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Magnesium 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:

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

Magnesium binding site 1 out of 4 in 5cjt

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

b:55.4
occ:1.00
 OD1 A:ASP262 2.1 90.2 1.0
O3B A:GDP1104 2.2 0.0 1.0
OG A:SER223 2.2 71.3 1.0
O1B A:GDP1104 2.7 98.2 1.0
OE2 A:GLU310 2.7 88.5 1.0
MG A:MG1106 2.9 67.4 1.0
PB A:GDP1104 2.9 98.4 1.0
CG A:ASP262 3.3 91.6 1.0
CB A:SER223 3.3 73.1 1.0
O2A A:GDP1104 3.6 85.0 1.0
CD A:GLU310 3.8 86.5 1.0
O2B A:GDP1104 4.0 98.3 1.0
O A:GLY261 4.0 0.3 1.0
OD2 A:ASP262 4.1 91.1 1.0
N A:SER223 4.1 81.1 1.0
O3A A:GDP1104 4.1 68.2 1.0
CB A:ASP262 4.3 94.4 1.0
OE1 A:GLU310 4.3 84.5 1.0
PA A:GDP1104 4.3 82.1 1.0
CA A:SER223 4.3 76.8 1.0
OD1 A:ASP249 4.3 0.0 1.0
CA A:ASP262 4.4 96.6 1.0
O1A A:GDP1104 4.5 79.5 1.0
C A:GLY261 4.9 0.7 1.0
NZ A:LYS222 5.0 0.8 1.0

Magnesium binding site 2 out of 4 in 5cjt

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

b:67.4
occ:1.00
 OD1 A:ASP249 2.6 0.0 1.0
OE2 A:GLU310 2.6 88.5 1.0
OD1 A:ASP262 2.8 90.2 1.0
MG A:MG1105 2.9 55.4 1.0
OD2 A:ASP262 3.0 91.1 1.0
O A:THR311 3.2 0.3 1.0
CG A:ASP262 3.3 91.6 1.0
CD A:GLU310 3.5 86.5 1.0
O A:ILE248 3.5 93.9 1.0
CG A:ASP249 3.8 0.5 1.0
CG A:GLU310 3.9 85.0 1.0
CE A:LYS222 4.0 0.9 1.0
O3B A:GDP1104 4.1 0.0 1.0
OG A:SER223 4.2 71.3 1.0
C A:THR311 4.2 0.9 1.0
CA A:SER312 4.2 0.1 1.0
OE1 A:GLU310 4.4 84.5 1.0
O1B A:GDP1104 4.4 98.2 1.0
C A:ILE248 4.5 93.7 1.0
NZ A:LYS222 4.5 0.8 1.0
OD2 A:ASP249 4.5 99.0 1.0
N A:SER312 4.7 0.1 1.0
CA A:ASP249 4.7 0.0 1.0
PB A:GDP1104 4.7 98.4 1.0
CB A:ASP262 4.8 94.4 1.0
CB A:ASP249 4.8 99.0 1.0
C A:SER312 4.9 0.0 1.0
O2B A:GDP1104 4.9 98.3 1.0

Magnesium binding site 3 out of 4 in 5cjt

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

b:58.3
occ:1.00
 O3B B:GDP1103 2.1 73.3 1.0
OD1 B:ASP262 2.1 92.3 1.0
OG B:SER223 2.2 68.1 1.0
O1B B:GDP1103 2.7 75.5 1.0
OE2 B:GLU310 2.7 64.8 1.0
PB B:GDP1103 2.9 73.2 1.0
CG B:ASP262 3.3 86.9 1.0
CB B:SER223 3.3 70.0 1.0
MG B:MG1105 3.4 51.5 1.0
O2A B:GDP1103 3.6 75.8 1.0
CD B:GLU310 3.8 70.6 1.0
O2B B:GDP1103 4.0 69.7 1.0
N B:SER223 4.0 77.1 1.0
O3A B:GDP1103 4.0 0.3 1.0
O B:GLY261 4.0 80.2 1.0
OD2 B:ASP262 4.1 87.8 1.0
OE1 B:GLU310 4.2 77.7 1.0
PA B:GDP1103 4.2 78.8 1.0
CA B:SER223 4.3 72.5 1.0
CB B:ASP262 4.3 81.2 1.0
OD1 B:ASP249 4.3 77.8 1.0
CA B:ASP262 4.4 78.8 1.0
O1A B:GDP1103 4.5 82.6 1.0
C B:GLY261 4.9 77.9 1.0
NZ B:LYS222 5.0 70.3 1.0

Magnesium binding site 4 out of 4 in 5cjt

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

b:51.5
occ:1.00
 OD2 B:ASP262 2.6 87.8 1.0
OD1 B:ASP249 2.6 77.8 1.0
OE2 B:GLU310 2.7 64.8 1.0
OD1 B:ASP262 2.9 92.3 1.0
O B:ILE248 2.9 70.6 1.0
O B:THR311 3.0 71.5 1.0
CG B:ASP262 3.0 86.9 1.0
CD B:GLU310 3.2 70.6 1.0
MG B:MG1104 3.4 58.3 1.0
CG B:GLU310 3.6 68.2 1.0
CG B:ASP249 3.7 84.1 1.0
C B:ILE248 3.8 73.2 1.0
C B:THR311 3.9 74.0 1.0
OE1 B:GLU310 4.1 77.7 1.0
CA B:SER312 4.2 73.8 1.0
OG B:SER223 4.3 68.1 1.0
CA B:ASP249 4.4 77.6 1.0
CE B:LYS222 4.4 70.9 1.0
N B:SER312 4.4 72.8 1.0
N B:ASP249 4.5 76.9 1.0
CB B:ASP262 4.5 81.2 1.0
N B:ILE248 4.5 74.0 1.0
CB B:ASP249 4.5 82.5 1.0
OD2 B:ASP249 4.6 90.2 1.0
O3B B:GDP1103 4.6 73.3 1.0
CB B:GLU310 4.7 68.7 1.0
O B:GLU310 4.7 75.5 1.0
CA B:ILE248 4.8 72.9 1.0
C B:GLU310 4.9 74.3 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: Mon Dec 14 20:07:22 2020

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