Cobalt in PDB 7qbg: Tc:CD320 in Complex with Nanobody Tc-NB4

The structure of Tc:CD320 in Complex with Nanobody Tc-NB4, PDB code: 7qbg 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)	48.92 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.339, 116.418, 125.498, 90, 90, 90
R / Rfree (%)	22.7 / 28.5

The structure of Tc:CD320 in Complex with Nanobody Tc-NB4 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-NB4 (pdb code 7qbg). 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-NB4, PDB code: 7qbg:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB4


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-NB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:41.2 occ:1.00 CO A:CNC501 0.0 41.2 1.0 N24 A:CNC501 1.7 46.7 1.0 N21 A:CNC501 1.8 47.1 1.0 N22 A:CNC501 1.9 42.4 0.0 N23 A:CNC501 1.9 50.3 1.0 C1A A:CNC501 2.0 45.5 1.0 C19 A:CNC501 2.7 42.4 1.0 C4 A:CNC501 2.8 44.6 0.7 C1 A:CNC501 2.9 36.2 1.0 N3B A:CNC501 2.9 27.8 1.0 C16 A:CNC501 2.9 45.0 1.0 C9 A:CNC501 2.9 45.9 1.0 C14 A:CNC501 3.0 51.4 1.0 C6 A:CNC501 3.0 43.7 1.0 C11 A:CNC501 3.0 44.7 1.0 N1A A:CNC501 3.2 44.6 1.0 C5 A:CNC501 3.3 44.4 1.0 C15 A:CNC501 3.5 47.1 1.0 C10 A:CNC501 3.5 40.4 0.6 C2B A:CNC501 3.7 32.4 1.0 C20 A:CNC501 3.7 37.8 0.4 C26 A:CNC501 3.9 37.0 1.0 C9B A:CNC501 3.9 37.6 1.0 C18 A:CNC501 3.9 42.2 1.0 C3 A:CNC501 3.9 41.9 1.0 C7 A:CNC501 3.9 43.6 1.0 C12 A:CNC501 4.0 45.2 1.0 C47 A:CNC501 4.0 43.7 1.0 C2 A:CNC501 4.0 43.3 1.0 C8 A:CNC501 4.0 37.6 1.0 C17 A:CNC501 4.1 43.9 1.0 C13 A:CNC501 4.2 43.6 1.0 C4B A:CNC501 4.3 36.8 1.0 C41 A:CNC501 4.7 31.0 1.0 C37 A:CNC501 4.7 40.3 1.0 C35 A:CNC501 4.8 43.3 1.0 N1B A:CNC501 4.9 35.9 0.4 C53 A:CNC501 4.9 53.1 1.0

Cobalt binding site 2 out of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB4


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-NB4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co501 b:56.0 occ:1.00 CO C:CNC501 0.0 56.0 1.0 N24 C:CNC501 1.7 50.3 1.0 N21 C:CNC501 1.8 49.7 1.0 N22 C:CNC501 1.9 51.9 0.4 N23 C:CNC501 1.9 51.1 1.0 C1A C:CNC501 2.0 55.6 1.0 N3B C:CNC501 2.5 38.8 1.0 C19 C:CNC501 2.7 49.4 1.0 C1 C:CNC501 2.8 47.9 1.0 C9 C:CNC501 2.9 51.8 1.0 C4 C:CNC501 2.9 47.9 0.0 C6 C:CNC501 3.0 53.6 1.0 C14 C:CNC501 3.0 48.9 1.0 C16 C:CNC501 3.0 50.6 1.0 C11 C:CNC501 3.0 51.7 1.0 N1A C:CNC501 3.2 58.9 1.0 C2B C:CNC501 3.3 39.3 1.0 C5 C:CNC501 3.4 47.8 1.0 C10 C:CNC501 3.5 51.4 1.0 C15 C:CNC501 3.6 50.7 1.0 C9B C:CNC501 3.6 43.8 1.0 C26 C:CNC501 3.7 42.9 1.0 C20 C:CNC501 3.8 43.5 0.5 C2 C:CNC501 3.9 49.0 1.0 C3 C:CNC501 3.9 49.2 1.0 C18 C:CNC501 4.0 44.0 1.0 C8 C:CNC501 4.0 49.8 1.0 C7 C:CNC501 4.0 48.9 1.0 C12 C:CNC501 4.1 51.4 1.0 C47 C:CNC501 4.1 49.7 1.0 C4B C:CNC501 4.2 41.5 1.0 C17 C:CNC501 4.2 48.2 1.0 C13 C:CNC501 4.3 44.6 1.0 C41 C:CNC501 4.5 45.3 1.0 N1B C:CNC501 4.5 42.9 1.0 C8B C:CNC501 4.7 42.4 1.0 C37 C:CNC501 4.8 51.7 1.0 C35 C:CNC501 4.9 50.0 0.2

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