Zinc in PDB 5v8u: 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: 5v8u 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) 37.56 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.095, 67.653, 98.087, 90.00, 105.22, 90.00
R / Rfree (%) 22.9 / 26

Other elements in 5v8u:

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 5v8u). 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: 5v8u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5v8u

Go back to Zinc Binding Sites List in 5v8u
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:46.4
occ:1.00
OE2 A:GLU262 2.0 69.9 1.0
NE2 A:HIS223 2.1 52.1 1.0
NE2 A:HIS227 2.1 66.2 1.0
S13 A:90M502 2.4 56.2 1.0
OE1 A:GLU262 2.7 71.3 1.0
CD A:GLU262 2.7 68.4 1.0
CD2 A:HIS227 2.9 65.5 1.0
C13 A:90M502 2.9 69.1 1.0
HD2 A:HIS227 3.0 78.6 1.0
CD2 A:HIS223 3.0 48.9 1.0
CE1 A:HIS223 3.1 51.7 1.0
CE1 A:HIS227 3.2 68.0 1.0
HD2 A:HIS223 3.2 58.7 1.0
HE1 A:HIS223 3.3 62.1 1.0
HE1 A:HIS227 3.5 81.6 1.0
HH A:TYR366 3.7 65.9 1.0
HE2 A:TYR366 3.8 66.1 1.0
C12 A:90M502 3.8 74.5 1.0
HA A:GLU262 4.0 43.3 1.0
CG A:HIS227 4.1 60.4 1.0
HG21 A:THR265 4.1 32.5 1.0
CG A:GLU262 4.1 60.2 1.0
ND1 A:HIS227 4.2 66.4 1.0
ND1 A:HIS223 4.2 50.1 1.0
CG A:HIS223 4.2 46.8 1.0
O12 A:90M502 4.3 69.6 1.0
OH A:TYR366 4.3 54.8 1.0
HB3 A:GLU262 4.5 58.5 1.0
O A:HOH750 4.5 41.2 1.0
CE2 A:TYR366 4.5 55.0 1.0
OE1 A:GLU224 4.5 45.1 1.0
HB A:THR265 4.5 32.0 1.0
HG2 A:GLU262 4.6 72.3 1.0
HG3 A:GLU262 4.6 72.3 1.0
CB A:GLU262 4.7 48.7 1.0
N5 A:90M502 4.8 86.1 1.0
CA A:GLU262 4.8 36.1 1.0
CZ A:TYR366 4.8 56.4 1.0
C4B A:90M502 4.9 0.5 1.0
CG2 A:THR265 4.9 27.1 1.0
HD1 A:HIS223 5.0 60.2 1.0
HD1 A:HIS227 5.0 79.8 1.0
OE2 A:GLU224 5.0 36.2 1.0

Zinc binding site 2 out of 2 in 5v8u

Go back to Zinc Binding Sites List in 5v8u
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:39.0
occ:1.00
OE2 B:GLU262 2.0 50.9 1.0
NE2 B:HIS223 2.1 42.3 1.0
NE2 B:HIS227 2.2 45.3 1.0
S13 B:90M502 2.4 32.2 1.0
CD B:GLU262 2.6 48.0 1.0
OE1 B:GLU262 2.7 46.7 1.0
CD2 B:HIS227 2.9 41.6 1.0
HD2 B:HIS227 3.0 50.0 1.0
C13 B:90M502 3.0 32.9 1.0
CD2 B:HIS223 3.0 34.1 1.0
HD2 B:HIS223 3.1 41.0 1.0
CE1 B:HIS223 3.2 38.6 1.0
CE1 B:HIS227 3.3 43.6 1.0
HE1 B:HIS223 3.5 46.4 1.0
HE1 B:HIS227 3.6 52.4 1.0
C12 B:90M502 3.8 39.6 1.0
HH B:TYR366 3.9 50.9 1.0
HE2 B:TYR366 3.9 49.2 1.0
HA B:GLU262 4.0 47.8 1.0
O12 B:90M502 4.1 40.3 1.0
CG B:GLU262 4.1 48.8 1.0
HG21 B:THR265 4.1 54.5 1.0
CG B:HIS227 4.1 40.8 1.0
CG B:HIS223 4.2 34.9 1.0
ND1 B:HIS227 4.3 39.9 1.0
ND1 B:HIS223 4.3 37.4 1.0
OE1 B:GLU224 4.4 71.9 1.0
O B:HOH672 4.4 32.2 1.0
HB3 B:GLU262 4.4 54.2 1.0
OH B:TYR366 4.5 42.4 1.0
CE2 B:TYR366 4.5 41.0 1.0
HB B:THR265 4.5 55.3 1.0
HG3 B:GLU262 4.6 58.6 1.0
HG2 B:GLU262 4.6 58.6 1.0
CB B:GLU262 4.6 45.1 1.0
CA B:GLU262 4.8 39.8 1.0
CZ B:TYR366 4.8 43.3 1.0
C4B B:90M502 4.9 41.1 1.0
OE2 B:GLU224 4.9 70.8 1.0
N5 B:90M502 4.9 31.9 1.0
CG2 B:THR265 4.9 45.4 1.0
CD B:GLU224 4.9 68.0 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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