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

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

All present enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isobutyryl-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 Isobutyryl-Coenzyme A, PDB code: 5cjt 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) 34.82 / 3.40
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 316.840, 316.840, 342.650, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 20.9

Other elements in 5cjt:

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

Cobalt binding site 1 out of 2 in 5cjt

Go back to Cobalt Binding Sites List in 5cjt
Cobalt binding site 1 out of 2 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isobutyryl-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 Isobutyryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1101

b:60.1
occ:1.00
 CO A:B121101 0.0 60.1 1.0
N21 A:B121101 1.9 64.0 1.0
N24 A:B121101 1.9 52.0 1.0
N23 A:B121101 1.9 61.0 1.0
N22 A:B121101 1.9 64.0 1.0
C5' A:5AD1102 2.2 0.6 0.5
NE2 A:HIS39 2.5 70.1 1.0
C19 A:B121101 2.8 48.0 1.0
C9 A:B121101 2.9 66.3 1.0
C1 A:B121101 2.9 62.6 1.0
C11 A:B121101 2.9 60.8 1.0
C4 A:B121101 2.9 65.5 1.0
C14 A:B121101 3.0 60.5 1.0
C16 A:B121101 3.0 56.6 1.0
C6 A:B121101 3.0 63.5 1.0
C10 A:B121101 3.2 63.3 1.0
CE1 A:HIS39 3.3 69.4 1.0
C5 A:B121101 3.4 68.4 1.0
C15 A:B121101 3.4 59.6 1.0
C5' A:5AD1102 3.4 0.3 0.5
C20 A:B121101 3.5 65.8 1.0
CD2 A:HIS39 3.5 71.3 1.0
C4' A:5AD1102 3.6 0.2 0.5
C2 A:B121101 4.1 64.5 1.0
C18 A:B121101 4.1 50.2 1.0
C3 A:B121101 4.2 62.6 1.0
C12 A:B121101 4.2 58.7 1.0
C8 A:B121101 4.2 70.6 1.0
C13 A:B121101 4.3 63.3 1.0
C17 A:B121101 4.3 52.5 1.0
C7 A:B121101 4.3 60.8 1.0
C3' A:5AD1102 4.4 0.5 0.5
ND1 A:HIS39 4.4 70.5 1.0
O4' A:5AD1102 4.5 0.2 0.5
C26 A:B121101 4.6 68.1 1.0
CG A:HIS39 4.6 71.8 1.0
C4' A:5AD1102 4.6 1.0 0.5
C3' A:5AD1102 4.7 0.4 0.5
C46 A:B121101 4.8 54.1 1.0
C35 A:B121101 4.8 73.5 1.0
C48 A:B121101 4.9 68.5 1.0
C53 A:B121101 4.9 60.5 1.0
O3' A:5AD1102 4.9 0.9 0.5

Cobalt binding site 2 out of 2 in 5cjt

Go back to Cobalt Binding Sites List in 5cjt
Cobalt binding site 2 out of 2 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Isobutyryl-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 Isobutyryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1101

b:89.3
occ:1.00
 CO B:B121101 0.0 89.3 1.0
N21 B:B121101 1.9 0.1 1.0
N24 B:B121101 1.9 93.8 1.0
N23 B:B121101 1.9 99.5 1.0
N22 B:B121101 1.9 0.1 1.0
NE2 B:HIS39 2.4 91.5 1.0
C19 B:B121101 2.8 93.3 1.0
C1 B:B121101 2.9 0.2 1.0
C9 B:B121101 2.9 0.3 1.0
C4 B:B121101 2.9 0.9 1.0
C11 B:B121101 2.9 99.8 1.0
C14 B:B121101 3.0 98.0 1.0
C16 B:B121101 3.0 95.8 1.0
C6 B:B121101 3.0 0.1 1.0
CD2 B:HIS39 3.2 91.7 1.0
C10 B:B121101 3.3 0.9 1.0
C5 B:B121101 3.3 0.1 1.0
C15 B:B121101 3.4 97.0 1.0
C20 B:B121101 3.4 0.8 1.0
CE1 B:HIS39 3.6 92.9 1.0
C18 B:B121101 4.1 95.1 1.0
C2 B:B121101 4.1 99.6 1.0
C3 B:B121101 4.2 0.9 1.0
C8 B:B121101 4.2 0.3 1.0
C12 B:B121101 4.2 96.6 1.0
C17 B:B121101 4.3 96.2 1.0
C13 B:B121101 4.3 98.0 1.0
C7 B:B121101 4.3 0.8 1.0
CG B:HIS39 4.4 91.8 1.0
ND1 B:HIS39 4.6 92.4 1.0
C26 B:B121101 4.6 99.4 1.0
C35 B:B121101 4.8 0.1 1.0
C48 B:B121101 4.8 99.7 1.0
C53 B:B121101 4.9 97.2 1.0
C46 B:B121101 5.0 96.3 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: Sun Dec 13 10:46:54 2020

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