Chlorine in PDB 7kd0: Ricin Bound to Vhh Antibody V2C11
Enzymatic activity of Ricin Bound to Vhh Antibody V2C11
All present enzymatic activity of Ricin Bound to Vhh Antibody V2C11:
3.2.2.22;
Protein crystallography data
The structure of Ricin Bound to Vhh Antibody V2C11, PDB code: 7kd0
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)
|
32.43 /
2.77
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.223,
100.817,
129.712,
90,
90,
90
|
R / Rfree (%)
|
20.7 /
25.5
|
Other elements in 7kd0:
The structure of Ricin Bound to Vhh Antibody V2C11 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Ricin Bound to Vhh Antibody V2C11
(pdb code 7kd0). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Ricin Bound to Vhh Antibody V2C11, PDB code: 7kd0:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 7kd0
Go back to
Chlorine Binding Sites List in 7kd0
Chlorine binding site 1 out
of 6 in the Ricin Bound to Vhh Antibody V2C11
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Ricin Bound to Vhh Antibody V2C11 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl305
b:43.4
occ:1.00
|
O
|
A:HOH434
|
3.3
|
33.7
|
1.0
|
N
|
A:TYR243
|
3.3
|
32.8
|
1.0
|
OG1
|
B:THR134
|
3.4
|
37.3
|
1.0
|
N
|
A:ASP244
|
3.6
|
38.5
|
1.0
|
ND2
|
B:ASN136
|
3.7
|
42.3
|
1.0
|
CB
|
B:THR134
|
4.1
|
32.9
|
1.0
|
CA
|
A:TYR243
|
4.1
|
35.9
|
1.0
|
CA
|
A:VAL242
|
4.1
|
33.1
|
1.0
|
CB
|
A:ASP244
|
4.2
|
38.2
|
1.0
|
CG1
|
A:VAL242
|
4.2
|
32.5
|
1.0
|
C
|
A:VAL242
|
4.2
|
31.1
|
1.0
|
C
|
A:TYR243
|
4.2
|
37.2
|
1.0
|
O
|
A:ASP244
|
4.3
|
39.5
|
1.0
|
CB
|
A:TYR243
|
4.3
|
40.4
|
1.0
|
CE2
|
B:PHE140
|
4.3
|
78.8
|
1.0
|
CA
|
A:ASP244
|
4.4
|
39.3
|
1.0
|
CD1
|
A:TYR243
|
4.4
|
40.6
|
1.0
|
CD2
|
B:LEU132
|
4.6
|
30.9
|
1.0
|
CB
|
A:VAL242
|
4.7
|
33.3
|
1.0
|
CZ
|
B:PHE140
|
4.8
|
82.8
|
1.0
|
O
|
A:SER241
|
4.8
|
42.6
|
1.0
|
C
|
A:ASP244
|
4.8
|
36.6
|
1.0
|
CG
|
B:ASN136
|
4.8
|
45.3
|
1.0
|
CG2
|
A:ILE247
|
4.8
|
25.6
|
1.0
|
CG
|
A:TYR243
|
4.9
|
41.4
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 7kd0
Go back to
Chlorine Binding Sites List in 7kd0
Chlorine binding site 2 out
of 6 in the Ricin Bound to Vhh Antibody V2C11
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Ricin Bound to Vhh Antibody V2C11 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl306
b:76.6
occ:1.00
|
O
|
A:HOH480
|
2.4
|
57.4
|
1.0
|
O
|
A:HOH461
|
2.4
|
41.6
|
1.0
|
NE2
|
A:HIS94
|
2.6
|
58.8
|
1.0
|
O
|
A:HOH474
|
2.7
|
41.9
|
1.0
|
CE1
|
A:HIS94
|
3.1
|
58.3
|
1.0
|
CD2
|
A:HIS94
|
3.8
|
54.5
|
1.0
|
ND1
|
A:HIS94
|
4.4
|
55.0
|
1.0
|
CG
|
A:HIS94
|
4.7
|
51.6
|
1.0
|
O
|
A:HOH483
|
4.8
|
42.8
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 7kd0
Go back to
Chlorine Binding Sites List in 7kd0
Chlorine binding site 3 out
of 6 in the Ricin Bound to Vhh Antibody V2C11
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Ricin Bound to Vhh Antibody V2C11 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl307
b:73.2
occ:1.00
|
CD2
|
A:HIS106
|
3.4
|
42.6
|
1.0
|
NE2
|
A:HIS106
|
3.5
|
45.5
|
1.0
|
O
|
A:HOH478
|
3.6
|
23.9
|
1.0
|
OG1
|
A:THR105
|
3.9
|
38.0
|
1.0
|
O
|
A:THR105
|
4.1
|
43.1
|
1.0
|
O
|
A:HOH437
|
4.2
|
53.8
|
1.0
|
ZN
|
A:ZN304
|
4.3
|
39.1
|
1.0
|
CG
|
A:HIS106
|
4.4
|
37.3
|
1.0
|
CE1
|
A:HIS106
|
4.4
|
46.3
|
1.0
|
C
|
A:THR105
|
4.5
|
32.8
|
1.0
|
CB
|
A:THR105
|
4.7
|
37.1
|
1.0
|
N
|
A:HIS106
|
4.9
|
30.8
|
1.0
|
ND1
|
A:HIS106
|
4.9
|
42.5
|
1.0
|
CA
|
A:HIS106
|
4.9
|
33.0
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 7kd0
Go back to
Chlorine Binding Sites List in 7kd0
Chlorine binding site 4 out
of 6 in the Ricin Bound to Vhh Antibody V2C11
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Ricin Bound to Vhh Antibody V2C11 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl308
b:45.1
occ:1.00
|
O
|
A:HOH460
|
3.1
|
18.6
|
1.0
|
N
|
A:ILE53
|
3.4
|
34.5
|
1.0
|
CA
|
A:PRO52
|
3.6
|
38.4
|
1.0
|
CB
|
A:PRO52
|
3.8
|
36.7
|
1.0
|
CG2
|
A:ILE53
|
3.8
|
35.5
|
1.0
|
C
|
A:PRO52
|
4.0
|
36.9
|
1.0
|
CB
|
A:ILE53
|
4.4
|
36.1
|
1.0
|
CA
|
A:ILE53
|
4.5
|
31.1
|
1.0
|
CG
|
A:PRO52
|
4.9
|
34.6
|
1.0
|
N
|
A:PRO52
|
4.9
|
38.8
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 7kd0
Go back to
Chlorine Binding Sites List in 7kd0
Chlorine binding site 5 out
of 6 in the Ricin Bound to Vhh Antibody V2C11
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Ricin Bound to Vhh Antibody V2C11 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl309
b:58.9
occ:1.00
|
O
|
A:HOH471
|
3.8
|
36.2
|
1.0
|
CG2
|
A:VAL256
|
3.9
|
40.9
|
1.0
|
NH2
|
A:ARG258
|
4.2
|
37.4
|
1.0
|
CZ3
|
A:TRP211
|
4.3
|
25.0
|
1.0
|
CA
|
A:GLY212
|
4.6
|
26.8
|
1.0
|
CE3
|
A:TRP211
|
4.6
|
26.5
|
1.0
|
NH1
|
A:ARG258
|
4.7
|
38.2
|
1.0
|
CZ
|
A:ARG258
|
4.9
|
38.5
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 7kd0
Go back to
Chlorine Binding Sites List in 7kd0
Chlorine binding site 6 out
of 6 in the Ricin Bound to Vhh Antibody V2C11
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Ricin Bound to Vhh Antibody V2C11 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl302
b:70.2
occ:1.00
|
O
|
B:HOH456
|
2.4
|
44.9
|
1.0
|
O
|
B:HOH449
|
3.2
|
44.9
|
1.0
|
N
|
B:ALA84
|
3.5
|
39.3
|
1.0
|
CA
|
B:ALA83
|
3.9
|
39.4
|
1.0
|
CB
|
B:ALA83
|
4.0
|
35.0
|
1.0
|
C
|
B:ALA83
|
4.3
|
42.5
|
1.0
|
CB
|
B:ALA84
|
4.3
|
41.0
|
1.0
|
CE
|
B:MET76
|
4.4
|
36.1
|
1.0
|
CA
|
B:ALA84
|
4.5
|
41.9
|
1.0
|
CZ
|
B:TYR78
|
4.6
|
36.8
|
1.0
|
CE1
|
B:TYR78
|
4.7
|
35.3
|
1.0
|
CE2
|
B:TYR78
|
4.8
|
37.0
|
1.0
|
CG2
|
B:THR65
|
4.9
|
29.6
|
1.0
|
CD1
|
B:TYR78
|
5.0
|
35.5
|
1.0
|
OH
|
B:TYR78
|
5.0
|
38.6
|
1.0
|
|
Reference:
M.J.Rudolph,
A.Y.Poon,
S.Kavaliauskiene,
A.G.Myrann,
C.Reynolds-Peterson,
S.A.Davis,
K.Sandvig,
D.J.Vance,
N.J.Mantis.
Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies That Bridge Ricin'S A-B Subunit Interface. J.Mol.Biol. V. 433 67086 2021.
ISSN: ESSN 1089-8638
PubMed: 34089718
DOI: 10.1016/J.JMB.2021.167086
Page generated: Mon Jul 29 23:30:50 2024
|