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Magnesium 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:

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 Isovaleryl-Coenzyme A (pdb code 5cjv). 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 Isovaleryl-Coenzyme A, PDB code: 5cjv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5cjv

Go back to Magnesium Binding Sites List in 5cjv
Magnesium binding site 1 out of 4 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 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 Isovaleryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:64.0
occ:1.00
 OG A:SER223 2.0 73.4 1.0
OD1 A:ASP262 2.1 0.3 1.0
O3B A:GDP1104 2.3 93.2 1.0
O2B A:GDP1104 2.6 92.7 1.0
OE2 A:GLU310 2.7 80.9 1.0
PB A:GDP1104 3.0 91.1 1.0
CB A:SER223 3.1 73.8 1.0
MG A:MG1106 3.2 78.1 1.0
CG A:ASP262 3.3 98.5 1.0
O1A A:GDP1104 3.6 80.5 1.0
CD A:GLU310 3.8 82.6 1.0
N A:SER223 4.0 83.0 1.0
O A:GLY261 4.0 99.8 1.0
O3A A:GDP1104 4.1 70.1 1.0
CA A:SER223 4.1 77.2 1.0
O1B A:GDP1104 4.2 88.6 1.0
CB A:ASP262 4.2 98.2 1.0
OD2 A:ASP262 4.2 96.9 1.0
PA A:GDP1104 4.2 78.8 1.0
OE1 A:GLU310 4.2 82.6 1.0
CA A:ASP262 4.2 96.9 1.0
O2A A:GDP1104 4.4 76.9 1.0
OD1 A:ASP249 4.5 0.2 1.0
C A:GLY261 4.8 98.6 1.0
N A:ASP262 4.9 97.0 1.0

Magnesium binding site 2 out of 4 in 5cjv

Go back to Magnesium Binding Sites List in 5cjv
Magnesium binding site 2 out of 4 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 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 Isovaleryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1106

b:78.1
occ:1.00
 OE2 A:GLU310 2.6 80.9 1.0
OD1 A:ASP249 2.7 0.2 1.0
OD1 A:ASP262 2.8 0.3 1.0
O A:THR311 3.0 0.1 1.0
OD2 A:ASP262 3.1 96.9 1.0
MG A:MG1105 3.2 64.0 1.0
O A:ILE248 3.3 93.2 1.0
CG A:ASP262 3.3 98.5 1.0
CD A:GLU310 3.4 82.6 1.0
CG A:GLU310 3.8 84.3 1.0
CG A:ASP249 3.9 0.9 1.0
CE A:LYS222 4.0 93.6 1.0
C A:THR311 4.0 0.6 1.0
CA A:SER312 4.1 0.7 1.0
O3B A:GDP1104 4.2 93.2 1.0
OG A:SER223 4.2 73.4 1.0
C A:ILE248 4.3 93.9 1.0
OE1 A:GLU310 4.4 82.6 1.0
NZ A:LYS222 4.4 95.0 1.0
O2B A:GDP1104 4.4 92.7 1.0
N A:SER312 4.6 0.5 1.0
OD2 A:ASP249 4.6 98.9 1.0
CA A:ASP249 4.6 99.1 1.0
CB A:ASP249 4.8 99.0 1.0
CB A:ASP262 4.8 98.2 1.0
PB A:GDP1104 4.8 91.1 1.0
C A:SER312 4.8 0.3 1.0
N A:ASP249 4.9 97.1 1.0

Magnesium binding site 3 out of 4 in 5cjv

Go back to Magnesium Binding Sites List in 5cjv
Magnesium binding site 3 out of 4 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 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 Isovaleryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:42.2
occ:1.00
 OG B:SER223 2.0 65.3 1.0
OD1 B:ASP262 2.1 93.6 1.0
O3B B:GDP1103 2.4 65.7 1.0
O2B B:GDP1103 2.6 66.4 1.0
OE2 B:GLU310 2.7 61.3 1.0
PB B:GDP1103 3.0 64.2 1.0
CB B:SER223 3.1 67.2 1.0
CG B:ASP262 3.3 89.0 1.0
MG B:MG1105 3.4 43.5 1.0
O2A B:GDP1103 3.5 70.3 1.0
CD B:GLU310 3.8 64.8 1.0
N B:SER223 4.0 68.1 1.0
O B:GLY261 4.0 81.2 1.0
O3A B:GDP1103 4.1 0.6 1.0
CA B:SER223 4.1 67.7 1.0
O1B B:GDP1103 4.2 63.0 1.0
CB B:ASP262 4.2 83.5 1.0
PA B:GDP1103 4.2 72.6 1.0
OD2 B:ASP262 4.2 89.4 1.0
OE1 B:GLU310 4.2 67.2 1.0
CA B:ASP262 4.2 80.8 1.0
O1A B:GDP1103 4.4 74.1 1.0
OD1 B:ASP249 4.5 82.1 1.0
C B:GLY261 4.8 80.3 1.0
N B:ASP262 4.9 80.5 1.0

Magnesium binding site 4 out of 4 in 5cjv

Go back to Magnesium Binding Sites List in 5cjv
Magnesium binding site 4 out of 4 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 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 Isovaleryl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1105

b:43.5
occ:1.00
 OE2 B:GLU310 2.5 61.3 1.0
OD2 B:ASP262 2.8 89.4 1.0
OD1 B:ASP262 2.8 93.6 1.0
OD1 B:ASP249 2.8 82.1 1.0
O B:THR311 2.8 66.9 1.0
O B:ILE248 2.9 75.5 1.0
CG B:ASP262 3.1 89.0 1.0
CD B:GLU310 3.2 64.8 1.0
MG B:MG1104 3.4 42.2 1.0
CG B:GLU310 3.5 62.8 1.0
CG B:ASP249 3.9 85.2 1.0
C B:THR311 3.9 68.5 1.0
C B:ILE248 3.9 74.0 1.0
OE1 B:GLU310 4.1 67.2 1.0
CA B:SER312 4.2 64.5 1.0
CE B:LYS222 4.2 63.7 1.0
OG B:SER223 4.2 65.3 1.0
O3B B:GDP1103 4.5 65.7 1.0
N B:SER312 4.5 65.1 1.0
CA B:ASP249 4.5 74.5 1.0
CB B:ASP262 4.6 83.5 1.0
N B:ASP249 4.6 74.9 1.0
N B:ILE248 4.6 68.2 1.0
CB B:ASP249 4.7 80.9 1.0
CB B:GLU310 4.7 63.7 1.0
OD2 B:ASP249 4.7 90.3 1.0
NZ B:LYS222 4.8 64.5 1.0
O B:GLU310 4.9 77.7 1.0
O2B B:GDP1103 4.9 66.4 1.0
C B:GLU310 4.9 73.3 1.0
CA B:ILE248 4.9 70.5 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 02:11:16 2024

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