Cobalt 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:
Cobalt Binding Sites:
The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt where determined in the
Tc:CD320 in Complex with Nanobody Tc-NB34, PDB code: 7qbf:
Jump to Cobalt binding site number:
1;
2;
Cobalt binding site 1 out
of 2 in 7qbf
Go back to
Cobalt Binding Sites List in 7qbf
Cobalt 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 Cobalt with other atoms in the Co 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:Co536
b:21.7
occ:0.42
|
CO
|
A:CNC536
|
0.0
|
21.7
|
0.4
|
CO
|
A:CNC536
|
0.7
|
19.7
|
0.6
|
C1A
|
A:CNC536
|
1.5
|
29.0
|
0.6
|
N24
|
A:CNC536
|
1.6
|
21.2
|
0.6
|
N24
|
A:CNC536
|
1.7
|
25.2
|
0.4
|
N21
|
A:CNC536
|
1.8
|
23.2
|
0.4
|
N23
|
A:CNC536
|
1.9
|
22.6
|
0.6
|
N22
|
A:CNC536
|
1.9
|
22.9
|
0.4
|
N21
|
A:CNC536
|
1.9
|
22.2
|
0.6
|
N23
|
A:CNC536
|
1.9
|
23.2
|
0.4
|
C1A
|
A:CNC536
|
2.0
|
27.4
|
0.4
|
N22
|
A:CNC536
|
2.1
|
22.2
|
0.6
|
N3B
|
A:CNC536
|
2.5
|
21.2
|
0.4
|
C19
|
A:CNC536
|
2.6
|
21.5
|
0.6
|
N1A
|
A:CNC536
|
2.6
|
29.2
|
0.6
|
C19
|
A:CNC536
|
2.8
|
22.6
|
0.4
|
N3B
|
A:CNC536
|
2.8
|
21.9
|
0.6
|
C16
|
A:CNC536
|
2.8
|
19.2
|
0.6
|
C9
|
A:CNC536
|
2.8
|
23.2
|
0.4
|
C16
|
A:CNC536
|
2.9
|
20.7
|
0.4
|
C14
|
A:CNC536
|
2.9
|
22.6
|
0.6
|
C4
|
A:CNC536
|
2.9
|
23.6
|
0.6
|
C1
|
A:CNC536
|
2.9
|
22.6
|
0.4
|
C11
|
A:CNC536
|
2.9
|
21.1
|
0.6
|
C4
|
A:CNC536
|
3.0
|
20.7
|
0.4
|
C1
|
A:CNC536
|
3.0
|
23.1
|
0.6
|
C14
|
A:CNC536
|
3.0
|
22.4
|
0.4
|
C11
|
A:CNC536
|
3.0
|
21.9
|
0.4
|
C6
|
A:CNC536
|
3.1
|
24.2
|
0.4
|
C9
|
A:CNC536
|
3.1
|
23.0
|
0.6
|
N1A
|
A:CNC536
|
3.2
|
29.9
|
0.4
|
C6
|
A:CNC536
|
3.2
|
19.2
|
0.6
|
C2B
|
A:CNC536
|
3.3
|
21.4
|
0.4
|
C15
|
A:CNC536
|
3.4
|
21.1
|
0.4
|
C15
|
A:CNC536
|
3.4
|
20.9
|
0.6
|
C10
|
A:CNC536
|
3.4
|
21.6
|
0.4
|
C5
|
A:CNC536
|
3.5
|
22.7
|
0.4
|
C10
|
A:CNC536
|
3.6
|
22.6
|
0.6
|
C9B
|
A:CNC536
|
3.6
|
21.9
|
0.4
|
C2B
|
A:CNC536
|
3.6
|
21.3
|
0.6
|
C5
|
A:CNC536
|
3.7
|
21.7
|
0.6
|
C20
|
A:CNC536
|
3.7
|
21.4
|
0.4
|
C20
|
A:CNC536
|
3.7
|
19.9
|
0.6
|
H12
|
A:EDO530
|
3.8
|
43.8
|
1.0
|
C9B
|
A:CNC536
|
3.8
|
21.9
|
0.6
|
C18
|
A:CNC536
|
3.9
|
22.3
|
0.6
|
C26
|
A:CNC536
|
4.0
|
24.1
|
0.4
|
C2
|
A:CNC536
|
4.0
|
25.2
|
0.4
|
C18
|
A:CNC536
|
4.0
|
23.4
|
0.4
|
C17
|
A:CNC536
|
4.0
|
22.9
|
0.6
|
C3
|
A:CNC536
|
4.0
|
21.2
|
0.4
|
C2
|
A:CNC536
|
4.1
|
24.8
|
0.6
|
C12
|
A:CNC536
|
4.2
|
23.3
|
0.4
|
C17
|
A:CNC536
|
4.2
|
23.0
|
0.4
|
C3
|
A:CNC536
|
4.2
|
19.1
|
0.6
|
C26
|
A:CNC536
|
4.2
|
23.7
|
0.6
|
C4B
|
A:CNC536
|
4.2
|
22.0
|
0.4
|
C13
|
A:CNC536
|
4.2
|
24.1
|
0.6
|
C8
|
A:CNC536
|
4.2
|
21.9
|
0.4
|
C12
|
A:CNC536
|
4.2
|
23.4
|
0.6
|
C7
|
A:CNC536
|
4.2
|
22.6
|
0.4
|
C13
|
A:CNC536
|
4.3
|
24.6
|
0.4
|
C4B
|
A:CNC536
|
4.3
|
21.9
|
0.6
|
C47
|
A:CNC536
|
4.4
|
23.9
|
0.4
|
HO1
|
A:EDO530
|
4.4
|
50.2
|
1.0
|
C8
|
A:CNC536
|
4.5
|
21.9
|
0.6
|
C7
|
A:CNC536
|
4.5
|
23.4
|
0.6
|
N1B
|
A:CNC536
|
4.5
|
22.7
|
0.4
|
C54
|
A:CNC536
|
4.6
|
21.7
|
0.6
|
C8B
|
A:CNC536
|
4.7
|
21.1
|
0.4
|
C47
|
A:CNC536
|
4.7
|
23.8
|
0.6
|
C1
|
A:EDO530
|
4.8
|
36.5
|
1.0
|
C48
|
A:CNC536
|
4.8
|
26.0
|
0.6
|
N1B
|
A:CNC536
|
4.8
|
22.2
|
0.6
|
C37
|
A:CNC536
|
4.8
|
20.7
|
0.4
|
O1
|
A:EDO530
|
4.9
|
41.9
|
1.0
|
C53
|
A:CNC536
|
4.9
|
21.4
|
0.4
|
C54
|
A:CNC536
|
4.9
|
21.4
|
0.4
|
C8B
|
A:CNC536
|
5.0
|
20.9
|
0.6
|
C53
|
A:CNC536
|
5.0
|
21.7
|
0.6
|
C37
|
A:CNC536
|
5.0
|
24.6
|
0.6
|
|
Cobalt binding site 2 out
of 2 in 7qbf
Go back to
Cobalt Binding Sites List in 7qbf
Cobalt 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 Cobalt with other atoms in the Co 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:Co536
b:19.7
occ:0.58
|
CO
|
A:CNC536
|
0.0
|
19.7
|
0.6
|
CO
|
A:CNC536
|
0.7
|
21.7
|
0.4
|
N21
|
A:CNC536
|
1.7
|
23.2
|
0.4
|
N24
|
A:CNC536
|
1.8
|
21.2
|
0.6
|
N22
|
A:CNC536
|
1.8
|
22.9
|
0.4
|
N3B
|
A:CNC536
|
1.8
|
21.2
|
0.4
|
N22
|
A:CNC536
|
1.9
|
22.2
|
0.6
|
N21
|
A:CNC536
|
1.9
|
22.2
|
0.6
|
N23
|
A:CNC536
|
1.9
|
23.2
|
0.4
|
N23
|
A:CNC536
|
1.9
|
22.6
|
0.6
|
C1A
|
A:CNC536
|
2.1
|
29.0
|
0.6
|
N24
|
A:CNC536
|
2.1
|
25.2
|
0.4
|
N3B
|
A:CNC536
|
2.1
|
21.9
|
0.6
|
C9
|
A:CNC536
|
2.5
|
23.2
|
0.4
|
C1A
|
A:CNC536
|
2.7
|
27.4
|
0.4
|
C2B
|
A:CNC536
|
2.7
|
21.4
|
0.4
|
C4
|
A:CNC536
|
2.8
|
20.7
|
0.4
|
C19
|
A:CNC536
|
2.9
|
21.5
|
0.6
|
C9
|
A:CNC536
|
2.9
|
23.0
|
0.6
|
C1
|
A:CNC536
|
2.9
|
22.6
|
0.4
|
C11
|
A:CNC536
|
2.9
|
21.9
|
0.4
|
C9B
|
A:CNC536
|
2.9
|
21.9
|
0.4
|
C11
|
A:CNC536
|
2.9
|
21.1
|
0.6
|
C4
|
A:CNC536
|
2.9
|
23.6
|
0.6
|
C16
|
A:CNC536
|
3.0
|
19.2
|
0.6
|
C1
|
A:CNC536
|
3.0
|
23.1
|
0.6
|
C14
|
A:CNC536
|
3.0
|
22.4
|
0.4
|
C6
|
A:CNC536
|
3.0
|
19.2
|
0.6
|
C14
|
A:CNC536
|
3.1
|
22.6
|
0.6
|
C6
|
A:CNC536
|
3.1
|
24.2
|
0.4
|
C2B
|
A:CNC536
|
3.1
|
21.3
|
0.6
|
C19
|
A:CNC536
|
3.1
|
22.6
|
0.4
|
C16
|
A:CNC536
|
3.1
|
20.7
|
0.4
|
C9B
|
A:CNC536
|
3.2
|
21.9
|
0.6
|
N1A
|
A:CNC536
|
3.2
|
29.2
|
0.6
|
C10
|
A:CNC536
|
3.3
|
21.6
|
0.4
|
C10
|
A:CNC536
|
3.3
|
22.6
|
0.6
|
C20
|
A:CNC536
|
3.5
|
19.9
|
0.6
|
C20
|
A:CNC536
|
3.5
|
21.4
|
0.4
|
C5
|
A:CNC536
|
3.5
|
22.7
|
0.4
|
C15
|
A:CNC536
|
3.6
|
20.9
|
0.6
|
C4B
|
A:CNC536
|
3.6
|
22.0
|
0.4
|
C5
|
A:CNC536
|
3.6
|
21.7
|
0.6
|
C15
|
A:CNC536
|
3.7
|
21.1
|
0.4
|
C4B
|
A:CNC536
|
3.7
|
21.9
|
0.6
|
N1A
|
A:CNC536
|
3.8
|
29.9
|
0.4
|
N1B
|
A:CNC536
|
3.9
|
22.7
|
0.4
|
C8
|
A:CNC536
|
3.9
|
21.9
|
0.4
|
C8B
|
A:CNC536
|
4.0
|
21.1
|
0.4
|
C3
|
A:CNC536
|
4.0
|
21.2
|
0.4
|
C7
|
A:CNC536
|
4.0
|
22.6
|
0.4
|
C2
|
A:CNC536
|
4.1
|
25.2
|
0.4
|
C18
|
A:CNC536
|
4.1
|
22.3
|
0.6
|
C8
|
A:CNC536
|
4.2
|
21.9
|
0.6
|
C2
|
A:CNC536
|
4.2
|
24.8
|
0.6
|
C7
|
A:CNC536
|
4.2
|
23.4
|
0.6
|
C3
|
A:CNC536
|
4.2
|
19.1
|
0.6
|
C12
|
A:CNC536
|
4.2
|
23.3
|
0.4
|
N1B
|
A:CNC536
|
4.2
|
22.2
|
0.6
|
C18
|
A:CNC536
|
4.2
|
23.4
|
0.4
|
C17
|
A:CNC536
|
4.3
|
22.9
|
0.6
|
C26
|
A:CNC536
|
4.3
|
24.1
|
0.4
|
C13
|
A:CNC536
|
4.3
|
24.1
|
0.6
|
C8B
|
A:CNC536
|
4.3
|
20.9
|
0.6
|
C13
|
A:CNC536
|
4.3
|
24.6
|
0.4
|
C12
|
A:CNC536
|
4.3
|
23.4
|
0.6
|
C17
|
A:CNC536
|
4.4
|
23.0
|
0.4
|
H12
|
A:EDO530
|
4.4
|
43.8
|
1.0
|
C26
|
A:CNC536
|
4.5
|
23.7
|
0.6
|
C47
|
A:CNC536
|
4.6
|
23.9
|
0.4
|
C41
|
A:CNC536
|
4.6
|
21.7
|
0.4
|
C48
|
A:CNC536
|
4.7
|
26.0
|
0.6
|
C41
|
A:CNC536
|
4.7
|
20.3
|
0.6
|
C37
|
A:CNC536
|
4.8
|
20.7
|
0.4
|
C30
|
A:CNC536
|
4.9
|
25.2
|
0.6
|
C37
|
A:CNC536
|
4.9
|
24.6
|
0.6
|
C5B
|
A:CNC536
|
4.9
|
24.2
|
0.4
|
C54
|
A:CNC536
|
5.0
|
21.7
|
0.6
|
|
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 19:24:40 2024
|