Cobalt 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:
Cobalt Binding Sites:
The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt where determined in the
Tc:CD320 in Complex with Nanobody Tc-NB4, PDB code: 7qbg:
Jump to Cobalt binding site number:
1;
2;
Cobalt binding site 1 out
of 2 in 7qbg
Go back to
Cobalt Binding Sites List in 7qbg
Cobalt binding site 1 out
of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB4
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Tc:CD320 in Complex with Nanobody Tc-NB4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co501
b:41.2
occ:1.00
|
CO
|
A:CNC501
|
0.0
|
41.2
|
1.0
|
N24
|
A:CNC501
|
1.7
|
46.7
|
1.0
|
N21
|
A:CNC501
|
1.8
|
47.1
|
1.0
|
N22
|
A:CNC501
|
1.9
|
42.4
|
0.0
|
N23
|
A:CNC501
|
1.9
|
50.3
|
1.0
|
C1A
|
A:CNC501
|
2.0
|
45.5
|
1.0
|
C19
|
A:CNC501
|
2.7
|
42.4
|
1.0
|
C4
|
A:CNC501
|
2.8
|
44.6
|
0.7
|
C1
|
A:CNC501
|
2.9
|
36.2
|
1.0
|
N3B
|
A:CNC501
|
2.9
|
27.8
|
1.0
|
C16
|
A:CNC501
|
2.9
|
45.0
|
1.0
|
C9
|
A:CNC501
|
2.9
|
45.9
|
1.0
|
C14
|
A:CNC501
|
3.0
|
51.4
|
1.0
|
C6
|
A:CNC501
|
3.0
|
43.7
|
1.0
|
C11
|
A:CNC501
|
3.0
|
44.7
|
1.0
|
N1A
|
A:CNC501
|
3.2
|
44.6
|
1.0
|
C5
|
A:CNC501
|
3.3
|
44.4
|
1.0
|
C15
|
A:CNC501
|
3.5
|
47.1
|
1.0
|
C10
|
A:CNC501
|
3.5
|
40.4
|
0.6
|
C2B
|
A:CNC501
|
3.7
|
32.4
|
1.0
|
C20
|
A:CNC501
|
3.7
|
37.8
|
0.4
|
C26
|
A:CNC501
|
3.9
|
37.0
|
1.0
|
C9B
|
A:CNC501
|
3.9
|
37.6
|
1.0
|
C18
|
A:CNC501
|
3.9
|
42.2
|
1.0
|
C3
|
A:CNC501
|
3.9
|
41.9
|
1.0
|
C7
|
A:CNC501
|
3.9
|
43.6
|
1.0
|
C12
|
A:CNC501
|
4.0
|
45.2
|
1.0
|
C47
|
A:CNC501
|
4.0
|
43.7
|
1.0
|
C2
|
A:CNC501
|
4.0
|
43.3
|
1.0
|
C8
|
A:CNC501
|
4.0
|
37.6
|
1.0
|
C17
|
A:CNC501
|
4.1
|
43.9
|
1.0
|
C13
|
A:CNC501
|
4.2
|
43.6
|
1.0
|
C4B
|
A:CNC501
|
4.3
|
36.8
|
1.0
|
C41
|
A:CNC501
|
4.7
|
31.0
|
1.0
|
C37
|
A:CNC501
|
4.7
|
40.3
|
1.0
|
C35
|
A:CNC501
|
4.8
|
43.3
|
1.0
|
N1B
|
A:CNC501
|
4.9
|
35.9
|
0.4
|
C53
|
A:CNC501
|
4.9
|
53.1
|
1.0
|
|
Cobalt binding site 2 out
of 2 in 7qbg
Go back to
Cobalt Binding Sites List in 7qbg
Cobalt binding site 2 out
of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB4
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Tc:CD320 in Complex with Nanobody Tc-NB4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co501
b:56.0
occ:1.00
|
CO
|
C:CNC501
|
0.0
|
56.0
|
1.0
|
N24
|
C:CNC501
|
1.7
|
50.3
|
1.0
|
N21
|
C:CNC501
|
1.8
|
49.7
|
1.0
|
N22
|
C:CNC501
|
1.9
|
51.9
|
0.4
|
N23
|
C:CNC501
|
1.9
|
51.1
|
1.0
|
C1A
|
C:CNC501
|
2.0
|
55.6
|
1.0
|
N3B
|
C:CNC501
|
2.5
|
38.8
|
1.0
|
C19
|
C:CNC501
|
2.7
|
49.4
|
1.0
|
C1
|
C:CNC501
|
2.8
|
47.9
|
1.0
|
C9
|
C:CNC501
|
2.9
|
51.8
|
1.0
|
C4
|
C:CNC501
|
2.9
|
47.9
|
0.0
|
C6
|
C:CNC501
|
3.0
|
53.6
|
1.0
|
C14
|
C:CNC501
|
3.0
|
48.9
|
1.0
|
C16
|
C:CNC501
|
3.0
|
50.6
|
1.0
|
C11
|
C:CNC501
|
3.0
|
51.7
|
1.0
|
N1A
|
C:CNC501
|
3.2
|
58.9
|
1.0
|
C2B
|
C:CNC501
|
3.3
|
39.3
|
1.0
|
C5
|
C:CNC501
|
3.4
|
47.8
|
1.0
|
C10
|
C:CNC501
|
3.5
|
51.4
|
1.0
|
C15
|
C:CNC501
|
3.6
|
50.7
|
1.0
|
C9B
|
C:CNC501
|
3.6
|
43.8
|
1.0
|
C26
|
C:CNC501
|
3.7
|
42.9
|
1.0
|
C20
|
C:CNC501
|
3.8
|
43.5
|
0.5
|
C2
|
C:CNC501
|
3.9
|
49.0
|
1.0
|
C3
|
C:CNC501
|
3.9
|
49.2
|
1.0
|
C18
|
C:CNC501
|
4.0
|
44.0
|
1.0
|
C8
|
C:CNC501
|
4.0
|
49.8
|
1.0
|
C7
|
C:CNC501
|
4.0
|
48.9
|
1.0
|
C12
|
C:CNC501
|
4.1
|
51.4
|
1.0
|
C47
|
C:CNC501
|
4.1
|
49.7
|
1.0
|
C4B
|
C:CNC501
|
4.2
|
41.5
|
1.0
|
C17
|
C:CNC501
|
4.2
|
48.2
|
1.0
|
C13
|
C:CNC501
|
4.3
|
44.6
|
1.0
|
C41
|
C:CNC501
|
4.5
|
45.3
|
1.0
|
N1B
|
C:CNC501
|
4.5
|
42.9
|
1.0
|
C8B
|
C:CNC501
|
4.7
|
42.4
|
1.0
|
C37
|
C:CNC501
|
4.8
|
51.7
|
1.0
|
C35
|
C:CNC501
|
4.9
|
50.0
|
0.2
|
|
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 Jul 30 19:25:17 2024
|