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

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy