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 Oct 3 07:36:01 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