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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

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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

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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

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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

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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

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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 Oct 3 07:36:01 2024

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