Cobalt in PDB 7qbf: Tc:CD320 in Complex with Nanobody Tc-NB34

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

The structure of Tc:CD320 in Complex with Nanobody Tc-NB34 also contains other interesting chemical elements:

Iodine	(I)	16 atoms
Calcium	(Ca)	2 atoms

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 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 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

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