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Zinc in PDB 5n0c: Crystal Structure of the Tetanus Neurotoxin in Complex with GM1A

Enzymatic activity of Crystal Structure of the Tetanus Neurotoxin in Complex with GM1A

All present enzymatic activity of Crystal Structure of the Tetanus Neurotoxin in Complex with GM1A:
3.4.24.68;

Protein crystallography data

The structure of Crystal Structure of the Tetanus Neurotoxin in Complex with GM1A, PDB code: 5n0c was solved by G.Masuyer, J.Conrad, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.50 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.230, 137.450, 152.400, 90.00, 90.12, 90.00
R / Rfree (%) 22.1 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Tetanus Neurotoxin in Complex with GM1A (pdb code 5n0c). 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 Tetanus Neurotoxin in Complex with GM1A, PDB code: 5n0c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5n0c

Go back to Zinc Binding Sites List in 5n0c
Zinc binding site 1 out of 2 in the Crystal Structure of the Tetanus Neurotoxin in Complex with GM1A


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 Tetanus Neurotoxin in Complex with GM1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1406

b:42.7
occ:1.00
NE2 A:HIS237 2.2 27.5 1.0
NE2 A:HIS233 2.3 27.1 1.0
CD2 A:HIS233 3.1 26.6 1.0
CD2 A:HIS237 3.2 27.3 1.0
CE1 A:HIS237 3.2 27.6 1.0
CE1 A:HIS233 3.4 27.2 1.0
CG A:GLU271 4.0 47.0 1.0
OE2 A:GLU234 4.2 26.2 1.0
ND1 A:HIS237 4.3 27.3 1.0
CG A:HIS233 4.3 26.2 1.0
CG A:HIS237 4.3 26.7 1.0
ND1 A:HIS233 4.5 27.0 1.0
CA A:GLU271 4.6 39.9 1.0
CB A:GLU271 4.7 43.1 1.0
CD A:GLU271 4.8 50.8 1.0
OE1 A:GLU271 4.8 53.8 1.0
OE1 A:GLU234 4.9 26.8 1.0
CD A:GLU234 4.9 25.8 1.0
CG2 A:THR274 4.9 29.2 1.0

Zinc binding site 2 out of 2 in 5n0c

Go back to Zinc Binding Sites List in 5n0c
Zinc binding site 2 out of 2 in the Crystal Structure of the Tetanus Neurotoxin in Complex with GM1A


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 Tetanus Neurotoxin in Complex with GM1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1406

b:52.2
occ:1.00
NE2 B:HIS237 2.3 24.6 1.0
NE2 B:HIS233 2.3 26.2 1.0
O B:HOH1646 2.6 37.4 1.0
CD2 B:HIS233 3.0 26.3 1.0
CD2 B:HIS237 3.2 24.7 1.0
CE1 B:HIS237 3.3 25.2 1.0
CE1 B:HIS233 3.5 26.4 1.0
CG B:GLU271 4.2 51.1 1.0
CG B:HIS233 4.3 25.9 1.0
OE2 B:GLU234 4.3 27.5 1.0
CG B:HIS237 4.4 24.7 1.0
ND1 B:HIS237 4.4 25.0 1.0
OE1 B:GLU234 4.4 27.8 1.0
ND1 B:HIS233 4.5 26.6 1.0
CD B:GLU234 4.7 26.9 1.0
CB B:GLU271 4.7 47.3 1.0
CA B:GLU271 4.8 44.1 1.0
CG2 B:THR274 4.8 36.2 1.0

Reference:

G.Masuyer, J.Conrad, P.Stenmark. The Structure of the Tetanus Toxin Reveals pH-Mediated Domain Dynamics. Embo Rep. V. 18 1306 2017.
ISSN: ESSN 1469-3178
PubMed: 28645943
DOI: 10.15252/EMBR.201744198
Page generated: Wed Dec 16 06:33:59 2020

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