Atomistry » Magnesium » PDB 5chg-5cqz » 5cjt
Atomistry »
  Magnesium »
    PDB 5chg-5cqz »
      5cjt »

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: Sun Sep 29 02:11:06 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy