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

Protein crystallography data

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

Other elements in 3kq4:

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

Calcium (Ca) 12 atoms

Cobalt Binding Sites:

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 3kq4

Go back to Cobalt Binding Sites List in 3kq4
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 3kq4

Go back to Cobalt Binding Sites List in 3kq4
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 3kq4

Go back to Cobalt Binding Sites List in 3kq4
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

Reference:

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
Page generated: Sun Dec 13 10:41:19 2020

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