Cobalt in PDB 6d5x: Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate

All present enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate:
2.5.1.17;

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate, PDB code: 6d5x was solved by G.J.Dodge, G.Campanello, J.L.Smith, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.79 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.685, 112.685, 117.939, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 21.2

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Cobalt atom in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate (pdb code 6d5x). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate, PDB code: 6d5x:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:73.7 occ:0.88 CO A:B12302 0.0 73.7 0.9 N21 A:B12302 1.9 84.6 0.9 N24 A:B12302 1.9 77.1 0.9 N23 A:B12302 1.9 74.8 0.9 N22 A:B12302 1.9 82.1 0.9 C5' A:5AD301 2.1 74.7 0.9 C19 A:B12302 2.9 75.3 0.9 C9 A:B12302 2.9 65.9 0.9 C1 A:B12302 2.9 76.6 0.9 C4 A:B12302 2.9 82.0 0.9 C11 A:B12302 2.9 74.6 0.9 C14 A:B12302 3.0 73.7 0.9 C6 A:B12302 3.0 69.6 0.9 C16 A:B12302 3.0 72.9 0.9 C10 A:B12302 3.3 67.6 0.9 C5 A:B12302 3.3 81.9 0.9 C4' A:5AD301 3.3 76.3 0.9 C15 A:B12302 3.4 72.8 0.9 C20 A:B12302 3.5 75.7 0.9 CE1 A:PHE170 3.7 81.9 1.0 CZ A:PHE170 4.1 79.4 1.0 C18 A:B12302 4.1 78.7 0.9 C2 A:B12302 4.1 77.0 0.9 O4' A:5AD301 4.1 69.3 0.9 C3 A:B12302 4.2 82.1 0.9 C8 A:B12302 4.2 67.5 0.9 C12 A:B12302 4.2 57.5 0.9 C7 A:B12302 4.2 77.7 0.9 C13 A:B12302 4.2 65.6 0.9 C17 A:B12302 4.3 80.6 0.9 C3' A:5AD301 4.5 64.6 0.9 C26 A:B12302 4.5 66.3 0.9 O1G A:3PO305 4.5 83.4 0.8 C48 A:B12302 4.7 76.8 0.9 O3' A:5AD301 4.7 78.2 0.9 C37 A:B12302 4.7 70.4 0.9 C35 A:B12302 4.8 73.2 0.9 C47 A:B12302 4.8 58.1 0.9 C41 A:B12302 4.9 70.2 0.9 C53 A:B12302 4.9 62.5 0.9 CD1 A:PHE170 4.9 78.3 1.0

Cobalt binding site 2 out of 2 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:0.7 occ:0.84 CO B:B12302 0.0 0.7 0.8 N21 B:B12302 1.9 1.0 0.8 N24 B:B12302 1.9 0.8 0.8 N22 B:B12302 1.9 0.6 0.8 N23 B:B12302 1.9 0.6 0.8 C5' B:5AD301 2.1 98.0 0.8 C19 B:B12302 2.8 0.8 0.8 C9 B:B12302 2.9 94.2 0.8 C4 B:B12302 2.9 0.5 0.8 C1 B:B12302 2.9 0.4 0.8 C11 B:B12302 2.9 0.2 0.8 C6 B:B12302 2.9 96.2 0.8 C16 B:B12302 3.0 0.1 0.8 C14 B:B12302 3.0 0.8 0.8 C10 B:B12302 3.3 95.9 0.8 C5 B:B12302 3.3 92.2 0.8 C4' B:5AD301 3.4 98.5 0.8 C15 B:B12302 3.4 0.4 0.8 C20 B:B12302 3.5 99.3 0.8 CE2 B:PHE170 4.1 96.2 1.0 C18 B:B12302 4.1 99.7 0.8 C2 B:B12302 4.1 0.5 0.8 C3 B:B12302 4.2 0.2 0.8 CZ B:PHE170 4.2 0.7 1.0 C7 B:B12302 4.2 92.1 0.8 C8 B:B12302 4.2 91.3 0.8 C12 B:B12302 4.2 88.7 0.8 C17 B:B12302 4.3 0.8 0.8 O4' B:5AD301 4.3 0.0 0.8 C13 B:B12302 4.3 88.2 0.8 C3' B:5AD301 4.5 0.5 0.8 C26 B:B12302 4.6 95.8 0.8 O3' B:5AD301 4.7 99.9 0.8 C35 B:B12302 4.7 88.0 0.8 C37 B:B12302 4.7 90.3 0.8 C53 B:B12302 4.9 89.4 0.8 C49 B:B12302 4.9 92.2 0.8 C41 B:B12302 5.0 79.0 0.8 C47 B:B12302 5.0 81.6 0.8

G.C.Campanello, M.Ruetz, G.J.Dodge, H.Gouda, A.Gupta, U.T.Twahir, M.M.Killian, D.Watkins, D.S.Rosenblatt, T.C.Brunold, K.Warncke, J.L.Smith, R.Banerjee. Sacrificial Cobalt-Carbon Bond Homolysis in Coenzyme B12AS A Cofactor Conservation Strategy. J. Am. Chem. Soc. V. 140 13205 2018.
ISSN: ESSN 1520-5126
PubMed: 30282455
DOI: 10.1021/JACS.8B08659