Cobalt in PDB 7qbd: Tc:CD320 in Complex with Nanobody Tc-NB26
Protein crystallography data
The structure of Tc:CD320 in Complex with Nanobody Tc-NB26, PDB code: 7qbd
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)
|
49.14 /
4.18
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.129,
102.129,
360.998,
90,
90,
90
|
R / Rfree (%)
|
26.2 /
27.2
|
Other elements in 7qbd:
The structure of Tc:CD320 in Complex with Nanobody Tc-NB26 also contains other interesting chemical elements:
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Tc:CD320 in Complex with Nanobody Tc-NB26
(pdb code 7qbd). 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-NB26, PDB code: 7qbd:
Jump to Cobalt binding site number:
1;
2;
Cobalt binding site 1 out
of 2 in 7qbd
Go back to
Cobalt Binding Sites List in 7qbd
Cobalt binding site 1 out
of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB26
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-NB26 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co501
b:148.3
occ:1.00
|
CO
|
A:CNC501
|
0.0
|
148.3
|
1.0
|
N24
|
A:CNC501
|
1.7
|
160.1
|
0.6
|
N21
|
A:CNC501
|
1.8
|
154.8
|
1.0
|
N23
|
A:CNC501
|
1.9
|
157.3
|
1.0
|
N22
|
A:CNC501
|
1.9
|
158.2
|
0.1
|
C1A
|
A:CNC501
|
2.1
|
155.4
|
1.0
|
N3B
|
A:CNC501
|
2.5
|
151.4
|
1.0
|
C19
|
A:CNC501
|
2.6
|
160.9
|
1.0
|
C1
|
A:CNC501
|
2.8
|
159.2
|
1.0
|
C9
|
A:CNC501
|
2.9
|
158.9
|
1.0
|
C11
|
A:CNC501
|
2.9
|
160.6
|
1.0
|
C16
|
A:CNC501
|
2.9
|
162.2
|
1.0
|
C14
|
A:CNC501
|
3.0
|
160.1
|
1.0
|
C6
|
A:CNC501
|
3.0
|
157.8
|
1.0
|
C4
|
A:CNC501
|
3.0
|
156.1
|
1.0
|
N1A
|
A:CNC501
|
3.3
|
153.8
|
1.0
|
C10
|
A:CNC501
|
3.4
|
159.3
|
0.8
|
C2B
|
A:CNC501
|
3.4
|
154.1
|
1.0
|
C5
|
A:CNC501
|
3.4
|
155.7
|
1.0
|
C15
|
A:CNC501
|
3.5
|
163.7
|
1.0
|
C9B
|
A:CNC501
|
3.6
|
153.3
|
1.0
|
C20
|
A:CNC501
|
3.7
|
161.3
|
0.6
|
C18
|
A:CNC501
|
3.9
|
157.8
|
1.0
|
C26
|
A:CNC501
|
3.9
|
158.6
|
1.0
|
C2
|
A:CNC501
|
4.0
|
159.0
|
0.9
|
C4B
|
A:CNC501
|
4.0
|
151.1
|
1.0
|
C12
|
A:CNC501
|
4.1
|
157.6
|
1.0
|
C17
|
A:CNC501
|
4.1
|
157.9
|
1.0
|
C8
|
A:CNC501
|
4.1
|
156.7
|
1.0
|
C13
|
A:CNC501
|
4.2
|
161.8
|
1.0
|
C3
|
A:CNC501
|
4.2
|
162.1
|
1.0
|
C7
|
A:CNC501
|
4.3
|
155.9
|
1.0
|
C30
|
A:CNC501
|
4.3
|
159.9
|
1.0
|
C47
|
A:CNC501
|
4.6
|
160.7
|
1.0
|
N1B
|
A:CNC501
|
4.6
|
156.3
|
1.0
|
C41
|
A:CNC501
|
4.7
|
156.1
|
1.0
|
C8B
|
A:CNC501
|
4.7
|
155.4
|
1.0
|
C35
|
A:CNC501
|
4.9
|
155.2
|
1.0
|
C53
|
A:CNC501
|
4.9
|
165.3
|
1.0
|
|
Cobalt binding site 2 out
of 2 in 7qbd
Go back to
Cobalt Binding Sites List in 7qbd
Cobalt binding site 2 out
of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB26
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-NB26 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co501
b:138.2
occ:1.00
|
CO
|
B:CNC501
|
0.0
|
138.2
|
1.0
|
N24
|
B:CNC501
|
1.7
|
155.9
|
1.0
|
N21
|
B:CNC501
|
1.8
|
150.7
|
1.0
|
N23
|
B:CNC501
|
1.9
|
143.4
|
1.0
|
N22
|
B:CNC501
|
1.9
|
146.8
|
0.9
|
C1A
|
B:CNC501
|
2.1
|
148.2
|
1.0
|
N3B
|
B:CNC501
|
2.5
|
131.1
|
1.0
|
C19
|
B:CNC501
|
2.6
|
156.3
|
1.0
|
C1
|
B:CNC501
|
2.8
|
154.2
|
1.0
|
C9
|
B:CNC501
|
2.9
|
152.2
|
1.0
|
C11
|
B:CNC501
|
2.9
|
151.9
|
1.0
|
C16
|
B:CNC501
|
2.9
|
154.8
|
1.0
|
C14
|
B:CNC501
|
3.0
|
145.4
|
1.0
|
C6
|
B:CNC501
|
3.0
|
147.6
|
1.0
|
C4
|
B:CNC501
|
3.0
|
148.8
|
1.0
|
N1A
|
B:CNC501
|
3.3
|
146.0
|
1.0
|
C10
|
B:CNC501
|
3.4
|
155.4
|
0.4
|
C2B
|
B:CNC501
|
3.4
|
136.0
|
1.0
|
C5
|
B:CNC501
|
3.4
|
149.6
|
1.0
|
C15
|
B:CNC501
|
3.5
|
150.1
|
1.0
|
C9B
|
B:CNC501
|
3.6
|
137.6
|
1.0
|
C20
|
B:CNC501
|
3.7
|
152.7
|
1.0
|
C18
|
B:CNC501
|
3.9
|
151.6
|
1.0
|
C26
|
B:CNC501
|
3.9
|
150.1
|
1.0
|
C2
|
B:CNC501
|
4.0
|
150.5
|
0.8
|
C4B
|
B:CNC501
|
4.0
|
140.2
|
1.0
|
C12
|
B:CNC501
|
4.1
|
152.4
|
1.0
|
C17
|
B:CNC501
|
4.1
|
153.0
|
1.0
|
C8
|
B:CNC501
|
4.1
|
151.0
|
1.0
|
C13
|
B:CNC501
|
4.2
|
148.2
|
1.0
|
C3
|
B:CNC501
|
4.2
|
146.2
|
1.0
|
C7
|
B:CNC501
|
4.3
|
148.4
|
1.0
|
C30
|
B:CNC501
|
4.3
|
141.2
|
1.0
|
C47
|
B:CNC501
|
4.6
|
157.2
|
1.0
|
N1B
|
B:CNC501
|
4.6
|
139.5
|
0.7
|
C41
|
B:CNC501
|
4.7
|
146.0
|
1.0
|
C8B
|
B:CNC501
|
4.7
|
140.1
|
1.0
|
C35
|
B:CNC501
|
4.9
|
153.0
|
1.0
|
C53
|
B:CNC501
|
4.9
|
152.7
|
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: Tue Jul 30 19:22:44 2024
|