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Zinc in PDB 7t5f: Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10

Enzymatic activity of Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10

All present enzymatic activity of Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10:
3.4.24.69;

Protein crystallography data

The structure of Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10, PDB code: 7t5f was solved by R.Jin, K.-H.Lam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.84 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 149.32, 88.276, 114.481, 90, 97.03, 90
R / Rfree (%) 19.4 / 22.2

Other elements in 7t5f:

The structure of Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10 also contains other interesting chemical elements:

Iodine (I) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10 (pdb code 7t5f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10, PDB code: 7t5f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7t5f

Go back to Zinc Binding Sites List in 7t5f
Zinc binding site 1 out of 2 in the Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:58.4
occ:0.88
OE2 A:GLU268 2.0 41.8 1.0
NE2 A:HIS230 2.2 36.3 1.0
NE2 A:HIS234 2.2 28.6 1.0
OE1 A:GLU268 2.5 52.4 1.0
CD A:GLU268 2.6 40.0 1.0
O A:HOH647 2.6 50.7 1.0
CE1 A:HIS230 3.0 32.2 1.0
CE1 A:HIS234 3.2 34.4 1.0
CD2 A:HIS234 3.2 27.6 1.0
CD2 A:HIS230 3.2 34.6 1.0
OE2 A:GLU231 3.9 47.6 1.0
OH A:TYR373 3.9 44.9 1.0
O A:HOH646 4.0 37.7 1.0
CG A:GLU268 4.1 40.2 1.0
ND1 A:HIS230 4.2 43.5 1.0
ND1 A:HIS234 4.3 38.3 1.0
CE2 A:TYR373 4.3 37.0 1.0
CG A:HIS230 4.3 36.6 1.0
CG A:HIS234 4.3 31.8 1.0
CZ A:TYR373 4.5 42.9 1.0
OE1 A:GLU231 4.7 45.0 1.0
CD A:GLU231 4.7 44.2 1.0
CB A:GLU268 4.8 31.0 1.0
CG2 A:THR271 4.9 36.0 1.0
CA A:GLU268 4.9 37.2 1.0

Zinc binding site 2 out of 2 in 7t5f

Go back to Zinc Binding Sites List in 7t5f
Zinc binding site 2 out of 2 in the Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:52.9
occ:0.93
NE2 D:HIS234 2.1 44.2 1.0
OE2 D:GLU268 2.2 33.5 1.0
NE2 D:HIS230 2.5 37.8 1.0
O D:HOH637 2.5 50.2 1.0
OE1 D:GLU268 2.8 40.6 1.0
CD D:GLU268 2.8 40.4 1.0
CE1 D:HIS234 3.1 35.2 1.0
CD2 D:HIS234 3.1 30.7 1.0
CD2 D:HIS230 3.2 35.3 1.0
CE1 D:HIS230 3.5 39.0 1.0
OE1 D:GLU231 3.8 51.7 1.0
O D:HOH629 4.0 40.9 1.0
OH D:TYR373 4.1 49.4 1.0
ND1 D:HIS234 4.2 26.8 1.0
CG D:HIS234 4.2 28.9 1.0
CG D:GLU268 4.4 37.5 1.0
CG D:HIS230 4.4 35.8 1.0
CE2 D:TYR373 4.5 39.3 1.0
ND1 D:HIS230 4.6 38.7 1.0
CD D:GLU231 4.6 42.4 1.0
OE2 D:GLU231 4.6 49.5 1.0
CZ D:TYR373 4.7 44.8 1.0
CB D:GLU268 5.0 29.6 1.0

Reference:

R.Jin, K.-H.Lam, C.B.Shoemaker. Probing the Structure and Function of the Protease Domain of Botulinum Neurotoxins Using Single-Domain Antibodies Plos Pathog..
ISSN: ESSN 1553-7374
Page generated: Thu Mar 31 05:24:35 2022

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