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Iodine 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:

Zinc (Zn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 6 binding sites of Iodine where determined in the Botulinum Neurotoxin Type B Light Chain Complexed with Nanobodies Jlj- G3 and Jne-B10, PDB code: 7t5f:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 7t5f

Go back to Iodine Binding Sites List in 7t5f
Iodine binding site 1 out of 6 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 Iodine with other atoms in the I 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:I502

b:56.0
occ:1.00
NH2 A:ARG123 3.8 24.2 1.0
N A:ALA134 3.8 19.8 1.0
NH1 A:ARG123 3.9 26.7 1.0
CD1 A:ILE177 4.1 39.0 1.0
CB A:ILE133 4.1 18.4 1.0
CA A:ILE133 4.2 25.7 1.0
CB A:ALA134 4.3 30.4 1.0
CZ A:ARG123 4.3 33.8 1.0
CG2 A:ILE133 4.4 26.9 1.0
C A:ILE133 4.6 30.5 1.0
CD A:ARG28 4.6 24.9 1.0
CA A:ALA134 4.7 24.1 1.0
NE A:ARG28 4.9 34.2 1.0

Iodine binding site 2 out of 6 in 7t5f

Go back to Iodine Binding Sites List in 7t5f
Iodine binding site 2 out of 6 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 Iodine with other atoms in the I 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
A:I503

b:85.6
occ:0.60
N A:ARG42 3.7 35.1 1.0
O A:HOH619 3.8 22.0 1.0
OD2 A:ASP41 3.8 58.4 1.0
CA A:ASP41 4.1 32.0 1.0
CB A:ASP41 4.2 37.2 1.0
CD A:LYS38 4.2 29.0 1.0
CG A:ASP41 4.3 50.8 1.0
C A:ASP41 4.3 38.8 1.0
NZ A:LYS38 4.4 48.1 1.0
CD A:ARG42 4.4 39.2 1.0
CA A:ARG42 4.5 35.6 1.0
CE A:LYS38 4.6 38.8 1.0
CG A:ARG42 4.6 41.2 1.0
NE A:ARG42 4.9 49.8 1.0

Iodine binding site 3 out of 6 in 7t5f

Go back to Iodine Binding Sites List in 7t5f
Iodine binding site 3 out of 6 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 Iodine with other atoms in the I binding site number 3 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:I502

b:60.0
occ:1.00
N D:ALA134 3.7 32.2 1.0
O D:HOH626 3.8 26.9 1.0
NH1 D:ARG123 3.8 27.6 1.0
NH2 D:ARG123 3.8 38.5 1.0
CB D:ALA134 4.1 36.3 1.0
CB D:ILE133 4.3 35.2 1.0
CZ D:ARG123 4.3 31.6 1.0
CA D:ILE133 4.3 35.3 1.0
CD1 D:ILE177 4.4 44.9 1.0
CD D:ARG28 4.5 51.4 1.0
CA D:ALA134 4.6 32.4 1.0
C D:ILE133 4.6 36.0 1.0
CG2 D:ILE133 4.6 37.0 1.0
NE D:ARG28 4.8 53.4 1.0

Iodine binding site 4 out of 6 in 7t5f

Go back to Iodine Binding Sites List in 7t5f
Iodine binding site 4 out of 6 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 Iodine with other atoms in the I binding site number 4 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
C:I201

b:93.1
occ:0.62
CB C:ARG71 3.4 51.6 1.0
NE C:ARG71 3.7 37.8 1.0
N C:ARG71 3.7 45.1 1.0
CG C:ARG71 4.0 49.2 1.0
CA C:ARG71 4.1 45.3 1.0
C C:SER70 4.2 49.0 1.0
CD C:ARG71 4.4 40.8 1.0
NH2 C:ARG71 4.4 49.7 1.0
O C:ARG71 4.5 53.5 1.0
CZ C:ARG71 4.5 44.0 1.0
CA C:SER70 4.6 45.5 1.0
C C:ARG71 4.8 53.2 1.0
O C:SER70 4.8 50.8 1.0
O C:ILE69 4.9 44.4 1.0

Iodine binding site 5 out of 6 in 7t5f

Go back to Iodine Binding Sites List in 7t5f
Iodine binding site 5 out of 6 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 Iodine with other atoms in the I binding site number 5 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
B:I201

b:49.6
occ:0.77
N B:GLY54 3.6 37.6 1.0
N B:ILE56 3.7 28.9 1.0
N B:ASN53 3.7 36.8 1.0
C B:GLY52 3.8 44.9 1.0
CA B:GLY52 3.8 36.5 1.0
N B:ILE57 3.9 34.7 1.0
CB B:ILE56 3.9 28.3 1.0
N B:GLY55 4.1 33.2 1.0
O A:TYR33 4.1 30.8 1.0
CA B:GLY54 4.2 35.0 1.0
CG1 B:ILE56 4.2 28.5 1.0
CE A:MET21 4.2 30.2 1.0
CD1 B:ILE56 4.2 28.7 1.0
CA B:ILE56 4.3 28.9 1.0
CG1 B:ILE57 4.3 36.6 1.0
C B:GLY54 4.3 29.0 1.0
O B:GLY52 4.3 37.6 1.0
OH B:TYR33 4.5 25.2 1.0
CB B:ILE57 4.5 32.4 1.0
C B:ILE56 4.5 37.1 1.0
C B:ASN53 4.6 35.9 1.0
CA B:ASN53 4.6 38.5 1.0
N B:GLY52 4.7 27.4 1.0
C B:GLY55 4.7 38.6 1.0
CB B:ASN53 4.8 40.7 1.0
CA B:ILE57 4.8 38.1 1.0
CA B:GLY55 4.9 29.6 1.0
CZ B:TYR33 4.9 35.6 1.0

Iodine binding site 6 out of 6 in 7t5f

Go back to Iodine Binding Sites List in 7t5f
Iodine binding site 6 out of 6 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 Iodine with other atoms in the I binding site number 6 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
E:I201

b:62.6
occ:0.70
N E:GLY54 3.5 79.5 1.0
N E:ASN53 3.6 71.6 1.0
N E:ILE56 3.6 75.3 1.0
N E:ILE57 3.7 78.7 1.0
C E:GLY52 3.7 72.7 1.0
CA E:GLY52 3.8 78.9 1.0
N E:GLY55 3.9 74.6 1.0
CB E:ILE56 3.9 74.9 1.0
O D:HOH617 4.0 47.6 1.0
CG1 E:ILE57 4.1 75.3 1.0
CA E:GLY54 4.2 73.2 1.0
CA E:ILE56 4.2 75.8 1.0
O D:TYR33 4.3 58.5 1.0
C E:GLY54 4.3 80.8 1.0
CB E:ILE57 4.3 78.2 1.0
CE D:MET21 4.3 54.2 1.0
OH E:TYR33 4.4 65.5 1.0
O E:GLY52 4.4 73.5 1.0
CA E:ASN53 4.4 78.3 1.0
C E:ASN53 4.4 78.1 1.0
C E:ILE56 4.5 84.4 1.0
CG1 E:ILE56 4.5 75.0 1.0
C E:GLY55 4.6 79.4 1.0
CD1 E:ILE56 4.6 74.0 1.0
CA E:ILE57 4.6 81.0 1.0
CB E:ASN53 4.7 70.2 1.0
CA E:GLY55 4.7 77.6 1.0
N E:GLY52 4.8 74.0 1.0
CZ E:TYR33 4.9 66.8 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 03:26:29 2022

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