Calcium in PDB 7qbg: Tc:CD320 in Complex with Nanobody Tc-NB4
Protein crystallography data
The structure of Tc:CD320 in Complex with Nanobody Tc-NB4, PDB code: 7qbg
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)
|
48.92 /
2.69
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.339,
116.418,
125.498,
90,
90,
90
|
|
R / Rfree (%)
|
22.7 /
28.5
|
Other elements in 7qbg:
The structure of Tc:CD320 in Complex with Nanobody Tc-NB4 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Tc:CD320 in Complex with Nanobody Tc-NB4
(pdb code 7qbg). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Tc:CD320 in Complex with Nanobody Tc-NB4, PDB code: 7qbg:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7qbg
Go back to
Calcium Binding Sites List in 7qbg
Calcium binding site 1 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Tc:CD320 in Complex with Nanobody Tc-NB4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:70.2
occ:1.00
|
O
|
B:TRP72
|
2.1
|
82.7
|
1.0
|
|
OD1
|
B:ASP75
|
2.1
|
76.6
|
1.0
|
|
O
|
B:ASP77
|
2.2
|
69.8
|
1.0
|
|
OD2
|
B:ASP79
|
2.6
|
64.3
|
1.0
|
|
OD2
|
B:ASP85
|
2.6
|
75.2
|
1.0
|
|
OE2
|
B:GLU86
|
3.0
|
83.1
|
1.0
|
|
C
|
B:TRP72
|
3.2
|
78.1
|
1.0
|
|
CG
|
B:ASP75
|
3.3
|
77.1
|
1.0
|
|
C
|
B:ASP77
|
3.3
|
70.3
|
1.0
|
|
CG
|
B:ASP79
|
3.5
|
65.2
|
1.0
|
|
CG
|
B:ASP85
|
3.6
|
80.3
|
1.0
|
|
CB
|
B:ASP79
|
3.7
|
64.6
|
1.0
|
|
CB
|
B:ASP85
|
3.8
|
84.8
|
1.0
|
|
N
|
B:ASP79
|
3.8
|
64.1
|
1.0
|
|
CD
|
B:GLU86
|
3.9
|
79.7
|
1.0
|
|
OD2
|
B:ASP75
|
3.9
|
77.4
|
1.0
|
|
CG
|
B:GLU86
|
3.9
|
74.5
|
1.0
|
|
CA
|
B:TRP72
|
4.0
|
78.6
|
1.0
|
|
CA
|
B:ASP77
|
4.1
|
69.7
|
1.0
|
|
N
|
B:ASP77
|
4.1
|
71.1
|
1.0
|
|
CB
|
B:ASP77
|
4.2
|
70.6
|
1.0
|
|
N
|
B:ARG73
|
4.2
|
78.4
|
1.0
|
|
CB
|
B:TRP72
|
4.3
|
76.7
|
1.0
|
|
N
|
B:LEU78
|
4.4
|
70.2
|
1.0
|
|
CB
|
B:ASP75
|
4.4
|
76.6
|
1.0
|
|
CA
|
B:ASP79
|
4.4
|
64.8
|
1.0
|
|
CA
|
B:ARG73
|
4.5
|
85.8
|
1.0
|
|
N
|
B:ASP75
|
4.6
|
80.5
|
1.0
|
|
CA
|
B:LEU78
|
4.6
|
67.1
|
1.0
|
|
NZ
|
C:LYS105
|
4.6
|
63.9
|
1.0
|
|
C
|
B:LEU78
|
4.6
|
65.5
|
1.0
|
|
O
|
B:ASP85
|
4.6
|
86.0
|
1.0
|
|
C
|
B:ASP85
|
4.7
|
84.4
|
1.0
|
|
OD1
|
B:ASP79
|
4.7
|
62.6
|
1.0
|
|
OD1
|
B:ASP85
|
4.8
|
76.3
|
1.0
|
|
N
|
B:CYS74
|
4.8
|
87.2
|
1.0
|
|
CA
|
B:ASP85
|
4.9
|
83.0
|
1.0
|
|
C
|
B:ARG73
|
4.9
|
90.9
|
1.0
|
|
CA
|
B:ASP75
|
5.0
|
78.3
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7qbg
Go back to
Calcium Binding Sites List in 7qbg
Calcium binding site 2 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Tc:CD320 in Complex with Nanobody Tc-NB4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:50.1
occ:1.00
|
OD2
|
B:ASP163
|
1.8
|
50.4
|
1.0
|
|
OD1
|
B:ASP153
|
1.9
|
46.4
|
1.0
|
|
OD2
|
B:ASP157
|
2.2
|
49.7
|
1.0
|
|
O
|
B:TRP150
|
2.3
|
46.4
|
1.0
|
|
O
|
B:HIS155
|
2.4
|
49.1
|
1.0
|
|
CG
|
B:ASP153
|
2.6
|
46.3
|
1.0
|
|
OE2
|
B:GLU164
|
2.9
|
52.4
|
1.0
|
|
OD2
|
B:ASP153
|
2.9
|
49.1
|
1.0
|
|
CG
|
B:ASP163
|
3.1
|
51.5
|
1.0
|
|
CG
|
B:ASP157
|
3.3
|
48.5
|
1.0
|
|
C
|
B:TRP150
|
3.5
|
45.0
|
1.0
|
|
C
|
B:HIS155
|
3.6
|
51.4
|
1.0
|
|
CD
|
B:GLU164
|
3.7
|
52.4
|
1.0
|
|
CB
|
B:ASP163
|
3.9
|
51.1
|
1.0
|
|
CB
|
B:ASP153
|
3.9
|
48.0
|
1.0
|
|
N
|
B:ASP157
|
4.0
|
51.4
|
1.0
|
|
OD1
|
B:ASP163
|
4.0
|
49.0
|
1.0
|
|
CB
|
B:ASP157
|
4.0
|
42.0
|
1.0
|
|
N
|
B:HIS155
|
4.1
|
51.3
|
1.0
|
|
CG
|
B:GLU164
|
4.2
|
46.6
|
1.0
|
|
N
|
B:ASP153
|
4.2
|
44.0
|
1.0
|
|
NZ
|
C:LYS114
|
4.2
|
39.2
|
1.0
|
|
CB
|
B:TRP150
|
4.2
|
46.8
|
1.0
|
|
OD1
|
B:ASP157
|
4.2
|
41.5
|
1.0
|
|
CA
|
B:TRP150
|
4.3
|
47.1
|
1.0
|
|
CA
|
B:HIS155
|
4.3
|
47.3
|
1.0
|
|
N
|
B:ARG151
|
4.5
|
46.5
|
1.0
|
|
N
|
B:PRO156
|
4.6
|
51.3
|
1.0
|
|
CA
|
B:ASP153
|
4.6
|
51.2
|
1.0
|
|
CA
|
B:PRO156
|
4.6
|
51.4
|
1.0
|
|
CA
|
B:ARG151
|
4.7
|
52.3
|
1.0
|
|
CA
|
B:ASP157
|
4.7
|
48.4
|
1.0
|
|
C
|
B:PRO156
|
4.7
|
49.2
|
1.0
|
|
N
|
B:CYS152
|
4.7
|
52.7
|
1.0
|
|
CB
|
B:HIS155
|
4.7
|
51.9
|
1.0
|
|
OE1
|
B:GLU164
|
4.7
|
56.6
|
1.0
|
|
C
|
B:ARG151
|
4.8
|
54.3
|
1.0
|
|
N
|
B:GLY154
|
4.9
|
49.3
|
1.0
|
|
C
|
B:ASP153
|
4.9
|
51.7
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7qbg
Go back to
Calcium Binding Sites List in 7qbg
Calcium binding site 3 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Tc:CD320 in Complex with Nanobody Tc-NB4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:47.8
occ:1.00
|
O
|
D:HIS155
|
2.2
|
43.9
|
1.0
|
|
OD2
|
D:ASP157
|
2.3
|
46.5
|
1.0
|
|
O
|
D:TRP150
|
2.3
|
52.5
|
1.0
|
|
OD1
|
D:ASP163
|
2.5
|
49.8
|
1.0
|
|
OD1
|
D:ASP153
|
2.6
|
45.7
|
1.0
|
|
OE2
|
D:GLU164
|
3.0
|
51.7
|
1.0
|
|
CG
|
D:ASP157
|
3.2
|
46.3
|
1.0
|
|
CG
|
D:ASP153
|
3.3
|
46.8
|
1.0
|
|
CG
|
D:ASP163
|
3.4
|
53.7
|
1.0
|
|
C
|
D:HIS155
|
3.4
|
49.1
|
1.0
|
|
OD2
|
D:ASP153
|
3.4
|
44.8
|
1.0
|
|
C
|
D:TRP150
|
3.4
|
57.4
|
1.0
|
|
N
|
D:ASP157
|
3.5
|
54.4
|
1.0
|
|
CB
|
D:ASP157
|
3.7
|
40.8
|
1.0
|
|
CD
|
D:GLU164
|
3.8
|
53.0
|
1.0
|
|
CB
|
D:ASP163
|
3.8
|
57.2
|
1.0
|
|
CG
|
D:GLU164
|
3.9
|
47.8
|
1.0
|
|
CB
|
D:TRP150
|
4.1
|
42.9
|
1.0
|
|
CA
|
D:TRP150
|
4.2
|
48.4
|
1.0
|
|
CA
|
D:ASP157
|
4.2
|
47.9
|
1.0
|
|
N
|
D:HIS155
|
4.3
|
46.3
|
1.0
|
|
OD1
|
D:ASP157
|
4.3
|
46.9
|
1.0
|
|
N
|
D:PRO156
|
4.3
|
47.8
|
1.0
|
|
C
|
D:PRO156
|
4.3
|
46.6
|
1.0
|
|
CA
|
D:HIS155
|
4.3
|
45.2
|
1.0
|
|
CA
|
D:PRO156
|
4.3
|
48.3
|
1.0
|
|
OD2
|
D:ASP163
|
4.4
|
55.5
|
1.0
|
|
N
|
D:ARG151
|
4.4
|
56.0
|
1.0
|
|
N
|
D:ASP153
|
4.5
|
45.8
|
1.0
|
|
CB
|
D:ASP153
|
4.5
|
41.7
|
1.0
|
|
CA
|
D:ARG151
|
4.7
|
54.9
|
1.0
|
|
CB
|
D:HIS155
|
4.7
|
48.2
|
1.0
|
|
N
|
D:CYS152
|
4.7
|
52.1
|
1.0
|
|
OE1
|
D:GLU164
|
4.8
|
62.5
|
1.0
|
|
NZ
|
A:LYS114
|
4.8
|
45.0
|
1.0
|
|
C
|
D:ARG151
|
4.9
|
56.6
|
1.0
|
|
C
|
D:ASP163
|
5.0
|
53.5
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7qbg
Go back to
Calcium Binding Sites List in 7qbg
Calcium binding site 4 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Tc:CD320 in Complex with Nanobody Tc-NB4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:75.5
occ:1.00
|
O
|
D:TRP72
|
2.3
|
75.8
|
1.0
|
|
OD2
|
D:ASP79
|
2.3
|
69.3
|
1.0
|
|
O
|
D:ASP77
|
2.3
|
73.4
|
1.0
|
|
OD1
|
D:ASP75
|
2.3
|
76.0
|
1.0
|
|
OD2
|
D:ASP85
|
2.4
|
75.6
|
1.0
|
|
OE2
|
D:GLU86
|
2.8
|
77.7
|
1.0
|
|
CG
|
D:ASP75
|
3.3
|
76.3
|
1.0
|
|
CG
|
D:ASP79
|
3.4
|
70.7
|
1.0
|
|
CG
|
D:ASP85
|
3.4
|
81.2
|
1.0
|
|
C
|
D:TRP72
|
3.4
|
74.4
|
1.0
|
|
C
|
D:ASP77
|
3.4
|
71.4
|
1.0
|
|
OD2
|
D:ASP75
|
3.6
|
75.7
|
1.0
|
|
CD
|
D:GLU86
|
3.8
|
83.3
|
1.0
|
|
CB
|
D:ASP85
|
3.8
|
80.7
|
1.0
|
|
CG
|
D:GLU86
|
4.0
|
79.0
|
1.0
|
|
N
|
D:ASP79
|
4.1
|
69.6
|
1.0
|
|
CA
|
D:TRP72
|
4.1
|
72.5
|
1.0
|
|
N
|
D:ASP77
|
4.1
|
71.9
|
1.0
|
|
CB
|
D:ASP79
|
4.1
|
72.7
|
1.0
|
|
CA
|
D:ASP77
|
4.2
|
70.7
|
1.0
|
|
CB
|
D:TRP72
|
4.2
|
71.2
|
1.0
|
|
N
|
D:ASP75
|
4.2
|
73.3
|
1.0
|
|
CB
|
D:ASP77
|
4.3
|
72.8
|
1.0
|
|
OD1
|
D:ASP79
|
4.3
|
68.6
|
1.0
|
|
NZ
|
A:LYS105
|
4.4
|
66.7
|
1.0
|
|
N
|
D:CYS74
|
4.4
|
81.5
|
1.0
|
|
N
|
D:LEU78
|
4.5
|
69.6
|
1.0
|
|
N
|
D:ARG73
|
4.5
|
76.1
|
1.0
|
|
OD1
|
D:ASP85
|
4.5
|
80.0
|
1.0
|
|
CB
|
D:ASP75
|
4.5
|
75.8
|
1.0
|
|
CA
|
D:LEU78
|
4.7
|
70.0
|
1.0
|
|
CA
|
D:ARG73
|
4.7
|
79.5
|
1.0
|
|
CA
|
D:ASP79
|
4.7
|
70.4
|
1.0
|
|
CA
|
D:ASP75
|
4.8
|
76.2
|
1.0
|
|
C
|
D:LEU78
|
4.8
|
73.6
|
1.0
|
|
C
|
D:ARG73
|
4.9
|
82.2
|
1.0
|
|
OE1
|
D:GLU86
|
4.9
|
86.1
|
1.0
|
|
C
|
D:ASP75
|
5.0
|
77.6
|
1.0
|
|
Calcium binding site 5 out
of 6 in 7qbg
Go back to
Calcium Binding Sites List in 7qbg
Calcium binding site 5 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Tc:CD320 in Complex with Nanobody Tc-NB4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca201
b:59.9
occ:1.00
|
OD2
|
E:ASP54
|
2.3
|
61.6
|
1.0
|
|
O
|
E:GLY126
|
2.3
|
69.3
|
1.0
|
|
O
|
E:GLN122
|
2.5
|
62.8
|
1.0
|
|
CG
|
E:ASP54
|
3.1
|
61.9
|
1.0
|
|
C
|
E:GLY126
|
3.3
|
66.9
|
1.0
|
|
OD1
|
E:ASP54
|
3.3
|
67.1
|
1.0
|
|
C
|
E:GLN122
|
3.6
|
60.3
|
1.0
|
|
N
|
E:SER124
|
3.8
|
55.3
|
1.0
|
|
O
|
E:SER124
|
3.8
|
55.2
|
1.0
|
|
C
|
E:SER124
|
3.9
|
66.8
|
1.0
|
|
C
|
E:PRO123
|
3.9
|
69.9
|
1.0
|
|
N
|
E:GLY126
|
3.9
|
68.7
|
1.0
|
|
CA
|
E:SER124
|
4.0
|
66.8
|
1.0
|
|
O
|
E:PRO123
|
4.0
|
79.0
|
1.0
|
|
CA
|
E:GLY126
|
4.1
|
67.9
|
1.0
|
|
CB
|
E:GLN122
|
4.1
|
61.4
|
1.0
|
|
N
|
E:CYS127
|
4.2
|
68.5
|
1.0
|
|
CA
|
E:CYS127
|
4.4
|
64.5
|
1.0
|
|
N
|
E:PRO123
|
4.4
|
58.8
|
1.0
|
|
N
|
E:ASN125
|
4.4
|
68.5
|
1.0
|
|
CA
|
E:GLN122
|
4.5
|
56.5
|
1.0
|
|
C
|
E:ASN125
|
4.5
|
67.0
|
1.0
|
|
OG
|
E:SER74
|
4.5
|
70.7
|
1.0
|
|
CB
|
E:ASP54
|
4.5
|
58.6
|
1.0
|
|
CA
|
E:PRO123
|
4.6
|
60.6
|
1.0
|
|
OE1
|
E:GLN122
|
4.8
|
57.8
|
1.0
|
|
O
|
E:ASN125
|
4.9
|
69.6
|
1.0
|
|
CD
|
C:LYS81
|
4.9
|
61.7
|
1.0
|
|
CB
|
E:SER73
|
4.9
|
79.8
|
1.0
|
|
CG
|
E:GLN122
|
5.0
|
58.7
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7qbg
Go back to
Calcium Binding Sites List in 7qbg
Calcium binding site 6 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Tc:CD320 in Complex with Nanobody Tc-NB4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca201
b:56.0
occ:1.00
|
O
|
G:SER124
|
2.3
|
59.8
|
1.0
|
|
O
|
G:GLY126
|
2.3
|
78.4
|
1.0
|
|
O
|
G:GLN122
|
2.3
|
56.1
|
1.0
|
|
OD2
|
G:ASP54
|
2.5
|
62.8
|
1.0
|
|
OD1
|
G:ASP54
|
2.9
|
77.4
|
1.0
|
|
CG
|
G:ASP54
|
3.1
|
67.7
|
1.0
|
|
C
|
G:GLY126
|
3.2
|
77.4
|
1.0
|
|
C
|
G:SER124
|
3.4
|
58.2
|
1.0
|
|
C
|
G:GLN122
|
3.6
|
50.7
|
1.0
|
|
O
|
G:ASN125
|
3.8
|
80.4
|
1.0
|
|
N
|
G:CYS127
|
3.9
|
84.1
|
1.0
|
|
N
|
G:SER124
|
4.0
|
50.6
|
1.0
|
|
C
|
G:PRO123
|
4.0
|
51.1
|
1.0
|
|
C
|
G:ASN125
|
4.0
|
71.0
|
1.0
|
|
CA
|
G:CYS127
|
4.0
|
80.4
|
1.0
|
|
CA
|
G:SER124
|
4.2
|
52.0
|
1.0
|
|
CB
|
G:GLN122
|
4.2
|
54.5
|
1.0
|
|
N
|
G:GLY126
|
4.2
|
73.9
|
1.0
|
|
CA
|
G:GLY126
|
4.3
|
76.6
|
1.0
|
|
CA
|
G:PRO123
|
4.3
|
49.7
|
1.0
|
|
O
|
G:PRO123
|
4.3
|
55.6
|
1.0
|
|
N
|
G:PRO123
|
4.4
|
52.0
|
1.0
|
|
N
|
G:ASN125
|
4.5
|
61.9
|
1.0
|
|
CA
|
G:GLN122
|
4.5
|
47.5
|
1.0
|
|
CB
|
G:SER74
|
4.6
|
79.2
|
1.0
|
|
CB
|
G:ASP54
|
4.6
|
64.2
|
1.0
|
|
OE1
|
G:GLN122
|
4.6
|
65.7
|
1.0
|
|
CB
|
G:SER124
|
4.6
|
51.2
|
1.0
|
|
CA
|
G:ASN125
|
4.8
|
61.6
|
1.0
|
|
N
|
G:SER74
|
4.8
|
84.2
|
1.0
|
|
OG
|
G:SER73
|
4.8
|
101.8
|
1.0
|
|
CB
|
G:CYS127
|
4.9
|
84.8
|
1.0
|
|
O
|
G:HOH301
|
4.9
|
59.9
|
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: Tue Apr 4 18:31:50 2023
|
