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Magnesium in PDB 4xc8: Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp)

Enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp)

All present enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp):
5.4.99.2;

Protein crystallography data

The structure of Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp), PDB code: 4xc8 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) 99.16 / 3.25
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 316.510, 316.510, 342.270, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp) (pdb code 4xc8). 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 Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp), PDB code: 4xc8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4xc8

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Magnesium binding site 1 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp)


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 Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:77.9
occ:1.00
 OD1 A:ASP262 2.1 92.3 1.0
O2B A:GDP1102 2.1 96.5 1.0
OG A:SER223 2.7 73.0 1.0
O1B A:GDP1102 3.1 93.7 1.0
PB A:GDP1102 3.1 94.4 1.0
CG A:ASP262 3.3 88.9 1.0
O2A A:GDP1102 3.5 80.6 1.0
OE1 A:GLU310 3.6 93.9 1.0
O A:GLY261 3.7 0.7 1.0
MG A:MG1104 3.8 66.5 1.0
CB A:SER223 3.8 79.3 1.0
OD2 A:ASP262 4.0 84.8 1.0
OD2 A:ASP249 4.1 0.7 1.0
OD1 A:ASP249 4.1 0.7 1.0
O3A A:GDP1102 4.1 73.8 1.0
CA A:ASP262 4.2 88.9 1.0
O3B A:GDP1102 4.2 94.0 1.0
CB A:ASP262 4.3 88.6 1.0
PA A:GDP1102 4.3 79.2 1.0
C A:GLY261 4.4 0.8 1.0
CG A:ASP249 4.5 1.0 1.0
N A:ASP262 4.6 98.5 1.0
CD A:GLU310 4.7 96.8 1.0
O1A A:GDP1102 4.7 73.2 1.0
NH2 A:ARG265 4.8 96.5 1.0
N A:SER223 4.8 83.6 1.0
CA A:SER223 4.9 81.8 1.0

Magnesium binding site 2 out of 4 in 4xc8

Go back to Magnesium Binding Sites List in 4xc8
Magnesium binding site 2 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp)


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 Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:66.5
occ:1.00
 OD2 A:ASP262 2.4 84.8 1.0
O A:ILE248 2.5 0.8 1.0
OD1 A:ASP249 2.7 0.7 1.0
OE1 A:GLU310 2.9 93.9 1.0
OD1 A:ASP262 3.0 92.3 1.0
CG A:ASP262 3.0 88.9 1.0
O A:THR311 3.2 0.6 1.0
CG A:ASP249 3.3 1.0 1.0
C A:ILE248 3.4 0.3 1.0
CD A:GLU310 3.5 96.8 1.0
MG A:MG1103 3.8 77.9 1.0
OD2 A:ASP249 3.8 0.7 1.0
CG A:GLU310 4.0 94.8 1.0
CA A:SER312 4.0 0.7 1.0
CA A:ASP249 4.0 0.4 1.0
C A:THR311 4.1 0.3 1.0
N A:ASP249 4.1 0.9 1.0
CB A:ASP249 4.2 0.2 1.0
N A:ILE248 4.3 98.8 1.0
O2B A:GDP1102 4.3 96.5 1.0
OE2 A:GLU310 4.4 99.3 1.0
N A:SER312 4.4 0.6 1.0
CA A:ILE248 4.5 0.1 1.0
CB A:ASP262 4.5 88.6 1.0
OG A:SER223 4.6 73.0 1.0
CB A:SER312 4.7 0.8 1.0
CE A:LYS222 4.8 76.5 1.0
O A:GLU310 4.8 87.3 1.0
C A:SER312 5.0 0.8 1.0

Magnesium binding site 3 out of 4 in 4xc8

Go back to Magnesium Binding Sites List in 4xc8
Magnesium binding site 3 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp)


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 Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:83.0
occ:1.00
 OD1 B:ASP262 2.0 75.5 1.0
OG B:SER223 2.5 60.8 1.0
O3B B:GDP1102 3.0 74.2 1.0
O2B B:GDP1102 3.1 73.5 1.0
CG B:ASP262 3.3 77.9 1.0
O2A B:GDP1102 3.3 76.9 1.0
O B:GLY261 3.5 68.9 1.0
CB B:SER223 3.5 60.7 1.0
PB B:GDP1102 3.6 72.3 1.0
OE1 B:GLU310 3.7 83.3 1.0
MG B:MG1104 3.8 62.0 1.0
CA B:ASP262 4.0 72.4 1.0
OD2 B:ASP262 4.1 82.0 1.0
CB B:ASP262 4.1 76.1 1.0
C B:GLY261 4.2 68.4 1.0
PA B:GDP1102 4.3 75.0 1.0
OD2 B:ASP249 4.3 74.7 1.0
O3A B:GDP1102 4.3 66.6 1.0
N B:ASP262 4.4 70.2 1.0
OD1 B:ASP249 4.4 75.9 1.0
O1A B:GDP1102 4.5 74.8 1.0
N B:SER223 4.7 67.2 1.0
CA B:SER223 4.7 62.4 1.0
CD B:GLU310 4.7 83.3 1.0
CG B:ASP249 4.8 72.2 1.0
NH2 B:ARG265 4.8 65.4 1.0
O1B B:GDP1102 4.9 68.4 1.0

Magnesium binding site 4 out of 4 in 4xc8

Go back to Magnesium Binding Sites List in 4xc8
Magnesium binding site 4 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp)


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 Butyryl-Coa, Gdp, and Mg and Without Cobalamin (Apo-Icmf/Gdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:62.0
occ:1.00
 OE1 B:GLU310 2.5 83.3 1.0
OD2 B:ASP262 2.7 82.0 1.0
OD1 B:ASP249 2.9 75.9 1.0
O B:ILE248 2.9 65.9 1.0
OD1 B:ASP262 2.9 75.5 1.0
O B:THR311 3.1 64.8 1.0
CG B:ASP262 3.2 77.9 1.0
CD B:GLU310 3.3 83.3 1.0
CG B:ASP249 3.6 72.2 1.0
CG B:GLU310 3.8 77.0 1.0
MG B:MG1103 3.8 83.0 1.0
C B:ILE248 3.9 66.3 1.0
CA B:SER312 4.0 68.2 1.0
C B:THR311 4.1 64.0 1.0
OD2 B:ASP249 4.1 74.7 1.0
OE2 B:GLU310 4.2 85.1 1.0
OG B:SER223 4.3 60.8 1.0
CE B:LYS222 4.4 61.1 1.0
N B:SER312 4.5 58.1 1.0
CA B:ASP249 4.5 60.9 1.0
N B:ASP249 4.6 65.0 1.0
CB B:ASP249 4.6 64.9 1.0
CB B:ASP262 4.7 76.1 1.0
N B:ILE248 4.7 67.9 1.0
O2B B:GDP1102 4.7 73.5 1.0
NZ B:LYS222 4.8 59.0 1.0
O3B B:GDP1102 4.8 74.2 1.0
C B:SER312 4.8 69.0 1.0
CB B:SER312 4.9 70.3 1.0
CA B:ILE248 4.9 65.9 1.0
O B:GLU310 5.0 72.0 1.0

Reference:

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
Page generated: Tue Aug 12 03:01:37 2025

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