Atomistry » Magnesium » PDB 4x7w-4xgp » 4xc6
Atomistry »
  Magnesium »
    PDB 4x7w-4xgp »
      4xc6 »

Magnesium in PDB 4xc6: Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp)

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

All present enzymatic activity of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp):
5.4.99.13;

Protein crystallography data

The structure of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp), PDB code: 4xc6 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) 48.69 / 3.35
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 318.760, 318.760, 343.520, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 19.8

Other elements in 4xc6:

The structure of Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp) 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, and Mg (Holo-Icmf/Gdp) (pdb code 4xc6). 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, and Mg (Holo-Icmf/Gdp), PDB code: 4xc6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4xc6

Go back to Magnesium Binding Sites List in 4xc6
Magnesium binding site 1 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp)


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, and Mg (Holo-Icmf/Gdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:60.2
occ:1.00
 OD1 A:ASP262 2.1 1.0 1.0
O3B A:GDP1103 2.1 87.5 1.0
OG A:SER223 2.3 61.6 1.0
OE2 A:GLU310 2.6 80.5 1.0
O2B A:GDP1103 2.7 84.0 1.0
PB A:GDP1103 2.9 84.1 1.0
MG A:MG1105 3.0 73.3 1.0
CG A:ASP262 3.2 0.8 1.0
CB A:SER223 3.4 63.2 1.0
CD A:GLU310 3.8 81.2 1.0
O1A A:GDP1103 3.8 71.5 1.0
OD2 A:ASP262 3.9 0.9 1.0
O1B A:GDP1103 3.9 82.8 1.0
N A:SER223 4.0 74.4 1.0
O3A A:GDP1103 4.1 65.8 1.0
OE1 A:GLU310 4.2 80.2 1.0
CB A:ASP262 4.3 0.3 1.0
OD1 A:ASP249 4.3 0.1 1.0
CA A:SER223 4.3 68.5 1.0
O A:GLY261 4.3 94.2 1.0
PA A:GDP1103 4.4 71.7 1.0
CA A:ASP262 4.5 96.8 1.0
O2A A:GDP1103 4.6 70.8 1.0
NZ A:LYS222 4.9 86.1 1.0
CE A:LYS222 5.0 85.3 1.0
CB A:LYS222 5.0 74.5 1.0
CG A:GLU310 5.0 82.0 1.0

Magnesium binding site 2 out of 4 in 4xc6

Go back to Magnesium Binding Sites List in 4xc6
Magnesium binding site 2 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp)


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, and Mg (Holo-Icmf/Gdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:73.3
occ:1.00
 OD1 A:ASP249 2.5 0.1 1.0
OE2 A:GLU310 2.7 80.5 1.0
OD2 A:ASP262 2.9 0.9 1.0
MG A:MG1104 3.0 60.2 1.0
OD1 A:ASP262 3.0 1.0 1.0
O A:THR311 3.1 0.6 1.0
O A:ILE248 3.2 95.0 1.0
CG A:ASP262 3.3 0.8 1.0
CD A:GLU310 3.5 81.2 1.0
CG A:ASP249 3.7 0.3 1.0
CG A:GLU310 3.9 82.0 1.0
CA A:SER312 4.0 0.5 1.0
C A:THR311 4.1 0.3 1.0
CE A:LYS222 4.1 85.3 1.0
C A:ILE248 4.2 93.4 1.0
OG A:SER223 4.3 61.6 1.0
O3B A:GDP1103 4.4 87.5 1.0
OE1 A:GLU310 4.4 80.2 1.0
OD2 A:ASP249 4.4 99.1 1.0
N A:SER312 4.5 0.4 1.0
NZ A:LYS222 4.6 86.1 1.0
CA A:ASP249 4.6 98.0 1.0
CB A:ASP249 4.7 98.2 1.0
O2B A:GDP1103 4.7 84.0 1.0
C A:SER312 4.7 0.3 1.0
CB A:ASP262 4.8 0.3 1.0
N A:ASP249 4.8 96.3 1.0
N A:GLY313 5.0 0.6 1.0
CB A:SER312 5.0 0.7 1.0

Magnesium binding site 3 out of 4 in 4xc6

Go back to Magnesium Binding Sites List in 4xc6
Magnesium binding site 3 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp)


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, and Mg (Holo-Icmf/Gdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:39.1
occ:1.00
 O3B B:GDP1102 2.1 67.7 1.0
OD1 B:ASP262 2.1 85.9 1.0
OG B:SER223 2.2 58.4 1.0
OE2 B:GLU310 2.6 58.8 1.0
O2B B:GDP1102 2.7 71.3 1.0
PB B:GDP1102 2.9 69.0 1.0
CG B:ASP262 3.2 80.8 1.0
MG B:MG1104 3.3 38.1 1.0
CB B:SER223 3.4 62.2 1.0
CD B:GLU310 3.8 63.9 1.0
O2A B:GDP1102 3.8 72.3 1.0
OD2 B:ASP262 3.9 82.2 1.0
O1B B:GDP1102 3.9 65.2 1.0
N B:SER223 4.0 67.5 1.0
O3A B:GDP1102 4.1 76.6 1.0
OE1 B:GLU310 4.2 73.1 1.0
CA B:SER223 4.3 66.0 1.0
CB B:ASP262 4.3 75.5 1.0
OD1 B:ASP249 4.3 73.4 1.0
PA B:GDP1102 4.4 76.1 1.0
O B:GLY261 4.4 76.5 1.0
CA B:ASP262 4.5 73.0 1.0
O1A B:GDP1102 4.6 80.0 1.0
NZ B:LYS222 4.9 64.2 1.0
CB B:LYS222 4.9 61.5 1.0
CE B:LYS222 5.0 61.6 1.0
CG B:GLU310 5.0 60.6 1.0

Magnesium binding site 4 out of 4 in 4xc6

Go back to Magnesium Binding Sites List in 4xc6
Magnesium binding site 4 out of 4 in the Isobutyryl-Coa Mutase Fused with Bound Adenosylcobalamin, Gdp, and Mg (Holo-Icmf/Gdp)


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, and Mg (Holo-Icmf/Gdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:38.1
occ:1.00
 OD2 B:ASP262 2.5 82.2 1.0
OE2 B:GLU310 2.6 58.8 1.0
OD1 B:ASP249 2.6 73.4 1.0
O B:ILE248 2.8 67.0 1.0
O B:THR311 2.9 68.4 1.0
OD1 B:ASP262 3.1 85.9 1.0
CG B:ASP262 3.1 80.8 1.0
CD B:GLU310 3.2 63.9 1.0
MG B:MG1103 3.3 39.1 1.0
CG B:GLU310 3.5 60.6 1.0
CG B:ASP249 3.8 79.5 1.0
C B:ILE248 3.8 67.5 1.0
C B:THR311 3.8 67.5 1.0
CA B:SER312 4.1 61.5 1.0
OE1 B:GLU310 4.1 73.1 1.0
N B:SER312 4.3 59.9 1.0
CE B:LYS222 4.4 61.6 1.0
OG B:SER223 4.4 58.4 1.0
CA B:ASP249 4.5 65.0 1.0
N B:ILE248 4.5 61.0 1.0
N B:ASP249 4.5 66.4 1.0
CB B:ASP262 4.6 75.5 1.0
OD2 B:ASP249 4.6 88.4 1.0
CB B:ASP249 4.6 73.2 1.0
O B:GLU310 4.6 71.5 1.0
CB B:GLU310 4.7 58.7 1.0
O3B B:GDP1102 4.7 67.7 1.0
CA B:ILE248 4.8 60.2 1.0
C B:GLU310 4.8 67.8 1.0
C B:SER312 4.9 62.5 1.0
NZ B:LYS222 5.0 64.2 1.0
CA B:THR311 5.0 66.2 1.0

Reference:

M.Jost, V.Cracan, P.A.Hubbard, R.Banerjee, C.L.Drennan. Visualization of A Radical B12 Enzyme with Its G-Protein Chaperone Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490
Page generated: Tue Aug 20 15:24:53 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