

Enzymatic activity of 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;

Protein crystallography data

The structure of Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain, PDB code: 5v8r 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) 29.48 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.534, 67.635, 98.112, 90.00, 104.91, 90.00
R / Rfree (%) 17.5 / 22.2

Other elements in 5v8r:

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

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Small Molecule Inhibitor Abs-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain (pdb code 5v8r). 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: 5v8r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5v8r

Go back to Zinc Binding Sites List in 5v8r
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:53.9
occ:1.00
NE2 A:HIS223 2.1 29.7 1.0
NE2 A:HIS227 2.3 47.0 1.0
OE1 A:GLU262 2.3 56.6 1.0
S13 A:90J502 2.5 55.2 1.0
OE2 A:GLU262 2.8 49.8 1.0
CD2 A:HIS223 2.8 28.9 1.0
CD A:GLU262 2.9 47.9 1.0
C13 A:90J502 2.9 76.8 1.0
CD2 A:HIS227 3.0 46.8 1.0
CE1 A:HIS223 3.3 36.6 1.0
CE1 A:HIS227 3.4 55.2 1.0
C12 A:90J502 4.0 74.7 1.0
CG A:HIS223 4.1 37.6 1.0
O A:HOH744 4.2 39.0 1.0
CG A:HIS227 4.2 36.8 1.0
ND1 A:HIS223 4.2 35.4 1.0
OE1 A:GLU224 4.3 37.0 1.0
CG A:GLU262 4.4 46.1 1.0
ND1 A:HIS227 4.4 42.1 1.0
OH A:TYR366 4.5 44.4 1.0
O12 A:90J502 4.6 74.0 1.0
CE2 A:TYR366 4.8 48.6 1.0
N5 A:90J502 4.8 68.3 1.0
CA A:GLU262 4.8 30.6 1.0
CG2 A:THR265 4.8 27.1 1.0
OE2 A:GLU224 4.8 36.0 1.0
CD A:GLU224 4.9 40.3 1.0
CB A:GLU262 4.9 40.2 1.0
C11 A:90J502 5.0 79.6 1.0
CB A:THR265 5.0 33.8 1.0

Zinc binding site 2 out of 2 in 5v8r

Go back to Zinc Binding Sites List in 5v8r
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:Zn501

b:38.5
occ:1.00
NE2 B:HIS227 2.1 41.4 1.0
NE2 B:HIS223 2.1 36.1 1.0
OE2 B:GLU262 2.1 54.7 1.0
S13 B:90J502 2.3 46.8 1.0
OE1 B:GLU262 2.4 46.4 1.0
CD B:GLU262 2.5 27.7 1.0
CD2 B:HIS227 2.9 38.7 1.0
CD2 B:HIS223 3.0 31.0 1.0
CE1 B:HIS227 3.1 37.0 1.0
C13 B:90J502 3.1 49.6 1.0
CE1 B:HIS223 3.1 31.6 1.0
CG B:GLU262 4.1 50.2 1.0
CG B:HIS227 4.1 37.5 1.0
CG B:HIS223 4.2 35.9 1.0
ND1 B:HIS227 4.2 37.0 1.0
C12 B:90J502 4.2 45.5 1.0
ND1 B:HIS223 4.2 35.0 1.0
OE1 B:GLU224 4.5 39.4 1.0
OE2 B:GLU224 4.6 41.1 1.0
O12 B:90J502 4.6 43.6 1.0
OH B:TYR366 4.8 66.1 1.0
CG2 B:THR265 4.8 37.2 1.0
CA B:GLU262 4.8 39.0 1.0
CD B:GLU224 4.9 41.1 1.0
CE2 B:TYR366 4.9 76.1 1.0
C7 B:90J502 4.9 42.9 1.0
CB B:GLU262 4.9 47.4 1.0
C8 B:90J502 5.0 42.8 1.0

Reference:

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
Page generated: Wed Dec 16 11:07:52 2020

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