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Cobalt in PDB 5cjv: Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A

Enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A

All present enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A:
5.4.99.2;

Protein crystallography data

The structure of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A, PDB code: 5cjv 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) 34.91 / 3.45
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 317.560, 317.560, 343.520, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 21.4

Other elements in 5cjv:

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

Magnesium (Mg) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A (pdb code 5cjv). 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, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A, PDB code: 5cjv:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 5cjv

Go back to Cobalt Binding Sites List in 5cjv
Cobalt binding site 1 out of 2 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A


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, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1101

b:60.0
occ:1.00
 CO A:B121101 0.0 60.0 1.0
N21 A:B121101 1.9 57.9 1.0
N24 A:B121101 1.9 54.7 1.0
N23 A:B121101 1.9 60.0 1.0
N22 A:B121101 1.9 61.6 1.0
C5' A:5AD1102 2.2 0.9 0.5
NE2 A:HIS39 2.4 63.0 1.0
C19 A:B121101 2.8 54.0 1.0
C9 A:B121101 2.9 63.3 1.0
C1 A:B121101 2.9 59.7 1.0
C4 A:B121101 2.9 58.2 1.0
C11 A:B121101 2.9 60.2 1.0
C14 A:B121101 3.0 58.0 1.0
C16 A:B121101 3.0 55.5 1.0
C6 A:B121101 3.0 60.4 1.0
C10 A:B121101 3.2 62.1 1.0
CE1 A:HIS39 3.3 61.7 1.0
C5 A:B121101 3.4 62.9 1.0
C15 A:B121101 3.4 56.8 1.0
CD2 A:HIS39 3.5 65.0 1.0
C20 A:B121101 3.5 63.9 1.0
C5' A:5AD1102 3.6 0.2 0.5
C4' A:5AD1102 3.6 0.9 0.5
C2 A:B121101 4.1 55.0 1.0
C18 A:B121101 4.1 53.8 1.0
C3 A:B121101 4.2 55.9 1.0
C12 A:B121101 4.2 58.8 1.0
C8 A:B121101 4.2 64.5 1.0
C17 A:B121101 4.3 52.6 1.0
C13 A:B121101 4.3 58.9 1.0
C7 A:B121101 4.3 57.9 1.0
ND1 A:HIS39 4.4 63.6 1.0
C3' A:5AD1102 4.5 0.8 0.5
C26 A:B121101 4.5 58.2 1.0
O4' A:5AD1102 4.5 0.6 0.5
C4' A:5AD1102 4.6 0.8 0.5
CG A:HIS39 4.6 66.4 1.0
C3' A:5AD1102 4.6 0.8 0.5
C35 A:B121101 4.8 68.3 1.0
C53 A:B121101 4.9 56.2 1.0
C46 A:B121101 4.9 54.8 1.0
C48 A:B121101 4.9 62.5 1.0
O4' A:5AD1102 4.9 0.5 0.5

Cobalt binding site 2 out of 2 in 5cjv

Go back to Cobalt Binding Sites List in 5cjv
Cobalt binding site 2 out of 2 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A


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, Mg (Holo-Icmf/Gdp), and Substrate Isovaleryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1101

b:0.2
occ:1.00
 CO B:B121101 0.0 0.2 1.0
N21 B:B121101 1.9 0.1 1.0
N24 B:B121101 1.9 0.4 1.0
N23 B:B121101 1.9 0.5 1.0
N22 B:B121101 1.9 0.8 1.0
NE2 B:HIS39 2.5 94.1 1.0
C19 B:B121101 2.8 0.2 1.0
C9 B:B121101 2.9 0.8 1.0
C1 B:B121101 2.9 0.3 1.0
C4 B:B121101 2.9 0.1 1.0
C11 B:B121101 2.9 0.9 1.0
C14 B:B121101 3.0 0.9 1.0
C16 B:B121101 3.0 0.5 1.0
C6 B:B121101 3.0 0.7 1.0
CD2 B:HIS39 3.3 94.0 1.0
C10 B:B121101 3.3 0.7 1.0
C5 B:B121101 3.3 0.6 1.0
C15 B:B121101 3.4 0.6 1.0
C20 B:B121101 3.5 0.7 1.0
CE1 B:HIS39 3.5 96.0 1.0
C18 B:B121101 4.1 0.5 1.0
C2 B:B121101 4.1 0.8 1.0
C3 B:B121101 4.2 0.7 1.0
C8 B:B121101 4.2 0.2 1.0
C12 B:B121101 4.2 0.5 1.0
C17 B:B121101 4.3 0.5 1.0
C13 B:B121101 4.3 0.5 1.0
C7 B:B121101 4.3 0.1 1.0
CG B:HIS39 4.5 92.9 1.0
ND1 B:HIS39 4.6 94.8 1.0
C26 B:B121101 4.6 1.0 1.0
C35 B:B121101 4.8 0.1 1.0
C48 B:B121101 4.8 0.7 1.0
C53 B:B121101 4.9 0.4 1.0
C46 B:B121101 4.9 0.8 1.0

Reference:

M.Jost, D.A.Born, V.Cracan, R.Banerjee, C.L.Drennan. Structural Basis For Substrate Specificity in Adenosylcobalamin-Dependent Isobutyryl-Coa Mutase and Related Acyl-Coa Mutases. J.Biol.Chem. V. 290 26882 2015.
ISSN: ESSN 1083-351X
PubMed: 26318610
DOI: 10.1074/JBC.M115.676890
Page generated: Tue Jul 30 17:46:43 2024

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