Cobalt in PDB 7qbe: Tc:CD320 in Complex with Nanobody Tc-NB11
Protein crystallography data
The structure of Tc:CD320 in Complex with Nanobody Tc-NB11, PDB code: 7qbe
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)
|
48.96 /
3.00
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.717,
195.831,
198.385,
90,
90,
90
|
R / Rfree (%)
|
25.2 /
28.4
|
Other elements in 7qbe:
The structure of Tc:CD320 in Complex with Nanobody Tc-NB11 also contains other interesting chemical elements:
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Tc:CD320 in Complex with Nanobody Tc-NB11
(pdb code 7qbe). 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-NB11, PDB code: 7qbe:
Jump to Cobalt binding site number:
1;
2;
Cobalt binding site 1 out
of 2 in 7qbe
Go back to
Cobalt Binding Sites List in 7qbe
Cobalt binding site 1 out
of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB11
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-NB11 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co501
b:96.9
occ:1.00
|
CO
|
A:CNC501
|
0.0
|
96.9
|
1.0
|
N24
|
A:CNC501
|
1.7
|
55.0
|
1.0
|
N21
|
A:CNC501
|
1.8
|
57.6
|
1.0
|
N22
|
A:CNC501
|
1.8
|
59.2
|
1.0
|
N23
|
A:CNC501
|
1.8
|
59.5
|
1.0
|
C1A
|
A:CNC501
|
2.1
|
61.2
|
1.0
|
N3B
|
A:CNC501
|
2.3
|
48.4
|
1.0
|
C19
|
A:CNC501
|
2.7
|
55.9
|
1.0
|
C9
|
A:CNC501
|
2.8
|
54.8
|
1.0
|
C1
|
A:CNC501
|
2.9
|
55.2
|
1.0
|
C4
|
A:CNC501
|
2.9
|
53.0
|
0.0
|
C11
|
A:CNC501
|
2.9
|
67.4
|
1.0
|
C6
|
A:CNC501
|
2.9
|
59.6
|
1.0
|
C14
|
A:CNC501
|
2.9
|
64.9
|
1.0
|
C16
|
A:CNC501
|
2.9
|
58.7
|
1.0
|
C2B
|
A:CNC501
|
3.2
|
47.7
|
1.0
|
N1A
|
A:CNC501
|
3.3
|
71.1
|
1.0
|
C9B
|
A:CNC501
|
3.3
|
51.6
|
1.0
|
C5
|
A:CNC501
|
3.4
|
52.9
|
1.0
|
C10
|
A:CNC501
|
3.4
|
52.8
|
1.0
|
C15
|
A:CNC501
|
3.4
|
55.5
|
1.0
|
C20
|
A:CNC501
|
3.7
|
43.8
|
1.0
|
C3
|
A:CNC501
|
3.9
|
54.2
|
1.0
|
C2
|
A:CNC501
|
3.9
|
48.5
|
1.0
|
C26
|
A:CNC501
|
3.9
|
45.7
|
1.0
|
C4B
|
A:CNC501
|
3.9
|
47.0
|
1.0
|
C18
|
A:CNC501
|
4.0
|
47.8
|
1.0
|
C12
|
A:CNC501
|
4.1
|
56.5
|
1.0
|
C8
|
A:CNC501
|
4.1
|
43.5
|
1.0
|
C17
|
A:CNC501
|
4.2
|
45.8
|
1.0
|
C47
|
A:CNC501
|
4.3
|
40.4
|
1.0
|
C7
|
A:CNC501
|
4.3
|
49.6
|
1.0
|
N1B
|
A:CNC501
|
4.4
|
48.2
|
1.0
|
C13
|
A:CNC501
|
4.4
|
69.8
|
1.0
|
C48
|
A:CNC501
|
4.4
|
72.7
|
1.0
|
C8B
|
A:CNC501
|
4.5
|
47.7
|
1.0
|
C41
|
A:CNC501
|
4.6
|
41.4
|
1.0
|
C35
|
A:CNC501
|
4.8
|
51.4
|
1.0
|
C56
|
A:CNC501
|
5.0
|
45.2
|
1.0
|
|
Cobalt binding site 2 out
of 2 in 7qbe
Go back to
Cobalt Binding Sites List in 7qbe
Cobalt binding site 2 out
of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB11
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-NB11 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co501
b:82.3
occ:1.00
|
CO
|
C:CNC501
|
0.0
|
82.3
|
1.0
|
N24
|
C:CNC501
|
1.7
|
80.5
|
1.0
|
N21
|
C:CNC501
|
1.7
|
75.0
|
1.0
|
N22
|
C:CNC501
|
1.8
|
80.5
|
1.0
|
N23
|
C:CNC501
|
1.8
|
81.9
|
1.0
|
C1A
|
C:CNC501
|
2.1
|
84.4
|
1.0
|
N3B
|
C:CNC501
|
2.5
|
69.5
|
1.0
|
C19
|
C:CNC501
|
2.6
|
75.6
|
1.0
|
C1
|
C:CNC501
|
2.8
|
74.5
|
1.0
|
C9
|
C:CNC501
|
2.8
|
77.6
|
1.0
|
C4
|
C:CNC501
|
2.8
|
74.4
|
0.2
|
C11
|
C:CNC501
|
2.9
|
85.1
|
1.0
|
C16
|
C:CNC501
|
2.9
|
79.5
|
1.0
|
C6
|
C:CNC501
|
2.9
|
77.7
|
1.0
|
C14
|
C:CNC501
|
2.9
|
88.5
|
1.0
|
N1A
|
C:CNC501
|
3.3
|
86.2
|
1.0
|
C2B
|
C:CNC501
|
3.3
|
77.7
|
1.0
|
C5
|
C:CNC501
|
3.4
|
73.2
|
1.0
|
C15
|
C:CNC501
|
3.4
|
80.8
|
1.0
|
C10
|
C:CNC501
|
3.4
|
82.4
|
1.0
|
C20
|
C:CNC501
|
3.7
|
69.9
|
1.0
|
C9B
|
C:CNC501
|
3.7
|
72.1
|
1.0
|
C26
|
C:CNC501
|
3.9
|
64.1
|
1.0
|
C2
|
C:CNC501
|
3.9
|
71.7
|
1.0
|
C3
|
C:CNC501
|
3.9
|
73.6
|
1.0
|
C18
|
C:CNC501
|
3.9
|
71.4
|
1.0
|
C17
|
C:CNC501
|
4.0
|
69.1
|
1.0
|
C12
|
C:CNC501
|
4.1
|
84.3
|
1.0
|
C8
|
C:CNC501
|
4.1
|
76.7
|
1.0
|
C47
|
C:CNC501
|
4.2
|
74.2
|
1.0
|
C7
|
C:CNC501
|
4.2
|
76.8
|
0.3
|
C4B
|
C:CNC501
|
4.3
|
73.0
|
1.0
|
C13
|
C:CNC501
|
4.4
|
107.1
|
1.0
|
C48
|
C:CNC501
|
4.4
|
107.1
|
1.0
|
C41
|
C:CNC501
|
4.5
|
73.1
|
1.0
|
N1B
|
C:CNC501
|
4.6
|
77.5
|
1.0
|
C35
|
C:CNC501
|
4.7
|
72.8
|
1.0
|
C8B
|
C:CNC501
|
4.7
|
77.0
|
1.0
|
C56
|
C:CNC501
|
4.9
|
76.9
|
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 Jul 30 19:24:16 2024
|