Atomistry » Cobalt » PDB 4xim-5d6e » 5cjt
Atomistry »
  Cobalt »
    PDB 4xim-5d6e »
      5cjt »

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: Tue Jul 30 17:45:42 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy