Cobalt in PDB 3kq4: Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin

The structure of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin, PDB code: 3kq4 was solved by C.B.F.Andersen, M.Madsen, S.K.Moestrup, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.85 / 3.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.684, 204.179, 410.023, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.3

The structure of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Cobalt atom in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin (pdb code 3kq4). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin, PDB code: 3kq4:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2007 b:74.1 occ:1.00 CO A:B122007 0.0 74.1 1.0 N24 A:B122007 1.8 63.0 1.0 N23 A:B122007 1.9 66.7 1.0 N22 A:B122007 1.9 60.3 1.0 N21 A:B122007 1.9 61.7 1.0 N3B A:B122007 2.1 48.4 1.0 C19 A:B122007 2.7 63.0 1.0 C14 A:B122007 2.8 63.7 1.0 C4 A:B122007 2.9 67.3 1.0 C6 A:B122007 2.9 63.6 1.0 C9 A:B122007 2.9 59.8 1.0 C1 A:B122007 2.9 61.6 1.0 C11 A:B122007 2.9 61.4 1.0 C16 A:B122007 2.9 67.5 1.0 C9B A:B122007 3.0 69.3 1.0 C2B A:B122007 3.1 71.9 1.0 C5 A:B122007 3.3 73.1 1.0 C10 A:B122007 3.3 56.4 1.0 C15 A:B122007 3.3 68.0 1.0 C4B A:B122007 3.5 70.3 1.0 C20 A:B122007 3.9 79.1 1.0 C2 A:B122007 4.0 71.8 1.0 C18 A:B122007 4.1 68.5 1.0 C3 A:B122007 4.1 70.5 1.0 C13 A:B122007 4.1 66.2 1.0 C7 A:B122007 4.1 64.5 1.0 C17 A:B122007 4.2 73.9 1.0 C8 A:B122007 4.2 61.0 1.0 C8B A:B122007 4.2 58.9 1.0 N1B A:B122007 4.3 62.4 1.0 C12 A:B122007 4.3 58.6 1.0 C26 A:B122007 4.3 76.7 1.0 C35 A:B122007 4.7 79.2 1.0 C53 A:B122007 4.8 69.6 1.0 C54 A:B122007 4.9 83.9 1.0 C5B A:B122007 4.9 67.6 1.0 C37 A:B122007 4.9 80.4 1.0 C48 A:B122007 5.0 62.5 1.0

Cobalt binding site 2 out of 3 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range: probe atom residue distance (Å) B Occ C:Co2007 b:74.4 occ:1.00 CO C:B122007 0.0 74.4 1.0 N24 C:B122007 1.8 62.0 1.0 N23 C:B122007 1.9 70.6 1.0 N22 C:B122007 1.9 61.8 1.0 N21 C:B122007 1.9 58.7 1.0 N3B C:B122007 2.1 50.0 1.0 C19 C:B122007 2.7 59.1 1.0 C14 C:B122007 2.8 68.2 1.0 C4 C:B122007 2.9 62.9 1.0 C6 C:B122007 2.9 63.5 1.0 C9 C:B122007 2.9 64.1 1.0 C1 C:B122007 2.9 56.3 1.0 C11 C:B122007 2.9 67.7 1.0 C16 C:B122007 2.9 67.3 1.0 C9B C:B122007 3.0 70.5 1.0 C2B C:B122007 3.1 74.4 1.0 C5 C:B122007 3.3 70.1 1.0 C10 C:B122007 3.3 63.0 1.0 C15 C:B122007 3.3 70.6 1.0 C4B C:B122007 3.5 70.7 1.0 C20 C:B122007 3.9 73.4 1.0 C2 C:B122007 4.0 63.7 1.0 C18 C:B122007 4.1 63.8 1.0 C3 C:B122007 4.1 62.8 1.0 C13 C:B122007 4.1 73.6 1.0 C7 C:B122007 4.1 66.2 1.0 C17 C:B122007 4.2 71.5 1.0 C8 C:B122007 4.2 65.8 1.0 C8B C:B122007 4.2 61.0 1.0 N1B C:B122007 4.3 65.1 1.0 C12 C:B122007 4.3 67.5 1.0 C26 C:B122007 4.3 67.9 1.0 C35 C:B122007 4.7 74.3 1.0 C53 C:B122007 4.8 73.2 1.0 C54 C:B122007 4.9 80.4 1.0 C5B C:B122007 4.9 68.0 1.0 C37 C:B122007 4.9 81.9 1.0 C48 C:B122007 5.0 69.9 1.0

Cobalt binding site 3 out of 3 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range: probe atom residue distance (Å) B Occ E:Co2007 b:78.9 occ:1.00 CO E:B122007 0.0 78.9 1.0 N24 E:B122007 1.8 66.2 1.0 N23 E:B122007 1.9 73.7 1.0 N22 E:B122007 1.9 65.6 1.0 N21 E:B122007 1.9 63.8 1.0 N3B E:B122007 2.1 50.5 1.0 C19 E:B122007 2.7 64.6 1.0 C14 E:B122007 2.8 70.0 1.0 C4 E:B122007 2.9 70.1 1.0 C6 E:B122007 2.9 69.5 1.0 C9 E:B122007 2.9 66.8 1.0 C1 E:B122007 2.9 62.3 1.0 C11 E:B122007 2.9 68.7 1.0 C16 E:B122007 2.9 71.4 1.0 C9B E:B122007 3.0 70.0 1.0 C2B E:B122007 3.1 73.0 1.0 C5 E:B122007 3.3 77.8 1.0 C10 E:B122007 3.3 63.7 1.0 C15 E:B122007 3.3 73.3 1.0 C4B E:B122007 3.5 71.1 1.0 C20 E:B122007 3.9 77.1 1.0 C2 E:B122007 4.0 72.5 1.0 C18 E:B122007 4.1 69.1 1.0 C3 E:B122007 4.1 71.7 1.0 C13 E:B122007 4.1 73.0 1.0 C7 E:B122007 4.1 72.3 1.0 C17 E:B122007 4.2 76.6 1.0 C8 E:B122007 4.2 69.1 1.0 C8B E:B122007 4.2 58.0 1.0 N1B E:B122007 4.3 61.7 1.0 C12 E:B122007 4.3 66.5 1.0 C26 E:B122007 4.3 79.5 1.0 C35 E:B122007 4.7 84.3 1.0 C53 E:B122007 4.8 75.6 1.0 C54 E:B122007 4.9 88.4 1.0 C5B E:B122007 4.9 66.8 1.0 C37 E:B122007 4.9 91.1 1.0 C48 E:B122007 5.0 67.2 1.0

C.B.Andersen, M.Madsen, T.Storm, S.K.Moestrup, G.R.Andersen. Structural Basis For Receptor Recognition of Vitamin-B(12)-Intrinsic Factor Complexes. Nature V. 464 445 2010.
ISSN: ISSN 0028-0836
PubMed: 20237569
DOI: 10.1038/NATURE08874