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

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

All present enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Pivalyl-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 Pivalyl-Coenzyme A, PDB code: 5cjw 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) 100.00 / 3.40
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 317.520, 317.520, 343.040, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 20

Other elements in 5cjw:

The structure of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Pivalyl-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 Pivalyl-Coenzyme A (pdb code 5cjw). 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 Pivalyl-Coenzyme A, PDB code: 5cjw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5cjw

Go back to Magnesium Binding Sites List in 5cjw
Magnesium binding site 1 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Pivalyl-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 Pivalyl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:78.0
occ:1.00
 OD1 A:ASP262 2.1 0.6 1.0
O3B A:GDP1104 2.1 0.6 1.0
OG A:SER223 2.2 91.5 1.0
OE2 A:GLU310 2.6 0.8 1.0
O2B A:GDP1104 2.9 0.6 1.0
PB A:GDP1104 3.0 0.9 1.0
MG A:MG1106 3.0 0.2 1.0
CG A:ASP262 3.3 0.9 1.0
CB A:SER223 3.3 93.8 1.0
CD A:GLU310 3.7 0.0 1.0
O1A A:GDP1104 3.7 96.7 1.0
N A:SER223 4.0 0.3 1.0
OD2 A:ASP262 4.0 0.2 1.0
O1B A:GDP1104 4.0 0.7 1.0
O3A A:GDP1104 4.2 95.0 1.0
OE1 A:GLU310 4.2 0.6 1.0
CA A:SER223 4.2 0.6 1.0
O A:GLY261 4.2 0.9 1.0
CB A:ASP262 4.3 0.1 1.0
OD1 A:ASP249 4.3 0.8 1.0
PA A:GDP1104 4.4 96.3 1.0
CA A:ASP262 4.5 0.7 1.0
O2A A:GDP1104 4.6 96.9 1.0
NZ A:LYS222 4.8 0.4 1.0
CG A:GLU310 4.9 1.0 1.0
CB A:LYS222 4.9 0.4 1.0
CE A:LYS222 4.9 0.6 1.0

Magnesium binding site 2 out of 4 in 5cjw

Go back to Magnesium Binding Sites List in 5cjw
Magnesium binding site 2 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Pivalyl-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 Pivalyl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1106

b:0.2
occ:1.00
 OD1 A:ASP249 2.6 0.8 1.0
OE2 A:GLU310 2.6 0.8 1.0
OD2 A:ASP262 2.9 0.2 1.0
OD1 A:ASP262 3.0 0.6 1.0
O A:THR311 3.0 0.9 1.0
MG A:MG1105 3.0 78.0 1.0
O A:ILE248 3.2 0.7 1.0
CD A:GLU310 3.3 0.0 1.0
CG A:ASP262 3.3 0.9 1.0
CG A:GLU310 3.6 1.0 1.0
CG A:ASP249 3.8 0.4 1.0
C A:THR311 4.0 0.1 1.0
CE A:LYS222 4.0 0.6 1.0
CA A:SER312 4.1 0.4 1.0
C A:ILE248 4.2 0.8 1.0
OE1 A:GLU310 4.3 0.6 1.0
OG A:SER223 4.3 91.5 1.0
O3B A:GDP1104 4.4 0.6 1.0
NZ A:LYS222 4.5 0.4 1.0
N A:SER312 4.5 0.5 1.0
OD2 A:ASP249 4.5 0.7 1.0
CA A:ASP249 4.6 0.5 1.0
CB A:ASP249 4.7 0.2 1.0
CB A:ASP262 4.8 0.1 1.0
O2B A:GDP1104 4.8 0.6 1.0
N A:ASP249 4.8 0.1 1.0
C A:SER312 4.9 0.3 1.0
CB A:GLU310 4.9 0.5 1.0
N A:ILE248 5.0 0.7 1.0

Magnesium binding site 3 out of 4 in 5cjw

Go back to Magnesium Binding Sites List in 5cjw
Magnesium binding site 3 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Pivalyl-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 Pivalyl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:70.7
occ:1.00
 O3B B:GDP1103 2.1 89.3 1.0
OD1 B:ASP262 2.1 0.7 1.0
OG B:SER223 2.2 80.9 1.0
OE2 B:GLU310 2.5 76.4 1.0
O2B B:GDP1103 2.9 87.0 1.0
PB B:GDP1103 3.0 88.0 1.0
CG B:ASP262 3.3 0.3 1.0
CB B:SER223 3.3 85.3 1.0
MG B:MG1105 3.3 70.8 1.0
CD B:GLU310 3.7 83.3 1.0
O2A B:GDP1103 3.7 89.3 1.0
N B:SER223 4.0 90.2 1.0
OD2 B:ASP262 4.0 0.9 1.0
O1B B:GDP1103 4.0 85.9 1.0
OE1 B:GLU310 4.2 89.8 1.0
O3A B:GDP1103 4.2 0.3 1.0
CA B:SER223 4.2 88.3 1.0
O B:GLY261 4.3 0.3 1.0
CB B:ASP262 4.3 0.8 1.0
OD1 B:ASP249 4.3 0.3 1.0
PA B:GDP1103 4.4 92.9 1.0
CA B:ASP262 4.5 0.6 1.0
O1A B:GDP1103 4.6 93.7 1.0
NZ B:LYS222 4.8 86.0 1.0
CG B:GLU310 4.9 78.9 1.0
CB B:LYS222 4.9 86.2 1.0
CE B:LYS222 4.9 86.3 1.0

Magnesium binding site 4 out of 4 in 5cjw

Go back to Magnesium Binding Sites List in 5cjw
Magnesium binding site 4 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, Mg (Holo-Icmf/Gdp), and Substrate Pivalyl-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 Pivalyl-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1105

b:70.8
occ:1.00
 OD1 B:ASP249 2.5 0.3 1.0
OE2 B:GLU310 2.7 76.4 1.0
OD2 B:ASP262 2.8 0.9 1.0
O B:ILE248 2.8 89.9 1.0
O B:THR311 2.9 84.5 1.0
OD1 B:ASP262 3.1 0.7 1.0
CG B:ASP262 3.3 0.3 1.0
CD B:GLU310 3.3 83.3 1.0
MG B:MG1104 3.3 70.7 1.0
CG B:GLU310 3.6 78.9 1.0
CG B:ASP249 3.7 0.9 1.0
C B:THR311 3.9 83.0 1.0
C B:ILE248 3.9 88.1 1.0
CA B:SER312 4.0 87.2 1.0
OE1 B:GLU310 4.2 89.8 1.0
CE B:LYS222 4.2 86.3 1.0
N B:SER312 4.3 83.6 1.0
CA B:ASP249 4.4 90.0 1.0
OG B:SER223 4.5 80.9 1.0
OD2 B:ASP249 4.5 0.9 1.0
N B:ASP249 4.5 89.5 1.0
CB B:ASP249 4.6 98.7 1.0
N B:ILE248 4.6 84.0 1.0
CB B:ASP262 4.7 0.8 1.0
O3B B:GDP1103 4.7 89.3 1.0
O B:GLU310 4.7 95.2 1.0
NZ B:LYS222 4.8 86.0 1.0
CB B:GLU310 4.8 78.8 1.0
C B:SER312 4.9 91.3 1.0
CA B:ILE248 4.9 85.0 1.0
C B:GLU310 4.9 87.8 1.0
CB B:SER312 5.0 90.7 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 02:11:40 2024

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