Cobalt in PDB 6d5k: Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin

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

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin, PDB code: 6d5k 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)	48.61 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.252, 112.252, 117.993, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 23.9

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

Magnesium

(Mg)

2 atoms

The binding sites of Cobalt atom in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin (pdb code 6d5k). 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, and Adenosylcobalamin, PDB code: 6d5k:
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, and Adenosylcobalamin


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, and Adenosylcobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:78.9 occ:1.00 CO A:B12302 0.0 78.9 1.0 N21 A:B12302 1.9 80.9 1.0 N24 A:B12302 1.9 86.2 1.0 N23 A:B12302 1.9 76.9 1.0 N22 A:B12302 1.9 80.7 1.0 C5' A:5AD301 2.1 79.3 0.9 C9 A:B12302 2.8 75.2 1.0 C19 A:B12302 2.8 81.9 1.0 C11 A:B12302 2.9 67.8 1.0 C1 A:B12302 2.9 81.4 1.0 C4 A:B12302 2.9 84.7 1.0 C16 A:B12302 3.0 77.4 1.0 C6 A:B12302 3.0 80.1 1.0 C14 A:B12302 3.0 77.8 1.0 C10 A:B12302 3.2 76.3 1.0 C4' A:5AD301 3.3 77.6 0.9 C5 A:B12302 3.3 84.5 1.0 C15 A:B12302 3.4 75.0 1.0 C20 A:B12302 3.5 80.8 1.0 CE1 A:PHE170 3.7 72.2 1.0 CZ A:PHE170 4.0 78.1 1.0 C18 A:B12302 4.1 75.9 1.0 C2 A:B12302 4.1 82.2 1.0 O4' A:5AD301 4.1 81.9 0.9 C8 A:B12302 4.2 64.9 1.0 C12 A:B12302 4.2 66.5 1.0 C3 A:B12302 4.2 86.3 1.0 C7 A:B12302 4.2 71.6 1.0 C17 A:B12302 4.3 73.2 1.0 C13 A:B12302 4.3 68.9 1.0 C3' A:5AD301 4.5 80.2 0.9 C26 A:B12302 4.5 85.8 1.0 O3' A:5AD301 4.7 81.0 0.9 C37 A:B12302 4.7 76.8 1.0 C35 A:B12302 4.8 81.1 1.0 C41 A:B12302 4.8 59.8 1.0 C47 A:B12302 4.8 75.0 1.0 CD1 A:PHE170 4.9 71.7 1.0 C53 A:B12302 4.9 65.5 1.0

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


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, and Adenosylcobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co303 b:0.9 occ:0.88 CO A:B12303 0.0 0.9 0.9 N21 A:B12303 1.9 0.9 0.9 N24 A:B12303 1.9 0.8 0.9 N23 A:B12303 1.9 0.9 0.9 N22 A:B12303 1.9 0.7 0.9 C5' B:5AD301 2.0 0.1 1.0 C19 A:B12303 2.8 0.7 0.9 C4 A:B12303 2.9 0.2 0.9 C9 A:B12303 2.9 1.0 0.9 C1 A:B12303 2.9 0.7 0.9 C11 A:B12303 2.9 0.2 0.9 C6 A:B12303 3.0 0.3 0.9 C16 A:B12303 3.0 0.2 0.9 C14 A:B12303 3.0 0.9 0.9 C10 A:B12303 3.3 0.7 0.9 C5 A:B12303 3.3 0.2 0.9 C4' B:5AD301 3.4 0.8 1.0 C15 A:B12303 3.5 0.4 0.9 C20 A:B12303 3.6 0.9 0.9 C2 A:B12303 4.1 0.8 0.9 C18 A:B12303 4.1 0.2 0.9 CZ B:PHE170 4.2 0.7 1.0 C3 A:B12303 4.2 0.7 0.9 O4' B:5AD301 4.2 0.6 1.0 C8 A:B12303 4.2 0.9 0.9 C7 A:B12303 4.2 0.8 0.9 C12 A:B12303 4.3 0.7 0.9 C17 A:B12303 4.3 0.1 0.9 C13 A:B12303 4.3 0.6 0.9 C3' B:5AD301 4.4 0.6 1.0 C26 A:B12303 4.5 0.1 0.9 CE2 B:PHE170 4.7 0.1 1.0 C35 A:B12303 4.7 0.8 0.9 C37 A:B12303 4.7 0.8 0.9 O3' B:5AD301 4.8 0.2 1.0 C41 A:B12303 4.9 0.6 0.9 C53 A:B12303 5.0 0.4 0.9 NH2 B:ARG190 5.0 0.8 1.0 C47 A:B12303 5.0 0.6 0.9

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