Cobalt in PDB 5nrp: Beta Domain of Human Transcobalamin Bound to Cobinamide

The structure of Beta Domain of Human Transcobalamin Bound to Cobinamide, PDB code: 5nrp 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)	41.68 / 1.57
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.859, 59.859, 70.114, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 20.9

The binding sites of Cobalt atom in the Beta Domain of Human Transcobalamin Bound to Cobinamide (pdb code 5nrp). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Beta Domain of Human Transcobalamin Bound to Cobinamide, PDB code: 5nrp:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Beta Domain of Human Transcobalamin Bound to Cobinamide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Beta Domain of Human Transcobalamin Bound to Cobinamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:57.8 occ:1.00 CO A:CBY501 0.0 57.8 1.0 N24 A:CBY501 1.9 53.7 1.0 N23 A:CBY501 1.9 62.3 1.0 N22 A:CBY501 1.9 61.8 1.0 N21 A:CBY501 1.9 55.6 1.0 NE2 A:HIS345 2.3 50.6 1.0 C19 A:CBY501 2.7 58.3 1.0 C1 A:CBY501 2.8 59.0 1.0 C4 A:CBY501 2.8 58.4 1.0 H19 A:CBY501 2.8 70.0 1.0 C14 A:CBY501 2.9 61.8 1.0 C6 A:CBY501 2.9 64.9 1.0 C9 A:CBY501 2.9 62.6 1.0 C11 A:CBY501 2.9 62.2 1.0 C16 A:CBY501 2.9 57.5 1.0 C5 A:CBY501 3.3 62.2 1.0 CE1 A:HIS345 3.3 49.9 1.0 CD2 A:HIS345 3.3 50.7 1.0 C10 A:CBY501 3.3 62.3 1.0 C15 A:CBY501 3.3 58.0 1.0 HE1 A:HIS345 3.4 60.0 1.0 HD2 A:HIS345 3.4 60.9 1.0 H20B A:CBY501 3.4 69.2 1.0 C20 A:CBY501 3.7 57.6 1.0 H26A A:CBY501 3.9 78.1 1.0 C2 A:CBY501 4.0 61.8 1.0 C18 A:CBY501 4.0 57.5 1.0 C3 A:CBY501 4.1 60.6 1.0 C13 A:CBY501 4.1 66.5 1.0 C17 A:CBY501 4.2 59.8 1.0 C7 A:CBY501 4.2 69.8 1.0 C8 A:CBY501 4.2 69.4 1.0 C12 A:CBY501 4.2 64.5 1.0 H20A A:CBY501 4.2 69.2 1.0 H48A A:CBY501 4.3 87.8 1.0 H311 A:CBY501 4.4 74.8 1.0 ND1 A:HIS345 4.4 47.9 1.0 H18 A:CBY501 4.4 69.1 1.0 CG A:HIS345 4.4 46.6 1.0 C26 A:CBY501 4.5 65.0 1.0 H49A A:CBY501 4.5 95.8 1.0 H20 A:CBY501 4.5 69.2 1.0 H37 A:CBY501 4.6 88.2 1.0 H47A A:CBY501 4.6 77.0 1.0 H54A A:CBY501 4.6 70.2 1.0 H56A A:CBY501 4.7 86.9 1.0 C48 A:CBY501 4.7 73.1 1.0 H56 A:CBY501 4.7 86.9 1.0 C35 A:CBY501 4.7 64.0 1.0 H3 A:CBY501 4.8 72.7 1.0 H41 A:CBY501 4.8 89.0 1.0 C37 A:CBY501 4.8 73.4 1.0 C53 A:CBY501 4.8 60.4 1.0 H37A A:CBY501 4.8 88.2 1.0 H8 A:CBY501 4.9 83.4 1.0 H30 A:CBY501 4.9 77.6 1.0 H26 A:CBY501 4.9 78.1 1.0 C54 A:CBY501 4.9 58.5 1.0 H13 A:CBY501 5.0 79.8 1.0 C30 A:CBY501 5.0 64.6 1.0

Cobalt binding site 2 out of 2 in the Beta Domain of Human Transcobalamin Bound to Cobinamide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Beta Domain of Human Transcobalamin Bound to Cobinamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Co502 b:52.8 occ:1.00 CO A:CBY502 0.0 52.8 1.0 C A:CYN503 1.8 46.4 1.0 N24 A:CBY502 1.9 55.9 1.0 N21 A:CBY502 1.9 52.5 1.0 N22 A:CBY502 1.9 47.9 1.0 N23 A:CBY502 1.9 51.4 1.0 C19 A:CBY502 2.7 55.7 1.0 H19 A:CBY502 2.8 66.9 1.0 C4 A:CBY502 2.8 49.2 1.0 C1 A:CBY502 2.8 55.3 1.0 C14 A:CBY502 2.8 53.2 1.0 C6 A:CBY502 2.9 44.8 1.0 C9 A:CBY502 2.9 43.5 1.0 C11 A:CBY502 2.9 46.9 1.0 C16 A:CBY502 2.9 56.0 1.0 N A:CYN503 3.0 51.6 1.0 C5 A:CBY502 3.2 46.7 1.0 C15 A:CBY502 3.3 55.5 1.0 C10 A:CBY502 3.3 44.2 1.0 H20B A:CBY502 3.5 68.4 1.0 C20 A:CBY502 3.8 57.0 1.0 H26 A:CBY502 3.9 77.3 1.0 C2 A:CBY502 4.0 59.4 1.0 C18 A:CBY502 4.0 60.3 1.0 C3 A:CBY502 4.1 54.5 1.0 C13 A:CBY502 4.1 54.5 1.0 C17 A:CBY502 4.2 59.3 1.0 C8 A:CBY502 4.2 40.3 1.0 C7 A:CBY502 4.2 40.6 1.0 C12 A:CBY502 4.2 47.8 1.0 H20 A:CBY502 4.2 68.4 1.0 H311 A:CBY502 4.3 53.1 1.0 H18 A:CBY502 4.3 72.5 1.0 C26 A:CBY502 4.4 64.4 1.0 H48 A:CBY502 4.4 73.5 1.0 H20A A:CBY502 4.5 68.4 1.0 H54 A:CBY502 4.5 69.7 1.0 H48A A:CBY502 4.6 73.5 1.0 C35 A:CBY502 4.6 49.4 1.0 H41A A:CBY502 4.6 46.4 1.0 H56A A:CBY502 4.6 76.1 1.0 H3 A:CBY502 4.7 65.5 1.0 C48 A:CBY502 4.7 61.2 1.0 H37 A:CBY502 4.7 45.0 1.0 H41 A:CBY502 4.7 46.4 1.0 H26A A:CBY502 4.7 77.3 1.0 C41 A:CBY502 4.8 38.6 1.0 C53 A:CBY502 4.8 57.6 1.0 H35B A:CBY502 4.8 59.3 1.0 H13 A:CBY502 4.8 65.5 1.0 H47B A:CBY502 4.8 61.5 1.0 H8 A:CBY502 4.9 48.4 1.0 C54 A:CBY502 4.9 58.0 1.0 H46A A:CBY502 4.9 58.0 1.0 H30 A:CBY502 4.9 69.0 1.0 C37 A:CBY502 4.9 37.4 1.0 H35 A:CBY502 5.0 59.3 1.0 C30 A:CBY502 5.0 57.4 1.0

J.S.Bloch, M.Ruetz, B.Krautler, K.P.Locher. Structure of the Human Transcobalamin Beta Domain in Four Distinct States. Plos One V. 12 84932 2017.
ISSN: ESSN 1932-6203
PubMed: 28910388
DOI: 10.1371/JOURNAL.PONE.0184932