Chlorine in PDB 7tgi: Single-Domain Vhh Intrabodies Neutralize Ricin Toxin
Enzymatic activity of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin
All present enzymatic activity of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin:
3.2.2.22;
Protein crystallography data
The structure of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin, PDB code: 7tgi
was solved by
M.J.Rudolph,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.20 /
2.10
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.129,
84.407,
109.945,
90,
97.06,
90
|
R / Rfree (%)
|
17.6 /
22.2
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin
(pdb code 7tgi). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the
Single-Domain Vhh Intrabodies Neutralize Ricin Toxin, PDB code: 7tgi:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
Chlorine binding site 1 out
of 5 in 7tgi
Go back to
Chlorine Binding Sites List in 7tgi
Chlorine binding site 1 out
of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl301
b:29.8
occ:0.50
|
N
|
A:ALA118
|
3.2
|
34.7
|
1.0
|
CA
|
A:PHE117
|
3.8
|
32.4
|
1.0
|
CE2
|
A:PHE119
|
3.9
|
30.8
|
1.0
|
CB
|
A:ALA118
|
3.9
|
32.2
|
1.0
|
CD1
|
A:PHE117
|
4.0
|
32.9
|
1.0
|
C
|
A:PHE117
|
4.0
|
33.1
|
1.0
|
CD2
|
A:PHE119
|
4.1
|
32.6
|
1.0
|
CA
|
A:ALA118
|
4.2
|
36.1
|
1.0
|
CB
|
A:PHE117
|
4.2
|
32.8
|
1.0
|
CG
|
A:PHE117
|
4.6
|
32.2
|
1.0
|
O
|
A:THR116
|
4.9
|
34.1
|
1.0
|
N
|
A:PHE119
|
4.9
|
31.2
|
1.0
|
CZ
|
A:PHE119
|
5.0
|
29.1
|
1.0
|
|
Chlorine binding site 2 out
of 5 in 7tgi
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Chlorine Binding Sites List in 7tgi
Chlorine binding site 2 out
of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl302
b:41.8
occ:1.00
|
OG1
|
A:THR13
|
3.0
|
29.9
|
1.0
|
OE2
|
A:GLU145
|
3.0
|
76.4
|
1.0
|
N
|
A:HIS65
|
3.2
|
44.4
|
1.0
|
O
|
A:HOH474
|
3.3
|
53.9
|
1.0
|
CG
|
A:GLU145
|
3.4
|
56.2
|
1.0
|
CB
|
A:HIS65
|
3.6
|
54.7
|
1.0
|
N
|
A:ALA14
|
3.6
|
35.1
|
1.0
|
CD
|
A:GLU145
|
3.7
|
71.1
|
1.0
|
CB
|
A:GLU145
|
3.7
|
44.4
|
1.0
|
C
|
A:THR13
|
3.7
|
35.3
|
1.0
|
CB
|
A:THR13
|
3.8
|
31.5
|
1.0
|
CB
|
A:ASN64
|
3.8
|
44.5
|
1.0
|
CA
|
A:ALA14
|
3.8
|
37.8
|
1.0
|
CA
|
A:HIS65
|
3.9
|
52.4
|
1.0
|
O
|
A:THR13
|
4.0
|
38.3
|
1.0
|
CA
|
A:ASN64
|
4.0
|
38.4
|
1.0
|
C
|
A:ASN64
|
4.0
|
41.9
|
1.0
|
O
|
A:HOH470
|
4.3
|
44.4
|
1.0
|
CA
|
A:THR13
|
4.3
|
29.2
|
1.0
|
CB
|
A:ALA14
|
4.4
|
37.9
|
1.0
|
O
|
A:HOH435
|
4.5
|
52.5
|
1.0
|
CA
|
A:GLU145
|
4.9
|
34.8
|
1.0
|
CG
|
A:ASN64
|
4.9
|
47.0
|
1.0
|
CG
|
A:HIS65
|
4.9
|
55.6
|
1.0
|
OE1
|
A:GLU145
|
4.9
|
79.1
|
1.0
|
ND2
|
A:ASN141
|
4.9
|
42.4
|
1.0
|
|
Chlorine binding site 3 out
of 5 in 7tgi
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Chlorine Binding Sites List in 7tgi
Chlorine binding site 3 out
of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl303
b:68.4
occ:1.00
|
O
|
A:GLU127
|
3.7
|
32.8
|
1.0
|
C
|
A:GLU127
|
4.1
|
34.1
|
1.0
|
CD2
|
A:LEU133
|
4.1
|
47.4
|
1.0
|
N
|
A:GLN128
|
4.3
|
34.6
|
1.0
|
CA
|
A:GLN128
|
4.4
|
36.2
|
1.0
|
CG
|
A:LEU133
|
4.5
|
48.2
|
1.0
|
C
|
A:ASN132
|
4.5
|
43.1
|
1.0
|
CB
|
A:GLU127
|
4.5
|
34.1
|
1.0
|
O
|
A:ASN132
|
4.5
|
38.6
|
1.0
|
N
|
A:ASN132
|
4.5
|
40.0
|
1.0
|
C
|
A:GLY131
|
4.7
|
41.4
|
1.0
|
N
|
A:LEU133
|
4.8
|
43.6
|
1.0
|
CA
|
A:ASN132
|
4.8
|
41.6
|
1.0
|
CA
|
A:GLU127
|
4.9
|
35.2
|
1.0
|
|
Chlorine binding site 4 out
of 5 in 7tgi
Go back to
Chlorine Binding Sites List in 7tgi
Chlorine binding site 4 out
of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl304
b:66.0
occ:1.00
|
N
|
A:PHE108
|
3.0
|
35.5
|
1.0
|
CD2
|
A:TYR6
|
3.8
|
45.7
|
1.0
|
CA
|
A:PHE108
|
3.8
|
39.2
|
1.0
|
CD1
|
A:PHE108
|
3.9
|
37.7
|
1.0
|
CD1
|
A:LEU59
|
3.9
|
31.1
|
1.0
|
CA
|
A:LEU107
|
3.9
|
34.3
|
1.0
|
C
|
A:LEU107
|
3.9
|
35.7
|
1.0
|
CD2
|
A:LEU107
|
4.1
|
36.2
|
1.0
|
CE2
|
A:TYR6
|
4.2
|
47.2
|
1.0
|
O
|
A:HIS106
|
4.3
|
42.8
|
1.0
|
CE1
|
A:PHE108
|
4.4
|
37.3
|
1.0
|
CG
|
A:PHE108
|
4.5
|
37.8
|
1.0
|
CD2
|
A:LEU59
|
4.6
|
34.4
|
1.0
|
CB
|
A:LEU107
|
4.6
|
38.4
|
1.0
|
CG
|
A:LEU59
|
4.7
|
33.9
|
1.0
|
CB
|
A:PHE108
|
4.8
|
34.0
|
1.0
|
N
|
A:THR109
|
4.8
|
44.0
|
1.0
|
C
|
A:PHE108
|
4.9
|
42.3
|
1.0
|
CG
|
A:TYR6
|
4.9
|
44.5
|
1.0
|
N
|
A:LEU107
|
5.0
|
35.6
|
1.0
|
|
Chlorine binding site 5 out
of 5 in 7tgi
Go back to
Chlorine Binding Sites List in 7tgi
Chlorine binding site 5 out
of 5 in the Single-Domain Vhh Intrabodies Neutralize Ricin Toxin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Single-Domain Vhh Intrabodies Neutralize Ricin Toxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl305
b:64.8
occ:1.00
|
N
|
A:GLU135
|
3.2
|
37.8
|
1.0
|
CG
|
A:GLU135
|
3.4
|
66.9
|
1.0
|
CD1
|
A:ILE205
|
3.5
|
44.1
|
1.0
|
N
|
A:ARG134
|
3.5
|
37.8
|
1.0
|
CB
|
A:LEU133
|
3.7
|
47.4
|
1.0
|
CB
|
A:GLU135
|
3.7
|
55.7
|
1.0
|
CB
|
A:ARG134
|
3.8
|
33.5
|
1.0
|
CA
|
A:ARG134
|
4.0
|
35.8
|
1.0
|
CD
|
A:GLU135
|
4.0
|
77.4
|
1.0
|
CA
|
A:GLU135
|
4.0
|
46.3
|
1.0
|
C
|
A:ARG134
|
4.0
|
37.4
|
1.0
|
OE2
|
A:GLU127
|
4.0
|
38.0
|
1.0
|
CG2
|
A:ILE205
|
4.1
|
38.4
|
1.0
|
C
|
A:LEU133
|
4.2
|
40.3
|
1.0
|
OE2
|
A:GLU135
|
4.3
|
82.7
|
1.0
|
CA
|
A:LEU133
|
4.4
|
42.9
|
1.0
|
CG
|
A:LEU133
|
4.6
|
48.2
|
1.0
|
CD2
|
A:LEU133
|
4.6
|
47.4
|
1.0
|
CG1
|
A:ILE205
|
4.6
|
41.1
|
1.0
|
OE1
|
A:GLU135
|
4.7
|
79.5
|
1.0
|
NE
|
A:ARG134
|
4.7
|
34.4
|
1.0
|
CD1
|
A:LEU133
|
4.7
|
50.5
|
1.0
|
CB
|
A:ILE205
|
4.9
|
39.2
|
1.0
|
CG
|
A:ARG134
|
5.0
|
32.1
|
1.0
|
CD
|
A:GLU127
|
5.0
|
38.8
|
1.0
|
|
Reference:
T.F.Czajka,
D.J.Vance,
S.Davis,
M.J.Rudolph,
N.J.Mantis.
Single-Domain Antibodies Neutralize Ricin Toxin Intracellularly By Blocking Access to Ribosomal P-Stalk Proteins. J.Biol.Chem. V. 298 01742 2022.
ISSN: ESSN 1083-351X
PubMed: 35182523
DOI: 10.1016/J.JBC.2022.101742
Page generated: Tue Apr 4 21:49:13 2023
|