Cobalt in PDB 7qbd: Tc:CD320 in Complex with Nanobody Tc-NB26

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

The structure of Tc:CD320 in Complex with Nanobody Tc-NB26 also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

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 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 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

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