Iodine in PDB 7qbf: Tc:CD320 in Complex with Nanobody Tc-NB34
Protein crystallography data
The structure of Tc:CD320 in Complex with Nanobody Tc-NB34, PDB code: 7qbf
was solved by
J.S.Bloch,
K.P.Locher,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.27 /
1.85
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.822,
104.822,
167.46,
90,
90,
90
|
R / Rfree (%)
|
17.4 /
20.5
|
Other elements in 7qbf:
The structure of Tc:CD320 in Complex with Nanobody Tc-NB34 also contains other interesting chemical elements:
Iodine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Iodine atom in the Tc:CD320 in Complex with Nanobody Tc-NB34
(pdb code 7qbf). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the
Tc:CD320 in Complex with Nanobody Tc-NB34, PDB code: 7qbf:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iodine binding site 1 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 1 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I501
b:37.8
occ:0.60
|
HD22
|
A:ASN192
|
2.8
|
53.6
|
1.0
|
HG3
|
A:ARG198
|
2.9
|
64.7
|
1.0
|
HA
|
A:ASN192
|
3.0
|
40.2
|
1.0
|
HA
|
A:PRO195
|
3.1
|
44.0
|
1.0
|
HA
|
A:ARG198
|
3.4
|
42.7
|
1.0
|
O
|
A:HOH746
|
3.6
|
44.3
|
1.0
|
HB2
|
A:ARG198
|
3.6
|
52.8
|
1.0
|
ND2
|
A:ASN192
|
3.7
|
44.7
|
1.0
|
CG
|
A:ARG198
|
3.8
|
53.9
|
1.0
|
HA
|
A:LYS189
|
3.8
|
33.3
|
0.4
|
HA
|
A:LYS189
|
3.8
|
33.2
|
0.6
|
HB3
|
A:PRO195
|
3.9
|
48.1
|
1.0
|
CA
|
A:ASN192
|
4.0
|
33.5
|
1.0
|
CB
|
A:ARG198
|
4.0
|
44.0
|
1.0
|
HD3
|
A:ARG198
|
4.0
|
74.7
|
1.0
|
CA
|
A:PRO195
|
4.0
|
36.7
|
1.0
|
HD21
|
A:ASN192
|
4.1
|
53.6
|
1.0
|
CA
|
A:ARG198
|
4.1
|
35.5
|
1.0
|
O
|
A:PHE193
|
4.1
|
43.3
|
1.0
|
HG3
|
A:LYS189
|
4.2
|
42.2
|
0.4
|
HG3
|
A:LYS189
|
4.4
|
42.2
|
0.6
|
HB3
|
A:ASN192
|
4.4
|
38.6
|
1.0
|
CD
|
A:ARG198
|
4.4
|
62.2
|
1.0
|
CB
|
A:PRO195
|
4.5
|
40.1
|
1.0
|
HG2
|
A:ARG198
|
4.5
|
64.7
|
1.0
|
N
|
A:PRO195
|
4.5
|
30.8
|
1.0
|
C
|
A:ASN192
|
4.5
|
34.7
|
1.0
|
CB
|
A:ASN192
|
4.6
|
32.1
|
1.0
|
H
|
A:ASN192
|
4.6
|
38.0
|
1.0
|
O
|
A:LYS189
|
4.6
|
28.5
|
0.6
|
O
|
A:ASN194
|
4.6
|
31.6
|
1.0
|
O
|
A:LYS189
|
4.6
|
28.5
|
0.4
|
CG
|
A:ASN192
|
4.6
|
37.7
|
1.0
|
HD2
|
A:ARG198
|
4.7
|
74.7
|
1.0
|
C
|
A:ASN194
|
4.8
|
36.5
|
1.0
|
HD12
|
A:ILE201
|
4.8
|
37.4
|
1.0
|
CA
|
A:LYS189
|
4.8
|
27.7
|
0.4
|
HD3
|
A:PRO195
|
4.8
|
42.5
|
1.0
|
CA
|
A:LYS189
|
4.8
|
27.7
|
0.6
|
N
|
A:ASN192
|
4.8
|
31.7
|
1.0
|
O
|
A:LEU188
|
4.9
|
28.1
|
1.0
|
O
|
A:ASN192
|
4.9
|
31.4
|
1.0
|
N
|
A:ARG198
|
4.9
|
33.3
|
1.0
|
HB3
|
A:ARG198
|
4.9
|
52.8
|
1.0
|
|
Iodine binding site 2 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 2 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I502
b:126.0
occ:1.00
|
HO2
|
A:EDO528
|
2.8
|
51.8
|
1.0
|
O2
|
A:EDO528
|
3.2
|
43.2
|
1.0
|
HG3
|
A:GLU211
|
3.3
|
49.7
|
1.0
|
O
|
A:HOH801
|
3.4
|
53.0
|
1.0
|
HB2
|
A:HIS173
|
3.5
|
38.4
|
1.0
|
HD2
|
A:HIS173
|
3.5
|
45.4
|
1.0
|
HB2
|
A:ALA178
|
3.7
|
32.9
|
1.0
|
HG21
|
B:THR28
|
3.8
|
48.3
|
1.0
|
HA
|
A:VAL165
|
3.9
|
36.0
|
1.0
|
HG12
|
A:VAL165
|
3.9
|
39.2
|
1.0
|
HG23
|
B:THR28
|
4.1
|
48.3
|
1.0
|
HB
|
A:VAL165
|
4.1
|
42.8
|
1.0
|
HB3
|
A:GLU211
|
4.1
|
41.5
|
1.0
|
HB1
|
A:ALA178
|
4.2
|
32.9
|
1.0
|
CG
|
A:GLU211
|
4.2
|
41.4
|
1.0
|
HB2
|
A:GLU211
|
4.2
|
41.5
|
1.0
|
CG2
|
B:THR28
|
4.3
|
40.3
|
1.0
|
HG22
|
B:THR28
|
4.3
|
48.3
|
1.0
|
CD2
|
A:HIS173
|
4.3
|
37.8
|
1.0
|
CB
|
A:ALA178
|
4.4
|
27.4
|
1.0
|
CB
|
A:GLU211
|
4.4
|
34.6
|
1.0
|
CB
|
A:HIS173
|
4.4
|
32.0
|
1.0
|
H
|
A:HIS173
|
4.4
|
48.5
|
1.0
|
HG22
|
A:THR207
|
4.5
|
38.8
|
1.0
|
C2
|
A:EDO528
|
4.5
|
43.6
|
1.0
|
HG22
|
A:VAL208
|
4.7
|
37.3
|
1.0
|
CG1
|
A:VAL165
|
4.7
|
32.6
|
1.0
|
CB
|
A:VAL165
|
4.7
|
35.7
|
1.0
|
HG
|
B:SER27
|
4.7
|
64.3
|
1.0
|
CA
|
A:VAL165
|
4.7
|
30.0
|
1.0
|
NE2
|
A:HIS169
|
4.7
|
35.8
|
0.5
|
CG
|
A:HIS173
|
4.8
|
31.8
|
1.0
|
H21
|
A:EDO528
|
4.8
|
52.3
|
1.0
|
OE2
|
A:GLU211
|
4.8
|
50.6
|
1.0
|
HE1
|
A:HIS169
|
4.8
|
47.0
|
0.5
|
HG2
|
A:GLU211
|
4.8
|
49.7
|
1.0
|
HA
|
A:VAL208
|
4.8
|
29.4
|
1.0
|
HB3
|
A:HIS173
|
4.9
|
38.4
|
1.0
|
HA
|
A:ALA178
|
4.9
|
30.6
|
1.0
|
HG11
|
A:VAL165
|
4.9
|
39.2
|
1.0
|
CD
|
A:GLU211
|
4.9
|
45.3
|
1.0
|
CE1
|
A:HIS169
|
5.0
|
39.1
|
0.5
|
H11
|
A:EDO528
|
5.0
|
60.8
|
1.0
|
|
Iodine binding site 3 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 3 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I503
b:37.6
occ:0.47
|
HO2
|
B:EDO203
|
2.6
|
65.0
|
1.0
|
HH22
|
A:ARG200
|
2.7
|
35.5
|
1.0
|
HE2
|
A:HIS128
|
2.7
|
54.0
|
1.0
|
O
|
A:HOH739
|
3.0
|
33.8
|
1.0
|
O2
|
B:EDO203
|
3.1
|
54.2
|
1.0
|
HB3
|
B:TYR117
|
3.1
|
49.5
|
1.0
|
HD2
|
A:TYR163
|
3.3
|
43.8
|
1.0
|
HD1
|
B:TYR115
|
3.3
|
38.7
|
1.0
|
NE2
|
A:HIS128
|
3.3
|
45.0
|
1.0
|
HH12
|
A:ARG200
|
3.4
|
38.9
|
1.0
|
NH2
|
A:ARG200
|
3.4
|
29.6
|
1.0
|
HB3
|
A:ASP159
|
3.4
|
34.6
|
1.0
|
HB2
|
A:TYR163
|
3.6
|
38.3
|
1.0
|
H11
|
A:EDO533
|
3.8
|
42.9
|
1.0
|
H21
|
A:EDO533
|
3.9
|
66.0
|
1.0
|
HH21
|
A:ARG200
|
3.9
|
35.5
|
1.0
|
HD2
|
B:TYR117
|
3.9
|
51.9
|
1.0
|
HE1
|
B:TYR115
|
3.9
|
40.8
|
1.0
|
HE1
|
A:HIS128
|
4.0
|
49.0
|
1.0
|
CE1
|
A:HIS128
|
4.0
|
40.8
|
1.0
|
NH1
|
A:ARG200
|
4.0
|
32.4
|
1.0
|
CD2
|
A:TYR163
|
4.1
|
36.5
|
1.0
|
CD1
|
B:TYR115
|
4.1
|
32.3
|
1.0
|
O1
|
A:EDO533
|
4.1
|
63.1
|
1.0
|
CB
|
B:TYR117
|
4.1
|
41.3
|
1.0
|
H
|
B:TYR117
|
4.1
|
53.7
|
1.0
|
CZ
|
A:ARG200
|
4.1
|
29.6
|
1.0
|
CB
|
A:ASP159
|
4.3
|
28.8
|
1.0
|
CD2
|
A:HIS128
|
4.3
|
39.8
|
1.0
|
C1
|
A:EDO533
|
4.3
|
35.8
|
1.0
|
CG
|
A:ASP159
|
4.3
|
29.8
|
1.0
|
HB2
|
B:TYR117
|
4.4
|
49.5
|
1.0
|
CE1
|
B:TYR115
|
4.4
|
34.0
|
1.0
|
O
|
A:ASP159
|
4.4
|
30.7
|
1.0
|
C2
|
B:EDO203
|
4.4
|
51.5
|
1.0
|
HD2
|
A:HIS128
|
4.4
|
47.7
|
1.0
|
OD2
|
A:ASP159
|
4.5
|
29.3
|
1.0
|
CB
|
A:TYR163
|
4.5
|
31.9
|
1.0
|
HO1
|
A:EDO533
|
4.5
|
75.8
|
1.0
|
C2
|
A:EDO533
|
4.6
|
55.0
|
1.0
|
H22
|
B:EDO203
|
4.6
|
61.8
|
1.0
|
O
|
B:TYR117
|
4.6
|
38.9
|
1.0
|
H
|
B:ASP116
|
4.6
|
46.2
|
1.0
|
CD2
|
B:TYR117
|
4.7
|
43.2
|
1.0
|
N
|
B:TYR117
|
4.7
|
44.7
|
1.0
|
CG
|
A:TYR163
|
4.7
|
30.6
|
1.0
|
OD1
|
A:ASP159
|
4.7
|
30.1
|
1.0
|
HH11
|
A:ARG200
|
4.8
|
38.9
|
1.0
|
HA
|
A:ASP159
|
4.8
|
31.5
|
1.0
|
H21
|
B:EDO203
|
4.8
|
61.8
|
1.0
|
HA
|
B:TYR115
|
4.9
|
40.1
|
1.0
|
CG
|
B:TYR117
|
4.9
|
45.6
|
1.0
|
CA
|
B:TYR117
|
4.9
|
43.4
|
1.0
|
HE2
|
A:TYR163
|
4.9
|
39.8
|
1.0
|
H
|
A:TYR163
|
5.0
|
36.9
|
1.0
|
CE2
|
A:TYR163
|
5.0
|
33.1
|
1.0
|
O
|
A:HOH710
|
5.0
|
34.9
|
1.0
|
CA
|
A:ASP159
|
5.0
|
26.2
|
1.0
|
C
|
A:ASP159
|
5.0
|
25.7
|
1.0
|
HB2
|
A:ASP159
|
5.0
|
34.6
|
1.0
|
HA
|
A:TYR163
|
5.0
|
33.7
|
1.0
|
|
Iodine binding site 4 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 4 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I504
b:74.2
occ:0.42
|
H
|
A:ASP9
|
2.7
|
53.2
|
1.0
|
HD21
|
A:LEU257
|
3.2
|
73.3
|
1.0
|
HA
|
A:MET8
|
3.2
|
44.1
|
1.0
|
HH22
|
A:ARG253
|
3.3
|
51.0
|
1.0
|
HG2
|
A:MET8
|
3.4
|
62.3
|
1.0
|
HD11
|
A:LEU257
|
3.4
|
67.2
|
1.0
|
N
|
A:ASP9
|
3.5
|
44.3
|
1.0
|
HB2
|
A:ASP9
|
3.5
|
75.5
|
1.0
|
HD22
|
A:LEU257
|
3.6
|
73.3
|
1.0
|
HD13
|
A:LEU257
|
3.7
|
67.2
|
1.0
|
CD2
|
A:LEU257
|
3.8
|
61.1
|
1.0
|
NH2
|
A:ARG253
|
3.9
|
42.5
|
1.0
|
CD1
|
A:LEU257
|
3.9
|
56.0
|
1.0
|
HB3
|
A:ASP9
|
4.0
|
75.5
|
1.0
|
CA
|
A:MET8
|
4.0
|
36.8
|
1.0
|
HB3
|
A:MET8
|
4.0
|
48.3
|
1.0
|
CB
|
A:ASP9
|
4.1
|
62.9
|
1.0
|
C
|
A:MET8
|
4.2
|
38.8
|
1.0
|
CG
|
A:MET8
|
4.2
|
52.0
|
1.0
|
HH21
|
A:ARG253
|
4.2
|
51.0
|
1.0
|
HH12
|
A:ARG253
|
4.3
|
49.5
|
1.0
|
CB
|
A:MET8
|
4.3
|
40.3
|
1.0
|
CA
|
A:ASP9
|
4.3
|
49.4
|
1.0
|
CG
|
A:LEU257
|
4.5
|
56.9
|
1.0
|
HD23
|
A:LEU257
|
4.6
|
73.3
|
1.0
|
HA
|
A:ASP9
|
4.6
|
59.2
|
1.0
|
CZ
|
A:ARG253
|
4.7
|
44.2
|
1.0
|
NH1
|
A:ARG253
|
4.8
|
41.2
|
1.0
|
HD22
|
A:LEU12
|
4.8
|
63.9
|
1.0
|
HD12
|
A:LEU257
|
4.8
|
67.2
|
1.0
|
HG3
|
A:MET8
|
4.8
|
62.3
|
1.0
|
O
|
A:GLU7
|
4.9
|
39.2
|
1.0
|
HD23
|
A:LEU12
|
5.0
|
63.9
|
1.0
|
|
Iodine binding site 5 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 5 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I505
b:45.4
occ:0.52
|
H
|
A:LEU388
|
2.5
|
38.0
|
1.0
|
HE21
|
A:GLN389
|
2.9
|
42.6
|
1.0
|
HE1
|
A:TYR394
|
3.0
|
50.3
|
1.0
|
HD1
|
A:TYR394
|
3.0
|
43.8
|
1.0
|
HB2
|
A:LEU388
|
3.3
|
36.3
|
1.0
|
N
|
A:LEU388
|
3.4
|
31.7
|
1.0
|
O
|
A:HOH816
|
3.4
|
45.1
|
1.0
|
HG3
|
A:GLN389
|
3.5
|
37.5
|
1.0
|
CE1
|
A:TYR394
|
3.6
|
41.9
|
1.0
|
HA
|
A:LEU387
|
3.6
|
33.0
|
1.0
|
CD1
|
A:TYR394
|
3.6
|
36.5
|
1.0
|
HG
|
A:LEU388
|
3.8
|
43.8
|
1.0
|
NE2
|
A:GLN389
|
3.8
|
35.5
|
1.0
|
HD22
|
A:LEU387
|
3.9
|
40.7
|
1.0
|
H
|
A:GLN389
|
3.9
|
30.9
|
1.0
|
HB3
|
A:LEU387
|
3.9
|
34.2
|
1.0
|
CB
|
A:LEU388
|
4.0
|
30.2
|
1.0
|
HE
|
A:ARG381
|
4.0
|
54.1
|
1.0
|
CA
|
A:LEU388
|
4.1
|
30.1
|
1.0
|
CA
|
A:LEU387
|
4.3
|
27.5
|
1.0
|
N
|
A:GLN389
|
4.3
|
25.8
|
1.0
|
HE22
|
A:GLN389
|
4.3
|
42.6
|
1.0
|
HB2
|
A:GLN389
|
4.3
|
34.2
|
1.0
|
C
|
A:LEU387
|
4.3
|
30.7
|
1.0
|
CG
|
A:GLN389
|
4.3
|
31.2
|
1.0
|
CG
|
A:LEU388
|
4.4
|
36.5
|
1.0
|
HD12
|
A:LEU388
|
4.4
|
45.8
|
1.0
|
C
|
A:LEU388
|
4.5
|
26.3
|
1.0
|
CB
|
A:LEU387
|
4.6
|
28.5
|
1.0
|
CD
|
A:GLN389
|
4.6
|
36.5
|
1.0
|
HD23
|
A:LEU387
|
4.6
|
40.7
|
1.0
|
CD2
|
A:LEU387
|
4.7
|
33.9
|
1.0
|
CB
|
A:GLN389
|
4.8
|
28.5
|
1.0
|
CZ
|
A:TYR394
|
4.8
|
38.0
|
1.0
|
NE
|
A:ARG381
|
4.8
|
45.1
|
1.0
|
CG
|
A:TYR394
|
4.8
|
34.9
|
1.0
|
HB3
|
A:LEU388
|
4.9
|
36.3
|
1.0
|
HD3
|
A:ARG381
|
4.9
|
54.3
|
1.0
|
CD1
|
A:LEU388
|
5.0
|
38.2
|
1.0
|
HB2
|
A:TYR394
|
5.0
|
38.9
|
1.0
|
HH21
|
A:ARG381
|
5.0
|
63.0
|
1.0
|
|
Iodine binding site 6 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 6 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I506
b:43.0
occ:0.37
|
H
|
A:TYR136
|
2.5
|
25.7
|
1.0
|
HH22
|
A:ARG374
|
2.8
|
65.9
|
1.0
|
HD2
|
A:TYR136
|
2.8
|
34.9
|
1.0
|
HH12
|
A:ARG374
|
3.0
|
68.7
|
1.0
|
O
|
A:HOH703
|
3.1
|
36.2
|
1.0
|
HA
|
A:SER135
|
3.1
|
27.7
|
1.0
|
HH2
|
A:TRP409
|
3.3
|
47.2
|
1.0
|
N
|
A:TYR136
|
3.3
|
21.4
|
1.0
|
HZ3
|
A:TRP409
|
3.3
|
52.7
|
1.0
|
HB2
|
A:SER135
|
3.4
|
32.4
|
1.0
|
O
|
A:HOH741
|
3.4
|
26.2
|
1.0
|
HB2
|
A:TYR136
|
3.5
|
28.4
|
1.0
|
NH2
|
A:ARG374
|
3.6
|
54.9
|
1.0
|
CH2
|
A:TRP409
|
3.6
|
39.4
|
1.0
|
CD2
|
A:TYR136
|
3.6
|
29.1
|
1.0
|
CZ3
|
A:TRP409
|
3.7
|
43.9
|
1.0
|
NH1
|
A:ARG374
|
3.8
|
57.3
|
1.0
|
CA
|
A:SER135
|
3.8
|
23.1
|
1.0
|
HG2
|
A:PRO132
|
3.8
|
41.9
|
1.0
|
CB
|
A:SER135
|
4.0
|
27.0
|
1.0
|
C
|
A:SER135
|
4.0
|
24.8
|
1.0
|
CB
|
A:TYR136
|
4.1
|
23.6
|
1.0
|
CZ
|
A:ARG374
|
4.2
|
60.8
|
1.0
|
HH21
|
A:ARG374
|
4.2
|
65.9
|
1.0
|
HG3
|
A:PRO132
|
4.3
|
41.9
|
1.0
|
CA
|
A:TYR136
|
4.3
|
22.1
|
1.0
|
HB3
|
A:SER135
|
4.3
|
32.4
|
1.0
|
CG
|
A:TYR136
|
4.3
|
25.2
|
1.0
|
CG
|
A:PRO132
|
4.5
|
34.9
|
1.0
|
HH11
|
A:ARG374
|
4.5
|
68.7
|
1.0
|
HE2
|
A:TYR136
|
4.5
|
30.8
|
1.0
|
HE1
|
A:HIS173
|
4.5
|
42.9
|
1.0
|
H
|
A:TYR137
|
4.6
|
27.9
|
1.0
|
CE2
|
A:TYR136
|
4.6
|
25.6
|
1.0
|
HD2
|
A:PRO132
|
4.6
|
38.8
|
1.0
|
CZ2
|
A:TRP409
|
4.7
|
38.1
|
1.0
|
CE3
|
A:TRP409
|
4.7
|
45.4
|
1.0
|
HG21
|
A:THR177
|
4.8
|
33.7
|
1.0
|
HA
|
A:TYR136
|
4.9
|
26.5
|
1.0
|
ND1
|
A:HIS173
|
5.0
|
32.8
|
1.0
|
O
|
A:THR134
|
5.0
|
30.1
|
1.0
|
O
|
A:HOH612
|
5.0
|
31.5
|
1.0
|
|
Iodine binding site 7 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 7 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I507
b:208.2
occ:1.00
|
HE3
|
A:MET367
|
2.9
|
76.3
|
1.0
|
HG23
|
A:THR351
|
2.9
|
67.0
|
1.0
|
HE2
|
A:MET367
|
3.4
|
76.3
|
1.0
|
CE
|
A:MET367
|
3.6
|
63.6
|
1.0
|
CG2
|
A:THR351
|
3.7
|
55.9
|
1.0
|
OG1
|
A:THR351
|
3.7
|
43.1
|
1.0
|
HG21
|
A:THR351
|
3.7
|
67.0
|
1.0
|
HG1
|
A:THR351
|
3.8
|
51.7
|
1.0
|
HA
|
A:MET367
|
3.9
|
48.5
|
1.0
|
HA
|
A:PHE350
|
4.0
|
57.6
|
1.0
|
H
|
A:THR351
|
4.0
|
51.9
|
1.0
|
HE1
|
A:MET367
|
4.0
|
76.3
|
1.0
|
HG2
|
A:MET367
|
4.1
|
60.0
|
1.0
|
N
|
A:THR351
|
4.2
|
43.2
|
1.0
|
C
|
A:GLY349
|
4.2
|
52.8
|
1.0
|
HA2
|
A:GLY349
|
4.2
|
60.7
|
1.0
|
O
|
A:GLY349
|
4.2
|
42.4
|
1.0
|
N
|
A:PHE350
|
4.3
|
48.9
|
1.0
|
CB
|
A:THR351
|
4.3
|
41.1
|
1.0
|
C
|
A:PHE350
|
4.3
|
47.1
|
1.0
|
HB3
|
A:MET367
|
4.4
|
52.9
|
1.0
|
CA
|
A:PHE350
|
4.4
|
48.0
|
1.0
|
HG22
|
A:THR351
|
4.5
|
67.0
|
1.0
|
H
|
A:PHE350
|
4.6
|
58.7
|
1.0
|
O
|
A:HOH875
|
4.7
|
63.4
|
1.0
|
CA
|
A:MET367
|
4.7
|
40.4
|
1.0
|
CA
|
A:GLY349
|
4.7
|
50.6
|
1.0
|
CG
|
A:MET367
|
4.8
|
50.0
|
1.0
|
CB
|
A:MET367
|
4.8
|
44.1
|
1.0
|
O
|
A:PHE350
|
4.9
|
45.2
|
1.0
|
CA
|
A:THR351
|
4.9
|
43.1
|
1.0
|
|
Iodine binding site 8 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 8 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I508
b:52.1
occ:0.43
|
H
|
A:GLY368
|
2.4
|
46.8
|
1.0
|
HG3
|
A:GLU353
|
2.9
|
62.0
|
1.0
|
HA
|
A:TYR352
|
3.0
|
43.1
|
1.0
|
OG
|
A:SER365
|
3.0
|
39.8
|
1.0
|
HG
|
A:SER365
|
3.0
|
47.7
|
1.0
|
N
|
A:GLY368
|
3.2
|
39.0
|
1.0
|
HA2
|
A:GLY368
|
3.3
|
47.0
|
1.0
|
HB3
|
A:SER365
|
3.3
|
41.1
|
1.0
|
HG1
|
A:THR351
|
3.5
|
51.7
|
1.0
|
CA
|
A:TYR352
|
3.6
|
35.9
|
1.0
|
OG1
|
A:THR351
|
3.6
|
43.1
|
1.0
|
H
|
A:MET367
|
3.6
|
46.2
|
1.0
|
N
|
A:TYR352
|
3.6
|
39.6
|
1.0
|
CB
|
A:SER365
|
3.7
|
34.3
|
1.0
|
C
|
A:TYR352
|
3.7
|
40.0
|
1.0
|
CA
|
A:GLY368
|
3.8
|
39.2
|
1.0
|
N
|
A:MET367
|
3.8
|
38.5
|
1.0
|
HB
|
A:THR351
|
3.8
|
49.4
|
1.0
|
CG
|
A:GLU353
|
3.8
|
51.6
|
1.0
|
H
|
A:TYR352
|
3.9
|
47.5
|
1.0
|
C
|
A:THR351
|
3.9
|
37.4
|
1.0
|
H
|
A:GLU353
|
4.0
|
42.1
|
1.0
|
N
|
A:GLU353
|
4.0
|
35.1
|
1.0
|
O
|
A:THR351
|
4.0
|
35.6
|
1.0
|
C
|
A:SER365
|
4.1
|
33.1
|
1.0
|
HA
|
A:VAL366
|
4.1
|
36.6
|
1.0
|
O
|
A:SER365
|
4.2
|
32.7
|
1.0
|
C
|
A:VAL366
|
4.2
|
33.5
|
1.0
|
CB
|
A:THR351
|
4.2
|
41.1
|
1.0
|
N
|
A:VAL366
|
4.2
|
32.3
|
1.0
|
HG2
|
A:GLU353
|
4.2
|
62.0
|
1.0
|
O
|
A:TYR352
|
4.2
|
39.2
|
1.0
|
HA
|
A:MET367
|
4.2
|
48.5
|
1.0
|
C
|
A:MET367
|
4.2
|
37.1
|
1.0
|
CA
|
A:MET367
|
4.3
|
40.4
|
1.0
|
O
|
A:HOH774
|
4.3
|
48.6
|
1.0
|
CD
|
A:GLU353
|
4.4
|
77.4
|
1.0
|
CA
|
A:VAL366
|
4.4
|
30.5
|
1.0
|
HB2
|
A:SER365
|
4.5
|
41.1
|
1.0
|
H
|
A:VAL366
|
4.5
|
38.7
|
1.0
|
HA3
|
A:GLY368
|
4.5
|
47.0
|
1.0
|
CA
|
A:SER365
|
4.5
|
31.9
|
1.0
|
C
|
A:GLY368
|
4.6
|
40.8
|
1.0
|
H
|
A:LYS369
|
4.6
|
41.6
|
1.0
|
OE2
|
A:GLU353
|
4.7
|
90.6
|
1.0
|
CA
|
A:THR351
|
4.7
|
43.1
|
1.0
|
HB2
|
A:GLU353
|
4.7
|
39.2
|
1.0
|
CB
|
A:GLU353
|
4.8
|
32.7
|
1.0
|
O
|
A:VAL366
|
4.8
|
32.4
|
1.0
|
N
|
A:LYS369
|
4.9
|
34.7
|
1.0
|
OE1
|
A:GLU353
|
5.0
|
87.7
|
1.0
|
CB
|
A:TYR352
|
5.0
|
35.8
|
1.0
|
CA
|
A:GLU353
|
5.0
|
34.9
|
1.0
|
|
Iodine binding site 9 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 9 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 9 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I509
b:153.6
occ:1.00
|
HH12
|
A:ARG108
|
2.5
|
55.9
|
1.0
|
HH22
|
A:ARG108
|
2.7
|
75.2
|
1.0
|
NH1
|
A:ARG108
|
3.3
|
46.6
|
1.0
|
OD2
|
A:ASP107
|
3.4
|
33.9
|
1.0
|
NH2
|
A:ARG108
|
3.5
|
62.7
|
1.0
|
HB2
|
C:PRO156
|
3.7
|
36.0
|
1.0
|
HB2
|
A:ASP107
|
3.8
|
36.3
|
1.0
|
O
|
C:PRO159
|
3.8
|
43.7
|
1.0
|
HA
|
C:PRO159
|
3.8
|
57.0
|
1.0
|
HA
|
A:HIS104
|
3.9
|
41.3
|
1.0
|
CZ
|
A:ARG108
|
3.9
|
65.9
|
1.0
|
HB3
|
A:ASP107
|
3.9
|
36.3
|
1.0
|
HH11
|
A:ARG108
|
4.0
|
55.9
|
1.0
|
HG2
|
C:PRO156
|
4.0
|
32.6
|
1.0
|
CB
|
A:ASP107
|
4.2
|
30.3
|
1.0
|
O
|
C:HOH303
|
4.2
|
44.0
|
1.0
|
HH21
|
A:ARG108
|
4.2
|
75.2
|
1.0
|
HG3
|
C:PRO156
|
4.2
|
32.6
|
1.0
|
CG
|
A:ASP107
|
4.3
|
29.7
|
1.0
|
OG
|
C:SER161
|
4.3
|
37.8
|
1.0
|
CG
|
C:PRO156
|
4.4
|
27.2
|
1.0
|
HB3
|
A:HIS104
|
4.4
|
43.5
|
1.0
|
HG
|
C:SER161
|
4.5
|
45.4
|
1.0
|
CB
|
C:PRO156
|
4.5
|
30.0
|
1.0
|
O
|
C:CYS158
|
4.5
|
30.3
|
1.0
|
HB2
|
A:HIS104
|
4.6
|
43.5
|
1.0
|
C
|
C:PRO159
|
4.6
|
45.7
|
1.0
|
CA
|
C:PRO159
|
4.6
|
47.5
|
1.0
|
O
|
A:HOH817
|
4.7
|
54.5
|
1.0
|
O
|
C:PRO156
|
4.7
|
30.8
|
1.0
|
CA
|
A:HIS104
|
4.7
|
34.4
|
1.0
|
CB
|
A:HIS104
|
4.8
|
36.2
|
1.0
|
HB3
|
C:PRO156
|
4.9
|
36.0
|
1.0
|
|
Iodine binding site 10 out
of 16 in 7qbf
Go back to
Iodine Binding Sites List in 7qbf
Iodine binding site 10 out
of 16 in the Tc:CD320 in Complex with Nanobody Tc-NB34
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 10 of Tc:CD320 in Complex with Nanobody Tc-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I510
b:118.0
occ:1.00
|
HG3
|
A:ARG108
|
3.2
|
40.8
|
1.0
|
ND1
|
A:HIS104
|
3.5
|
40.4
|
1.0
|
HA
|
A:LYS105
|
3.5
|
30.2
|
1.0
|
HD13
|
A:LEU67
|
3.6
|
32.9
|
1.0
|
HG2
|
A:LYS105
|
3.6
|
35.4
|
1.0
|
HB3
|
A:LEU67
|
3.7
|
34.2
|
1.0
|
O
|
A:HOH755
|
3.9
|
54.7
|
1.0
|
HE1
|
A:HIS104
|
3.9
|
50.2
|
1.0
|
HD22
|
A:LEU67
|
3.9
|
35.1
|
1.0
|
CE1
|
A:HIS104
|
4.1
|
41.8
|
1.0
|
CG
|
A:ARG108
|
4.1
|
34.0
|
1.0
|
HG2
|
A:ARG108
|
4.2
|
40.8
|
1.0
|
O
|
A:HIS104
|
4.3
|
29.7
|
1.0
|
CA
|
A:LYS105
|
4.4
|
25.2
|
1.0
|
HB2
|
A:ARG108
|
4.4
|
34.0
|
1.0
|
HG3
|
A:LYS105
|
4.4
|
35.4
|
1.0
|
CG
|
A:LYS105
|
4.4
|
29.5
|
1.0
|
O
|
A:HOH865
|
4.4
|
38.9
|
1.0
|
CD1
|
A:LEU67
|
4.5
|
27.4
|
1.0
|
HB2
|
A:HIS104
|
4.5
|
43.5
|
1.0
|
C
|
A:HIS104
|
4.5
|
31.2
|
1.0
|
N
|
A:LYS105
|
4.5
|
29.1
|
1.0
|
CB
|
A:LEU67
|
4.5
|
28.5
|
1.0
|
CG
|
A:HIS104
|
4.6
|
43.4
|
1.0
|
CD2
|
A:LEU67
|
4.8
|
29.2
|
1.0
|
CB
|
A:ARG108
|
4.8
|
28.4
|
1.0
|
HH21
|
A:ARG108
|
4.8
|
75.2
|
1.0
|
CG
|
A:LEU67
|
4.8
|
27.5
|
1.0
|
HB2
|
A:LEU67
|
4.8
|
34.2
|
1.0
|
HD12
|
A:LEU67
|
4.9
|
32.9
|
1.0
|
HD2
|
A:ARG108
|
4.9
|
51.7
|
1.0
|
H
|
A:LYS105
|
4.9
|
34.9
|
1.0
|
H
|
A:GLY68
|
5.0
|
50.9
|
1.0
|
CB
|
A:LYS105
|
5.0
|
25.4
|
1.0
|
|
Reference:
J.S.Bloch,
J.M.Sequeira,
A.S.Ramirez,
E.V.Quadros,
K.P.Locher.
Generation of Nanobodies Targeting the Human, Transcobalamin-Mediated Vitamin B 12 Uptake Route. Faseb J. V. 36 22222 2022.
ISSN: ESSN 1530-6860
PubMed: 35218573
DOI: 10.1096/FJ.202101376RR
Page generated: Mon Aug 12 01:59:17 2024
|