Calcium 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:
Calcium Binding Sites:
The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the
Tc:CD320 in Complex with Nanobody Tc-NB34, PDB code: 7qbf:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 7qbf
Go back to
Calcium Binding Sites List in 7qbf
Calcium binding site 1 out
of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB34
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-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:25.9
occ:1.00
|
OD2
|
C:ASP163
|
2.2
|
29.7
|
1.0
|
OD2
|
C:ASP157
|
2.2
|
27.0
|
1.0
|
O
|
C:HIS155
|
2.3
|
25.6
|
1.0
|
O
|
C:TRP150
|
2.3
|
23.8
|
1.0
|
OE2
|
C:GLU164
|
2.3
|
29.2
|
1.0
|
OD1
|
C:ASP153
|
2.4
|
28.3
|
1.0
|
CG
|
C:ASP153
|
3.2
|
27.5
|
1.0
|
H
|
C:ASP157
|
3.2
|
30.7
|
1.0
|
HB3
|
C:TRP150
|
3.3
|
30.7
|
1.0
|
H
|
C:ASP153
|
3.3
|
36.8
|
1.0
|
CG
|
C:ASP163
|
3.4
|
32.0
|
1.0
|
CD
|
C:GLU164
|
3.4
|
26.8
|
1.0
|
CG
|
C:ASP157
|
3.4
|
24.3
|
1.0
|
H
|
C:HIS155
|
3.4
|
37.6
|
1.0
|
C
|
C:HIS155
|
3.5
|
29.4
|
1.0
|
HG2
|
C:GLU164
|
3.5
|
37.8
|
1.0
|
C
|
C:TRP150
|
3.5
|
30.4
|
1.0
|
OD2
|
C:ASP153
|
3.6
|
24.4
|
1.0
|
HB2
|
C:ASP163
|
3.7
|
33.2
|
1.0
|
HZ3
|
A:LYS114
|
3.7
|
32.7
|
1.0
|
HB2
|
C:ASP157
|
3.9
|
30.3
|
1.0
|
CG
|
C:GLU164
|
3.9
|
31.5
|
1.0
|
N
|
C:ASP157
|
3.9
|
25.6
|
1.0
|
HB3
|
C:HIS155
|
4.0
|
32.7
|
1.0
|
HA
|
C:PRO156
|
4.1
|
33.9
|
1.0
|
N
|
C:HIS155
|
4.1
|
31.3
|
1.0
|
CB
|
C:ASP163
|
4.1
|
27.7
|
1.0
|
HZ2
|
A:LYS114
|
4.1
|
32.7
|
1.0
|
CB
|
C:TRP150
|
4.1
|
25.6
|
1.0
|
HA
|
C:ARG151
|
4.1
|
34.3
|
1.0
|
CB
|
C:ASP157
|
4.2
|
25.3
|
1.0
|
N
|
C:ASP153
|
4.2
|
30.7
|
1.0
|
HG3
|
C:GLU164
|
4.2
|
37.8
|
1.0
|
H
|
C:CYS152
|
4.3
|
33.3
|
1.0
|
CA
|
C:TRP150
|
4.3
|
24.1
|
1.0
|
CA
|
C:HIS155
|
4.3
|
27.9
|
1.0
|
NZ
|
A:LYS114
|
4.3
|
27.3
|
1.0
|
HA
|
C:TRP150
|
4.3
|
29.0
|
1.0
|
OD1
|
C:ASP163
|
4.3
|
31.2
|
1.0
|
OD1
|
C:ASP157
|
4.3
|
23.5
|
1.0
|
CB
|
C:ASP153
|
4.4
|
30.4
|
1.0
|
OE1
|
C:GLU164
|
4.4
|
32.6
|
1.0
|
HZ1
|
A:LYS114
|
4.5
|
32.7
|
1.0
|
N
|
C:PRO156
|
4.5
|
26.6
|
1.0
|
N
|
C:ARG151
|
4.5
|
30.1
|
1.0
|
HB2
|
C:TRP150
|
4.5
|
30.7
|
1.0
|
H
|
C:GLY154
|
4.5
|
36.5
|
1.0
|
N
|
C:CYS152
|
4.6
|
27.8
|
1.0
|
CA
|
C:PRO156
|
4.6
|
28.2
|
1.0
|
O
|
C:ASP163
|
4.6
|
30.6
|
1.0
|
CB
|
C:HIS155
|
4.6
|
27.2
|
1.0
|
HB3
|
C:ASP153
|
4.6
|
36.5
|
1.0
|
HD12
|
C:ILE146
|
4.7
|
42.5
|
1.0
|
CA
|
C:ARG151
|
4.7
|
28.6
|
1.0
|
CA
|
C:ASP153
|
4.7
|
27.6
|
1.0
|
C
|
C:PRO156
|
4.7
|
29.7
|
1.0
|
CA
|
C:ASP157
|
4.7
|
25.1
|
1.0
|
HB3
|
C:ASP163
|
4.7
|
33.2
|
1.0
|
C
|
C:ASP163
|
4.8
|
33.1
|
1.0
|
N
|
C:GLY154
|
4.8
|
30.4
|
1.0
|
C
|
C:ARG151
|
4.8
|
30.1
|
1.0
|
HD2
|
C:HIS155
|
4.9
|
29.9
|
1.0
|
C
|
C:ASP153
|
4.9
|
30.2
|
1.0
|
HD13
|
C:ILE146
|
5.0
|
42.5
|
1.0
|
|
Calcium binding site 2 out
of 2 in 7qbf
Go back to
Calcium Binding Sites List in 7qbf
Calcium binding site 2 out
of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB34
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-NB34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca202
b:30.5
occ:1.00
|
O
|
C:ASP77
|
2.2
|
28.9
|
1.0
|
O
|
C:TRP72
|
2.2
|
37.1
|
1.0
|
OD2
|
C:ASP79
|
2.3
|
27.7
|
1.0
|
OD1
|
C:ASP85
|
2.3
|
32.0
|
1.0
|
OD1
|
C:ASP75
|
2.3
|
32.6
|
1.0
|
OE2
|
C:GLU86
|
2.4
|
34.0
|
1.0
|
H
|
C:ASP75
|
3.2
|
46.7
|
1.0
|
H
|
C:ASP79
|
3.2
|
34.5
|
1.0
|
HG2
|
C:GLU86
|
3.3
|
42.7
|
1.0
|
CG
|
C:ASP75
|
3.4
|
41.7
|
1.0
|
CD
|
C:GLU86
|
3.4
|
33.8
|
1.0
|
C
|
C:ASP77
|
3.4
|
27.5
|
1.0
|
CG
|
C:ASP79
|
3.4
|
32.5
|
1.0
|
C
|
C:TRP72
|
3.4
|
35.8
|
1.0
|
CG
|
C:ASP85
|
3.5
|
33.0
|
1.0
|
HB3
|
C:TRP72
|
3.5
|
42.5
|
1.0
|
HB2
|
C:ASP79
|
3.5
|
31.9
|
1.0
|
HB2
|
C:ASP85
|
3.6
|
36.5
|
1.0
|
HB2
|
C:ASP77
|
3.6
|
35.4
|
1.0
|
CG
|
C:GLU86
|
3.8
|
35.6
|
1.0
|
HZ3
|
A:LYS105
|
3.9
|
39.7
|
1.0
|
N
|
C:ASP79
|
3.9
|
28.8
|
1.0
|
H
|
C:ASP77
|
3.9
|
42.7
|
1.0
|
OD2
|
C:ASP75
|
4.0
|
33.8
|
1.0
|
CB
|
C:ASP79
|
4.0
|
26.6
|
1.0
|
HA
|
C:TRP72
|
4.0
|
42.6
|
1.0
|
N
|
C:ASP75
|
4.0
|
39.0
|
1.0
|
HG3
|
C:GLU86
|
4.0
|
42.7
|
1.0
|
HA
|
C:LEU78
|
4.1
|
40.9
|
1.0
|
CB
|
C:ASP85
|
4.1
|
30.4
|
1.0
|
N
|
C:ASP77
|
4.1
|
35.6
|
1.0
|
CA
|
C:ASP77
|
4.1
|
31.6
|
1.0
|
H
|
C:CYS74
|
4.1
|
40.7
|
1.0
|
CA
|
C:TRP72
|
4.2
|
35.5
|
1.0
|
HA
|
C:ARG73
|
4.2
|
40.9
|
1.0
|
CB
|
C:TRP72
|
4.3
|
35.4
|
1.0
|
CB
|
C:ASP77
|
4.3
|
29.5
|
1.0
|
H
|
C:ARG76
|
4.4
|
44.6
|
1.0
|
N
|
C:LEU78
|
4.4
|
31.5
|
1.0
|
CB
|
C:ASP75
|
4.4
|
38.0
|
1.0
|
OE1
|
C:GLU86
|
4.4
|
33.3
|
1.0
|
OD1
|
C:ASP79
|
4.4
|
27.5
|
1.0
|
OD2
|
C:ASP85
|
4.5
|
32.0
|
1.0
|
N
|
C:ARG73
|
4.5
|
38.0
|
1.0
|
N
|
C:CYS74
|
4.5
|
34.0
|
1.0
|
CA
|
C:ASP75
|
4.5
|
36.6
|
1.0
|
N
|
C:ARG76
|
4.6
|
37.2
|
1.0
|
C
|
C:ASP75
|
4.6
|
42.9
|
1.0
|
CA
|
C:LEU78
|
4.6
|
34.0
|
1.0
|
HB3
|
C:ASP75
|
4.6
|
45.6
|
1.0
|
HB3
|
C:ASP77
|
4.6
|
35.4
|
1.0
|
CA
|
C:ASP79
|
4.6
|
26.2
|
1.0
|
HZ2
|
A:LYS105
|
4.6
|
39.7
|
1.0
|
O
|
C:ASP85
|
4.6
|
36.6
|
1.0
|
NZ
|
A:LYS105
|
4.7
|
33.1
|
1.0
|
CA
|
C:ARG73
|
4.7
|
34.1
|
1.0
|
C
|
C:LEU78
|
4.7
|
32.4
|
1.0
|
HB3
|
C:ASP85
|
4.7
|
36.5
|
1.0
|
HB3
|
C:ASP79
|
4.8
|
31.9
|
1.0
|
C
|
C:ASP85
|
4.8
|
36.0
|
1.0
|
C
|
C:ARG73
|
4.8
|
38.2
|
1.0
|
HB2
|
C:TRP72
|
4.8
|
42.5
|
1.0
|
C
|
C:ARG76
|
4.8
|
43.5
|
1.0
|
HZ1
|
A:LYS105
|
5.0
|
39.7
|
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: Fri Jul 19 03:25:45 2024
|