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

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

All present enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-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 N-Butyryl-Coenzyme A, PDB code: 5cju 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 / 3.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 316.760, 316.760, 342.670, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 20.9

Other elements in 5cju:

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

Cobalt (Co) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A (pdb code 5cju). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A, PDB code: 5cju:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5cju

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Magnesium binding site 1 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:70.5
occ:1.00
 OD1 A:ASP262 2.0 0.7 1.0
OG A:SER223 2.1 88.7 1.0
O3B A:GDP1104 2.4 0.4 1.0
OE2 A:GLU310 2.5 98.2 1.0
O2B A:GDP1104 2.6 0.0 1.0
PB A:GDP1104 3.1 0.2 1.0
CG A:ASP262 3.2 0.5 1.0
MG A:MG1106 3.2 75.3 1.0
CB A:SER223 3.2 90.1 1.0
CD A:GLU310 3.6 95.4 1.0
O1A A:GDP1104 3.8 90.2 1.0
OD2 A:ASP262 3.9 0.1 1.0
N A:SER223 4.0 98.0 1.0
O1B A:GDP1104 4.1 99.8 1.0
OE1 A:GLU310 4.1 93.5 1.0
CB A:ASP262 4.1 0.8 1.0
O A:GLY261 4.1 0.5 1.0
CA A:SER223 4.2 92.7 1.0
O3A A:GDP1104 4.2 74.1 1.0
OD1 A:ASP249 4.3 0.5 1.0
CA A:ASP262 4.3 0.7 1.0
PA A:GDP1104 4.4 89.7 1.0
O2A A:GDP1104 4.6 87.4 1.0
CG A:GLU310 4.9 93.8 1.0
C A:GLY261 4.9 0.2 1.0
NZ A:LYS222 4.9 0.5 1.0

Magnesium binding site 2 out of 4 in 5cju

Go back to Magnesium Binding Sites List in 5cju
Magnesium binding site 2 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1106

b:75.3
occ:1.00
 OD1 A:ASP249 2.7 0.5 1.0
OE2 A:GLU310 2.7 98.2 1.0
O A:THR311 2.8 0.1 1.0
OD2 A:ASP262 3.0 0.1 1.0
O A:ILE248 3.1 0.3 1.0
OD1 A:ASP262 3.1 0.7 1.0
MG A:MG1105 3.2 70.5 1.0
CG A:ASP262 3.4 0.5 1.0
CD A:GLU310 3.4 95.4 1.0
CG A:GLU310 3.7 93.8 1.0
C A:THR311 3.8 0.7 1.0
CG A:ASP249 3.9 0.1 1.0
CA A:SER312 4.0 0.5 1.0
CE A:LYS222 4.0 0.0 1.0
C A:ILE248 4.1 0.9 1.0
N A:SER312 4.3 0.9 1.0
NZ A:LYS222 4.4 0.5 1.0
OE1 A:GLU310 4.4 93.5 1.0
OG A:SER223 4.5 88.7 1.0
CA A:ASP249 4.5 0.6 1.0
O3B A:GDP1104 4.5 0.4 1.0
OD2 A:ASP249 4.7 0.8 1.0
N A:ASP249 4.7 0.1 1.0
O2B A:GDP1104 4.7 0.0 1.0
C A:SER312 4.7 0.0 1.0
CB A:ASP249 4.7 0.9 1.0
CB A:ASP262 4.9 0.8 1.0
CB A:SER312 4.9 0.0 1.0
N A:ILE248 4.9 0.5 1.0
CB A:GLU310 5.0 93.3 1.0

Magnesium binding site 3 out of 4 in 5cju

Go back to Magnesium Binding Sites List in 5cju
Magnesium binding site 3 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:59.8
occ:1.00
 OD1 B:ASP262 2.0 96.4 1.0
OG B:SER223 2.1 77.1 1.0
O3B B:GDP1103 2.4 83.3 1.0
OE2 B:GLU310 2.5 74.7 1.0
O2B B:GDP1103 2.6 85.1 1.0
PB B:GDP1103 3.1 82.5 1.0
CG B:ASP262 3.2 94.2 1.0
CB B:SER223 3.2 79.8 1.0
MG B:MG1105 3.4 55.1 1.0
CD B:GLU310 3.6 79.9 1.0
O2A B:GDP1103 3.8 82.8 1.0
OD2 B:ASP262 3.9 94.8 1.0
N B:SER223 4.0 83.9 1.0
O1B B:GDP1103 4.1 80.3 1.0
OE1 B:GLU310 4.1 82.8 1.0
CB B:ASP262 4.1 92.1 1.0
O B:GLY261 4.1 92.1 1.0
CA B:SER223 4.1 81.5 1.0
O3A B:GDP1103 4.2 0.4 1.0
OD1 B:ASP249 4.3 96.0 1.0
CA B:ASP262 4.3 91.2 1.0
PA B:GDP1103 4.4 85.4 1.0
O1A B:GDP1103 4.6 87.1 1.0
CG B:GLU310 4.9 77.0 1.0
C B:GLY261 4.9 90.5 1.0
NZ B:LYS222 4.9 88.6 1.0

Magnesium binding site 4 out of 4 in 5cju

Go back to Magnesium Binding Sites List in 5cju
Magnesium binding site 4 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate N-Butyryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1105

b:55.1
occ:1.00
 OD1 B:ASP249 2.6 96.0 1.0
OD2 B:ASP262 2.7 94.8 1.0
OE2 B:GLU310 2.8 74.7 1.0
O B:ILE248 2.8 92.2 1.0
O B:THR311 2.8 79.7 1.0
OD1 B:ASP262 3.0 96.4 1.0
CG B:ASP262 3.2 94.2 1.0
MG B:MG1104 3.4 59.8 1.0
CD B:GLU310 3.4 79.9 1.0
CG B:GLU310 3.7 77.0 1.0
CG B:ASP249 3.7 97.5 1.0
C B:ILE248 3.8 90.3 1.0
C B:THR311 3.8 78.0 1.0
CA B:SER312 4.0 81.7 1.0
CA B:ASP249 4.3 85.0 1.0
CE B:LYS222 4.3 86.5 1.0
N B:SER312 4.3 78.4 1.0
OE1 B:GLU310 4.4 82.8 1.0
N B:ASP249 4.4 86.5 1.0
CB B:ASP249 4.5 91.1 1.0
OG B:SER223 4.5 77.1 1.0
N B:ILE248 4.6 78.0 1.0
OD2 B:ASP249 4.6 0.6 1.0
CB B:ASP262 4.7 92.1 1.0
O3B B:GDP1103 4.8 83.3 1.0
NZ B:LYS222 4.8 88.6 1.0
CA B:ILE248 4.8 78.4 1.0
O B:GLU310 4.8 90.0 1.0
C B:SER312 4.8 83.0 1.0
CB B:GLU310 4.9 78.9 1.0
CB B:SER312 4.9 83.0 1.0
C B:GLU310 4.9 89.3 1.0
CA B:THR311 5.0 78.8 1.0
O2B B:GDP1103 5.0 85.1 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 Sep 29 02:11:09 2024

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