Cobalt in PDB 7qbe: Tc:CD320 in Complex with Nanobody Tc-NB11

The structure of Tc:CD320 in Complex with Nanobody Tc-NB11, PDB code: 7qbe 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)	48.96 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.717, 195.831, 198.385, 90, 90, 90
R / Rfree (%)	25.2 / 28.4

The structure of Tc:CD320 in Complex with Nanobody Tc-NB11 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Cobalt atom in the Tc:CD320 in Complex with Nanobody Tc-NB11 (pdb code 7qbe). 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-NB11, PDB code: 7qbe:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB11


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-NB11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:96.9 occ:1.00 CO A:CNC501 0.0 96.9 1.0 N24 A:CNC501 1.7 55.0 1.0 N21 A:CNC501 1.8 57.6 1.0 N22 A:CNC501 1.8 59.2 1.0 N23 A:CNC501 1.8 59.5 1.0 C1A A:CNC501 2.1 61.2 1.0 N3B A:CNC501 2.3 48.4 1.0 C19 A:CNC501 2.7 55.9 1.0 C9 A:CNC501 2.8 54.8 1.0 C1 A:CNC501 2.9 55.2 1.0 C4 A:CNC501 2.9 53.0 0.0 C11 A:CNC501 2.9 67.4 1.0 C6 A:CNC501 2.9 59.6 1.0 C14 A:CNC501 2.9 64.9 1.0 C16 A:CNC501 2.9 58.7 1.0 C2B A:CNC501 3.2 47.7 1.0 N1A A:CNC501 3.3 71.1 1.0 C9B A:CNC501 3.3 51.6 1.0 C5 A:CNC501 3.4 52.9 1.0 C10 A:CNC501 3.4 52.8 1.0 C15 A:CNC501 3.4 55.5 1.0 C20 A:CNC501 3.7 43.8 1.0 C3 A:CNC501 3.9 54.2 1.0 C2 A:CNC501 3.9 48.5 1.0 C26 A:CNC501 3.9 45.7 1.0 C4B A:CNC501 3.9 47.0 1.0 C18 A:CNC501 4.0 47.8 1.0 C12 A:CNC501 4.1 56.5 1.0 C8 A:CNC501 4.1 43.5 1.0 C17 A:CNC501 4.2 45.8 1.0 C47 A:CNC501 4.3 40.4 1.0 C7 A:CNC501 4.3 49.6 1.0 N1B A:CNC501 4.4 48.2 1.0 C13 A:CNC501 4.4 69.8 1.0 C48 A:CNC501 4.4 72.7 1.0 C8B A:CNC501 4.5 47.7 1.0 C41 A:CNC501 4.6 41.4 1.0 C35 A:CNC501 4.8 51.4 1.0 C56 A:CNC501 5.0 45.2 1.0

Cobalt binding site 2 out of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB11


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-NB11 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co501 b:82.3 occ:1.00 CO C:CNC501 0.0 82.3 1.0 N24 C:CNC501 1.7 80.5 1.0 N21 C:CNC501 1.7 75.0 1.0 N22 C:CNC501 1.8 80.5 1.0 N23 C:CNC501 1.8 81.9 1.0 C1A C:CNC501 2.1 84.4 1.0 N3B C:CNC501 2.5 69.5 1.0 C19 C:CNC501 2.6 75.6 1.0 C1 C:CNC501 2.8 74.5 1.0 C9 C:CNC501 2.8 77.6 1.0 C4 C:CNC501 2.8 74.4 0.2 C11 C:CNC501 2.9 85.1 1.0 C16 C:CNC501 2.9 79.5 1.0 C6 C:CNC501 2.9 77.7 1.0 C14 C:CNC501 2.9 88.5 1.0 N1A C:CNC501 3.3 86.2 1.0 C2B C:CNC501 3.3 77.7 1.0 C5 C:CNC501 3.4 73.2 1.0 C15 C:CNC501 3.4 80.8 1.0 C10 C:CNC501 3.4 82.4 1.0 C20 C:CNC501 3.7 69.9 1.0 C9B C:CNC501 3.7 72.1 1.0 C26 C:CNC501 3.9 64.1 1.0 C2 C:CNC501 3.9 71.7 1.0 C3 C:CNC501 3.9 73.6 1.0 C18 C:CNC501 3.9 71.4 1.0 C17 C:CNC501 4.0 69.1 1.0 C12 C:CNC501 4.1 84.3 1.0 C8 C:CNC501 4.1 76.7 1.0 C47 C:CNC501 4.2 74.2 1.0 C7 C:CNC501 4.2 76.8 0.3 C4B C:CNC501 4.3 73.0 1.0 C13 C:CNC501 4.4 107.1 1.0 C48 C:CNC501 4.4 107.1 1.0 C41 C:CNC501 4.5 73.1 1.0 N1B C:CNC501 4.6 77.5 1.0 C35 C:CNC501 4.7 72.8 1.0 C8B C:CNC501 4.7 77.0 1.0 C56 C:CNC501 4.9 76.9 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