Cobalt in PDB 4xc6: Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp)

All present enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp):
5.4.99.13;

The structure of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp), PDB code: 4xc6 was solved by M.Jost, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.69 / 3.35
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	318.760, 318.760, 343.520, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 19.8

The structure of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp) also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Cobalt atom in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp) (pdb code 4xc6). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp), PDB code: 4xc6:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1101 b:52.2 occ:1.00 CO A:B121101 0.0 52.2 1.0 N21 A:B121101 1.9 53.3 1.0 N24 A:B121101 1.9 47.3 1.0 N23 A:B121101 1.9 57.0 1.0 N22 A:B121101 1.9 57.5 1.0 NE2 A:HIS39 2.5 62.5 1.0 C19 A:B121101 2.8 47.7 1.0 C9 A:B121101 2.9 60.9 1.0 C1 A:B121101 2.9 48.2 1.0 C4 A:B121101 2.9 57.7 1.0 C11 A:B121101 2.9 56.5 1.0 C14 A:B121101 3.0 56.6 1.0 C16 A:B121101 3.0 59.8 1.0 C6 A:B121101 3.0 60.3 1.0 C10 A:B121101 3.2 57.8 1.0 CE1 A:HIS39 3.3 60.9 1.0 C5 A:B121101 3.3 61.0 1.0 C15 A:B121101 3.4 57.3 1.0 C5' A:5AD1102 3.4 0.7 1.0 C20 A:B121101 3.6 58.9 1.0 CD2 A:HIS39 3.6 63.6 1.0 C2 A:B121101 4.1 48.7 1.0 C18 A:B121101 4.1 47.9 1.0 C3 A:B121101 4.2 48.9 1.0 C12 A:B121101 4.2 49.0 1.0 C8 A:B121101 4.2 60.6 1.0 C13 A:B121101 4.3 54.9 1.0 C17 A:B121101 4.3 47.4 1.0 C7 A:B121101 4.3 54.9 1.0 C3' A:5AD1102 4.3 0.5 1.0 C4' A:5AD1102 4.4 0.7 1.0 ND1 A:HIS39 4.5 60.8 1.0 C26 A:B121101 4.5 62.9 1.0 CG A:HIS39 4.7 62.6 1.0 O3' A:5AD1102 4.7 1.0 1.0 C35 A:B121101 4.8 65.3 1.0 C46 A:B121101 4.8 45.9 1.0 C53 A:B121101 4.9 58.0 1.0 C48 A:B121101 4.9 58.0 1.0

Cobalt binding site 2 out of 2 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1101 b:88.1 occ:1.00 CO B:B121101 0.0 88.1 1.0 N21 B:B121101 1.9 0.1 1.0 N24 B:B121101 1.9 86.2 1.0 N23 B:B121101 1.9 96.3 1.0 N22 B:B121101 1.9 1.0 1.0 NE2 B:HIS39 2.4 90.9 1.0 C19 B:B121101 2.8 86.9 1.0 C1 B:B121101 2.9 0.3 1.0 C9 B:B121101 2.9 0.1 1.0 C4 B:B121101 2.9 0.0 1.0 C11 B:B121101 2.9 97.7 1.0 C14 B:B121101 3.0 92.2 1.0 C16 B:B121101 3.0 87.8 1.0 C6 B:B121101 3.0 0.9 1.0 CD2 B:HIS39 3.2 90.9 1.0 C10 B:B121101 3.3 0.1 1.0 C5 B:B121101 3.3 0.9 1.0 C15 B:B121101 3.4 89.2 1.0 C20 B:B121101 3.4 0.9 1.0 CE1 B:HIS39 3.6 92.3 1.0 C18 B:B121101 4.1 89.5 1.0 C2 B:B121101 4.1 0.7 1.0 C3 B:B121101 4.2 0.5 1.0 C8 B:B121101 4.2 0.4 1.0 C12 B:B121101 4.2 93.4 1.0 C13 B:B121101 4.3 89.9 1.0 C17 B:B121101 4.3 88.7 1.0 C7 B:B121101 4.3 0.4 1.0 CG B:HIS39 4.4 89.0 1.0 ND1 B:HIS39 4.6 90.6 1.0 C26 B:B121101 4.6 0.5 1.0 C35 B:B121101 4.8 0.9 1.0 C48 B:B121101 4.8 90.5 1.0 C53 B:B121101 4.9 87.6 1.0 C46 B:B121101 5.0 91.4 1.0

M.Jost, V.Cracan, P.A.Hubbard, R.Banerjee, C.L.Drennan. Visualization of A Radical B12 Enzyme with Its G-Protein Chaperone Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490