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Cobalt in PDB 2pmv: Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution

Protein crystallography data

The structure of Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution, PDB code: 2pmv was solved by F.S.Mathews, M.M.Gordon, Z.Chen, K.R.Rajashankar, S.E.Ealick, D.H.Alpers, N.Sukumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.53 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.100, 67.300, 147.700, 90.00, 96.80, 90.00
R / Rfree (%) 21.3 / 24.9

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution (pdb code 2pmv). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution, PDB code: 2pmv:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 2pmv

Go back to Cobalt Binding Sites List in 2pmv
Cobalt binding site 1 out of 2 in the Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1001

b:68.5
occ:1.00
CO A:B121001 0.0 68.5 1.0
N21 A:B121001 1.9 39.7 1.0
N24 A:B121001 1.9 39.5 1.0
N22 A:B121001 2.0 41.5 1.0
N23 A:B121001 2.0 42.1 1.0
N3B A:B121001 2.2 40.7 1.0
C19 A:B121001 2.9 36.4 1.0
C4 A:B121001 2.9 40.0 1.0
C1 A:B121001 3.0 35.9 1.0
C9 A:B121001 3.0 42.2 1.0
C16 A:B121001 3.0 39.8 1.0
C11 A:B121001 3.0 43.2 1.0
C14 A:B121001 3.0 40.5 1.0
C6 A:B121001 3.1 39.5 1.0
C2B A:B121001 3.2 39.9 1.0
C9B A:B121001 3.3 38.1 1.0
C10 A:B121001 3.4 41.4 1.0
C5 A:B121001 3.4 42.5 1.0
C15 A:B121001 3.5 40.9 1.0
C20 A:B121001 3.5 32.7 1.0
C4B A:B121001 3.8 38.2 1.0
C18 A:B121001 4.2 39.7 1.0
C3 A:B121001 4.3 37.7 1.0
C2 A:B121001 4.3 37.2 1.0
C17 A:B121001 4.3 42.4 1.0
C8 A:B121001 4.4 42.0 1.0
C13 A:B121001 4.4 44.5 1.0
C7 A:B121001 4.4 39.8 1.0
C12 A:B121001 4.4 42.6 1.0
N1B A:B121001 4.5 38.1 1.0
C8B A:B121001 4.6 35.8 1.0
C26 A:B121001 4.8 30.7 1.0
C35 A:B121001 5.0 42.3 1.0

Cobalt binding site 2 out of 2 in 2pmv

Go back to Cobalt Binding Sites List in 2pmv
Cobalt binding site 2 out of 2 in the Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1002

b:65.0
occ:1.00
CO C:B121002 0.0 65.0 1.0
N21 C:B121002 1.9 45.1 1.0
N22 C:B121002 1.9 48.7 1.0
N24 C:B121002 2.0 37.9 1.0
N23 C:B121002 2.0 45.8 1.0
N3B C:B121002 2.2 51.7 1.0
C4 C:B121002 2.9 43.7 1.0
C19 C:B121002 2.9 41.5 1.0
C9 C:B121002 2.9 48.4 1.0
C1 C:B121002 3.0 42.0 1.0
C6 C:B121002 3.0 46.7 1.0
C11 C:B121002 3.0 46.0 1.0
C16 C:B121002 3.1 38.6 1.0
C14 C:B121002 3.1 42.9 1.0
C2B C:B121002 3.2 48.4 1.0
C10 C:B121002 3.3 44.8 1.0
C9B C:B121002 3.3 50.3 1.0
C5 C:B121002 3.4 47.7 1.0
C15 C:B121002 3.5 40.4 1.0
C20 C:B121002 3.5 40.8 1.0
C4B C:B121002 3.9 49.3 1.0
C18 C:B121002 4.2 39.5 1.0
C3 C:B121002 4.2 41.3 1.0
C2 C:B121002 4.3 42.6 1.0
C8 C:B121002 4.3 50.7 1.0
C7 C:B121002 4.3 50.1 1.0
C17 C:B121002 4.4 41.0 1.0
C13 C:B121002 4.4 46.5 1.0
C12 C:B121002 4.4 46.9 1.0
N1B C:B121002 4.4 50.5 1.0
C8B C:B121002 4.5 50.9 1.0
C26 C:B121002 4.8 40.4 1.0
C35 C:B121002 4.9 51.6 1.0

Reference:

F.S.Mathews, M.M.Gordon, Z.Chen, K.R.Rajashankar, S.E.Ealick, D.H.Alpers, N.Sukumar. Crystal Structure of Human Intrinsic Factor: Cobalamin Complex at 2.6-A Resolution Proc.Natl.Acad.Sci.Usa V. 104 17311 2007.
ISSN: ISSN 0027-8424
PubMed: 17954916
DOI: 10.1073/PNAS.0703228104
Page generated: Sun Dec 13 10:38:37 2020

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