Atomistry » Magnesium » PDB 7r8p-7rf0 » 7rab
Atomistry »
  Magnesium »
    PDB 7r8p-7rf0 »
      7rab »

Magnesium in PDB 7rab: Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice

Enzymatic activity of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice

All present enzymatic activity of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice, PDB code: 7rab was solved by M.M.Georgiadis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.06 / 1.92
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 224.241, 224.241, 224.241, 90, 90, 90
R / Rfree (%) 27 / 29.8

Other elements in 7rab:

The structure of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice also contains other interesting chemical elements:

Copper (Cu) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice (pdb code 7rab). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice, PDB code: 7rab:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7rab

Go back to Magnesium Binding Sites List in 7rab
Magnesium binding site 1 out of 8 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:39.5
occ:1.00
OD1 A:ASP241 2.0 33.5 1.0
OD1 A:ASN243 2.2 36.1 1.0
O A:GLU247 2.2 26.6 1.0
OE2 A:GLU249 2.2 40.3 1.0
OE1 A:GLU249 2.3 39.9 1.0
OD1 A:ASP245 2.3 45.1 1.0
CD A:GLU249 2.5 39.8 1.0
CG A:ASP241 3.1 34.7 1.0
CG A:ASN243 3.2 47.4 1.0
CG A:ASP245 3.2 48.4 1.0
C A:GLU247 3.3 27.1 1.0
ND2 A:ASN243 3.7 43.2 1.0
OD2 A:ASP245 3.7 53.7 1.0
N A:GLU247 3.8 29.4 1.0
OD2 A:ASP241 3.9 34.1 1.0
CA A:GLU247 3.9 29.4 1.0
CB A:ASP241 3.9 28.0 1.0
CA A:ASP241 4.0 23.9 1.0
CB A:GLU247 4.0 32.4 1.0
CG A:GLU249 4.1 31.4 1.0
N A:ASP245 4.1 40.0 1.0
N A:ASN243 4.3 35.0 1.0
C A:ASP241 4.3 25.4 1.0
CB A:ASP245 4.4 38.1 1.0
N A:THR242 4.4 26.6 1.0
N A:ASN248 4.4 25.7 1.0
CB A:ASN243 4.5 36.9 1.0
N A:GLU249 4.5 23.2 1.0
CA A:ASP245 4.6 41.8 1.0
N A:PHE244 4.6 35.6 1.0
C A:ASN248 4.6 22.6 1.0
C A:ASP245 4.6 37.1 1.0
C A:ASN243 4.7 39.4 1.0
CA A:ASN243 4.7 37.7 1.0
CA A:ASN248 4.7 22.1 1.0
N A:GLU246 4.8 33.1 1.0
CB A:GLU249 4.8 21.1 1.0

Magnesium binding site 2 out of 8 in 7rab

Go back to Magnesium Binding Sites List in 7rab
Magnesium binding site 2 out of 8 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:41.2
occ:1.00
OD1 B:ASP241 2.1 36.9 1.0
O B:GLU247 2.2 27.2 1.0
OE1 B:GLU249 2.3 40.1 1.0
OE2 B:GLU249 2.3 38.7 1.0
OD1 B:ASP245 2.4 42.0 1.0
OD1 B:ASN243 2.4 43.0 1.0
CD B:GLU249 2.6 40.3 1.0
CG B:ASP241 3.0 38.7 1.0
CG B:ASP245 3.2 49.5 1.0
C B:GLU247 3.3 30.4 1.0
CG B:ASN243 3.4 47.9 1.0
OD2 B:ASP245 3.6 51.7 1.0
CB B:ASP241 3.8 31.4 1.0
N B:GLU247 3.8 28.2 1.0
OD2 B:ASP241 3.8 37.8 1.0
ND2 B:ASN243 3.9 45.2 1.0
CA B:GLU247 3.9 31.2 1.0
CA B:ASP241 4.0 28.5 1.0
CB B:GLU247 4.0 37.8 1.0
CG B:GLU249 4.1 33.2 1.0
N B:ASP245 4.2 39.6 1.0
C B:ASP241 4.4 28.4 1.0
N B:ASN248 4.4 27.1 1.0
N B:ASN243 4.4 32.1 1.0
CB B:ASP245 4.5 43.9 1.0
N B:THR242 4.5 30.6 1.0
N B:GLU249 4.5 23.4 1.0
CG B:GLU247 4.5 47.3 1.0
C B:ASN248 4.5 26.9 1.0
N B:PHE244 4.6 40.2 1.0
CA B:ASP245 4.7 41.5 1.0
CA B:ASN248 4.7 24.9 1.0
CB B:ASN243 4.7 38.2 1.0
C B:ASP245 4.8 37.5 1.0
CB B:GLU249 4.8 25.7 1.0
C B:ASN243 4.8 39.0 1.0
CA B:ASN243 4.9 36.8 1.0
N B:GLU246 4.9 34.8 1.0

Magnesium binding site 3 out of 8 in 7rab

Go back to Magnesium Binding Sites List in 7rab
Magnesium binding site 3 out of 8 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:42.5
occ:1.00
OD1 C:ASP241 2.1 36.9 1.0
OE1 C:GLU249 2.2 40.9 1.0
OE2 C:GLU249 2.3 41.1 1.0
O C:GLU247 2.3 27.1 1.0
OD1 C:ASP245 2.3 42.3 1.0
OD1 C:ASN243 2.3 41.1 1.0
CD C:GLU249 2.5 39.6 1.0
CG C:ASP241 3.0 38.5 1.0
CG C:ASP245 3.2 48.7 1.0
CG C:ASN243 3.3 47.1 1.0
C C:GLU247 3.4 31.7 1.0
OD2 C:ASP245 3.6 50.4 1.0
ND2 C:ASN243 3.8 44.7 1.0
OD2 C:ASP241 3.8 40.9 1.0
CB C:ASP241 3.8 33.0 1.0
N C:GLU247 4.0 29.7 1.0
CA C:ASP241 4.0 31.1 1.0
CG C:GLU249 4.0 35.5 1.0
CA C:GLU247 4.1 33.3 1.0
CB C:GLU247 4.2 41.6 1.0
N C:ASP245 4.2 39.1 1.0
N C:ASN243 4.3 33.0 1.0
C C:ASP241 4.4 27.8 1.0
N C:THR242 4.5 31.7 1.0
CB C:ASP245 4.5 47.2 1.0
N C:ASN248 4.5 25.4 1.0
N C:GLU249 4.5 24.6 1.0
N C:PHE244 4.6 41.3 1.0
C C:ASN248 4.6 26.1 1.0
CB C:ASN243 4.6 36.1 1.0
OE1 C:GLU247 4.7 71.1 1.0
CA C:ASP245 4.7 41.1 1.0
CA C:ASN248 4.8 22.2 1.0
CB C:GLU249 4.8 29.6 1.0
C C:ASP245 4.8 41.8 1.0
CA C:ASN243 4.8 37.0 1.0
C C:ASN243 4.8 38.7 1.0
N C:GLU246 4.9 34.2 1.0

Magnesium binding site 4 out of 8 in 7rab

Go back to Magnesium Binding Sites List in 7rab
Magnesium binding site 4 out of 8 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:41.8
occ:1.00
OD1 D:ASP241 2.1 31.4 1.0
OE2 D:GLU249 2.2 39.8 1.0
O D:GLU247 2.2 27.0 1.0
OD1 D:ASN243 2.2 39.2 1.0
OE1 D:GLU249 2.3 40.8 1.0
OD1 D:ASP245 2.4 42.2 1.0
CD D:GLU249 2.5 41.1 1.0
CG D:ASP245 3.2 45.3 1.0
CG D:ASP241 3.2 34.7 1.0
CG D:ASN243 3.2 45.6 1.0
C D:GLU247 3.3 30.2 1.0
OD2 D:ASP245 3.5 49.7 1.0
ND2 D:ASN243 3.6 41.3 1.0
N D:GLU247 3.9 29.6 1.0
CA D:GLU247 3.9 30.0 1.0
CB D:GLU247 4.0 36.6 1.0
CB D:ASP241 4.0 28.1 1.0
OD2 D:ASP241 4.0 37.9 1.0
CG D:GLU249 4.0 31.9 1.0
CA D:ASP241 4.0 26.5 1.0
N D:ASP245 4.2 39.4 1.0
N D:ASN243 4.3 36.1 1.0
CB D:ASP245 4.4 40.8 1.0
C D:ASP241 4.4 26.1 1.0
N D:ASN248 4.5 24.1 1.0
N D:THR242 4.5 27.6 1.0
N D:GLU249 4.5 24.7 1.0
CB D:ASN243 4.5 34.2 1.0
C D:ASN248 4.5 24.1 1.0
N D:PHE244 4.6 38.9 1.0
CA D:ASP245 4.6 41.7 1.0
CA D:ASN243 4.7 38.9 1.0
C D:ASP245 4.7 37.8 1.0
CA D:ASN248 4.7 21.5 1.0
C D:ASN243 4.7 37.5 1.0
CB D:GLU249 4.8 24.7 1.0
N D:GLU246 4.9 33.7 1.0
O D:ASN248 5.0 26.8 1.0

Magnesium binding site 5 out of 8 in 7rab

Go back to Magnesium Binding Sites List in 7rab
Magnesium binding site 5 out of 8 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:42.3
occ:1.00
OD1 E:ASP241 2.1 31.9 1.0
O E:GLU247 2.2 32.0 1.0
OE1 E:GLU249 2.2 44.2 1.0
OD1 E:ASN243 2.2 44.8 1.0
OD1 E:ASP245 2.3 45.0 1.0
OE2 E:GLU249 2.5 40.5 1.0
CD E:GLU249 2.7 43.6 1.0
CG E:ASP245 3.2 48.1 1.0
CG E:ASP241 3.2 38.8 1.0
C E:GLU247 3.2 33.4 1.0
CG E:ASN243 3.3 46.9 1.0
OD2 E:ASP245 3.6 49.8 1.0
ND2 E:ASN243 3.7 48.8 1.0
CB E:GLU247 3.7 35.7 1.0
N E:GLU247 3.7 31.6 1.0
CA E:GLU247 3.8 32.0 1.0
CB E:ASP241 4.1 28.8 1.0
OD2 E:ASP241 4.1 42.0 1.0
CA E:ASP241 4.1 29.0 1.0
N E:ASP245 4.2 40.1 1.0
CG E:GLU249 4.2 36.1 1.0
N E:ASN243 4.3 34.7 1.0
CB E:ASP245 4.4 41.1 1.0
N E:ASN248 4.4 25.2 1.0
C E:ASP241 4.5 26.9 1.0
N E:THR242 4.5 31.2 1.0
CB E:ASN243 4.6 41.3 1.0
N E:PHE244 4.6 35.5 1.0
N E:GLU249 4.6 24.9 1.0
CA E:ASP245 4.6 41.8 1.0
C E:ASN248 4.6 24.3 1.0
C E:ASP245 4.7 40.3 1.0
CA E:ASN248 4.8 23.7 1.0
CA E:ASN243 4.8 37.6 1.0
C E:ASN243 4.8 41.5 1.0
N E:GLU246 4.8 33.5 1.0
C E:GLU246 5.0 35.6 1.0
CB E:GLU249 5.0 24.0 1.0

Magnesium binding site 6 out of 8 in 7rab

Go back to Magnesium Binding Sites List in 7rab
Magnesium binding site 6 out of 8 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:41.3
occ:1.00
OD1 F:ASP241 2.1 37.5 1.0
O F:GLU247 2.2 32.4 1.0
OD1 F:ASP245 2.3 46.7 1.0
OD1 F:ASN243 2.3 43.2 1.0
OE2 F:GLU249 2.3 41.8 1.0
OE1 F:GLU249 2.5 44.1 1.0
CD F:GLU249 2.7 41.3 1.0
CG F:ASP241 3.0 39.0 1.0
CG F:ASP245 3.1 50.1 1.0
C F:GLU247 3.3 36.0 1.0
CG F:ASN243 3.4 47.5 1.0
OD2 F:ASP245 3.5 49.3 1.0
OD2 F:ASP241 3.6 43.4 1.0
N F:GLU247 3.8 34.4 1.0
CA F:GLU247 3.9 34.9 1.0
CB F:GLU247 3.9 41.3 1.0
CB F:ASP241 4.0 31.2 1.0
ND2 F:ASN243 4.0 50.2 1.0
N F:ASP245 4.0 40.1 1.0
CA F:ASP241 4.2 35.5 1.0
CG F:GLU249 4.2 36.7 1.0
CB F:ASP245 4.3 46.0 1.0
N F:ASN243 4.4 37.1 1.0
N F:PHE244 4.5 40.8 1.0
N F:ASN248 4.5 29.8 1.0
CA F:ASP245 4.5 40.1 1.0
C F:ASP241 4.6 30.9 1.0
C F:ASP245 4.6 40.0 1.0
N F:THR242 4.6 33.6 1.0
N F:GLU249 4.7 24.8 1.0
CG F:GLU247 4.7 52.7 1.0
C F:ASN248 4.7 25.8 1.0
CB F:ASN243 4.7 42.4 1.0
N F:GLU246 4.7 33.0 1.0
C F:ASN243 4.8 39.8 1.0
CA F:ASN248 4.8 27.3 1.0
CA F:ASN243 4.8 38.7 1.0
C F:GLU246 5.0 35.4 1.0
O F:ASP245 5.0 35.9 1.0

Magnesium binding site 7 out of 8 in 7rab

Go back to Magnesium Binding Sites List in 7rab
Magnesium binding site 7 out of 8 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg403

b:42.6
occ:1.00
OD1 G:ASP241 2.0 34.8 1.0
OD1 G:ASN243 2.2 38.4 1.0
OE2 G:GLU249 2.2 46.0 1.0
O G:GLU247 2.3 32.1 1.0
OD1 G:ASP245 2.3 45.0 1.0
OE1 G:GLU249 2.5 42.5 1.0
CD G:GLU249 2.7 40.0 1.0
CG G:ASP241 3.0 37.1 1.0
CG G:ASP245 3.1 48.4 1.0
CG G:ASN243 3.3 46.1 1.0
C G:GLU247 3.4 30.9 1.0
OD2 G:ASP245 3.6 53.2 1.0
OD2 G:ASP241 3.7 41.0 1.0
N G:GLU247 3.8 34.7 1.0
CB G:GLU247 3.8 33.2 1.0
CA G:GLU247 3.8 31.7 1.0
ND2 G:ASN243 3.9 49.9 1.0
N G:ASP245 4.0 37.3 1.0
CB G:ASP241 4.0 28.0 1.0
CA G:ASP241 4.2 27.7 1.0
CG G:GLU249 4.2 34.3 1.0
CB G:ASP245 4.2 40.7 1.0
N G:ASN243 4.3 35.4 1.0
CA G:ASP245 4.4 40.7 1.0
N G:PHE244 4.5 33.4 1.0
C G:ASP241 4.5 25.3 1.0
C G:ASP245 4.5 37.0 1.0
N G:THR242 4.5 25.9 1.0
N G:ASN248 4.5 26.8 1.0
CB G:ASN243 4.6 38.4 1.0
C G:ASN243 4.7 43.3 1.0
N G:GLU246 4.7 32.0 1.0
CA G:ASN243 4.7 41.2 1.0
N G:GLU249 4.8 25.6 1.0
C G:ASN248 4.8 23.4 1.0
CA G:ASN248 4.9 24.8 1.0
O G:ASP245 5.0 32.0 1.0
C G:GLU246 5.0 34.4 1.0

Magnesium binding site 8 out of 8 in 7rab

Go back to Magnesium Binding Sites List in 7rab
Magnesium binding site 8 out of 8 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg403

b:41.9
occ:1.00
OD1 H:ASP241 2.0 38.3 1.0
O H:GLU247 2.2 31.0 1.0
OE1 H:GLU249 2.3 45.2 1.0
OD1 H:ASP245 2.4 46.5 1.0
OD1 H:ASN243 2.5 44.8 1.0
OE2 H:GLU249 2.5 45.9 1.0
CD H:GLU249 2.7 44.1 1.0
CG H:ASP241 2.8 38.9 1.0
CG H:ASP245 3.3 49.7 1.0
C H:GLU247 3.3 34.4 1.0
OD2 H:ASP241 3.5 41.1 1.0
CG H:ASN243 3.6 50.9 1.0
OD2 H:ASP245 3.7 52.0 1.0
CB H:GLU247 3.8 42.6 1.0
N H:GLU247 3.8 34.1 1.0
CA H:GLU247 3.8 34.4 1.0
CB H:ASP241 3.8 30.0 1.0
CA H:ASP241 4.1 32.5 1.0
N H:ASP245 4.1 39.6 1.0
ND2 H:ASN243 4.2 52.3 1.0
CG H:GLU249 4.2 36.5 1.0
CB H:ASP245 4.4 45.6 1.0
N H:ASN243 4.4 39.0 1.0
N H:ASN248 4.4 30.8 1.0
C H:ASP241 4.5 31.5 1.0
N H:PHE244 4.5 39.1 1.0
N H:THR242 4.6 29.1 1.0
CA H:ASP245 4.6 42.9 1.0
C H:ASN248 4.6 25.6 1.0
N H:GLU249 4.6 25.7 1.0
C H:ASP245 4.7 38.5 1.0
N H:GLU246 4.8 33.6 1.0
CA H:ASN248 4.8 28.4 1.0
C H:ASN243 4.8 40.7 1.0
CB H:ASN243 4.9 42.1 1.0
CB H:GLU249 4.9 29.2 1.0
CA H:ASN243 4.9 40.8 1.0
CG H:GLU247 4.9 52.8 1.0

Reference:

J.L.Paavola, U.Battistin, C.M.Ogata, M.M.Georgiadis. Crystal Structures of A Dodecameric Multicopper Oxidase From Marinithermus Hydrothermalis. Acta Crystallogr D Struct V. 77 1336 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 34605435
DOI: 10.1107/S205979832100944X
Page generated: Thu Aug 14 14:55:28 2025

Last articles

Cl in 7HSY
Cl in 7HU9
Cl in 7HSQ
Cl in 7HRG
Cl in 7HRE
Cl in 7HRF
Cl in 7HR4
Cl in 7HQT
Cd in 9J00
Cd in 9J01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy