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Magnesium in PDB 3zxw: Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate

Enzymatic activity of Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate

All present enzymatic activity of Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate:
4.1.1.39;

Protein crystallography data

The structure of Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate, PDB code: 3zxw was solved by B.Terlecka, V.Wilhelmi, W.Bialek, B.Gubernator, A.Szczepaniak, E.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.500, 111.500, 397.000, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate (pdb code 3zxw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate, PDB code: 3zxw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3zxw

Go back to Magnesium Binding Sites List in 3zxw
Magnesium binding site 1 out of 4 in the Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg476

b:35.0
occ:1.00
 OD1 A:ASP203 1.9 27.5 1.0
OE1 A:GLU204 2.1 26.4 1.0
O7 A:CAP477 2.3 25.5 1.0
O2 A:CAP477 2.4 42.0 1.0
O3 A:CAP477 2.5 33.0 1.0
OQ1 A:KCX201 2.6 31.6 1.0
OQ2 A:KCX201 2.9 35.5 1.0
C A:CAP477 3.1 61.8 1.0
CG A:ASP203 3.1 26.8 1.0
C2 A:CAP477 3.1 70.6 1.0
CD A:GLU204 3.2 28.2 1.0
CX A:KCX201 3.2 32.8 1.0
C3 A:CAP477 3.3 34.3 1.0
OE2 A:GLU204 3.7 30.9 1.0
NZ A:LYS177 3.7 29.2 1.0
N A:GLU204 3.7 22.5 1.0
OD2 A:ASP203 3.8 31.0 1.0
NZ A:LYS175 3.9 32.0 1.0
CA A:ASP203 4.0 23.1 1.0
NE2 A:HIS294 4.0 21.5 1.0
CB A:ASP203 4.1 23.4 1.0
CG2 A:THR173 4.1 32.3 1.0
O6 A:CAP477 4.3 33.1 1.0
CG A:GLU204 4.4 24.7 1.0
C A:ASP203 4.4 23.0 1.0
CB A:GLU204 4.5 23.0 1.0
NZ A:KCX201 4.5 34.7 1.0
C1 A:CAP477 4.5 35.2 1.0
C4 A:CAP477 4.6 27.3 1.0
CD2 A:HIS294 4.6 22.7 1.0
CA A:GLU204 4.7 22.7 1.0
OG1 A:THR173 4.9 33.6 1.0
O1 A:CAP477 4.9 43.2 1.0
CE1 A:HIS294 5.0 21.3 1.0

Magnesium binding site 2 out of 4 in 3zxw

Go back to Magnesium Binding Sites List in 3zxw
Magnesium binding site 2 out of 4 in the Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg476

b:28.1
occ:1.00
 OD1 C:ASP203 1.9 25.2 1.0
OE1 C:GLU204 2.1 26.3 1.0
O6 C:CAP477 2.3 24.2 1.0
O2 C:CAP477 2.3 36.2 1.0
O3 C:CAP477 2.4 25.6 1.0
OQ1 C:KCX201 2.4 27.1 1.0
OQ2 C:KCX201 2.9 37.3 1.0
C2 C:CAP477 3.0 57.9 1.0
C C:CAP477 3.0 47.9 1.0
CX C:KCX201 3.1 31.5 1.0
CG C:ASP203 3.2 30.3 1.0
CD C:GLU204 3.2 31.0 1.0
C3 C:CAP477 3.2 25.9 1.0
OE2 C:GLU204 3.7 33.1 1.0
N C:GLU204 3.7 19.3 1.0
NZ C:LYS177 3.8 25.9 1.0
NZ C:LYS175 3.9 32.2 1.0
NE2 C:HIS294 3.9 18.9 1.0
OD2 C:ASP203 3.9 34.7 1.0
CA C:ASP203 4.0 21.0 1.0
CB C:ASP203 4.1 21.1 1.0
CG2 C:THR173 4.1 30.6 1.0
O7 C:CAP477 4.2 25.1 1.0
CG C:GLU204 4.4 23.5 1.0
NZ C:KCX201 4.4 38.4 1.0
C C:ASP203 4.4 26.1 1.0
C4 C:CAP477 4.4 24.9 1.0
C1 C:CAP477 4.4 28.7 1.0
CB C:GLU204 4.5 20.7 1.0
CD2 C:HIS294 4.5 23.5 1.0
CA C:GLU204 4.7 19.7 1.0
CE1 C:HIS294 4.9 19.2 1.0
O1 C:CAP477 4.9 34.5 1.0
C5 C:CAP477 4.9 22.6 1.0
OG1 C:THR173 4.9 35.4 1.0

Magnesium binding site 3 out of 4 in 3zxw

Go back to Magnesium Binding Sites List in 3zxw
Magnesium binding site 3 out of 4 in the Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg476

b:30.4
occ:1.00
 OD1 E:ASP203 2.1 28.6 1.0
OE1 E:GLU204 2.1 26.0 1.0
O3 E:CAP477 2.3 24.1 1.0
O7 E:CAP477 2.3 29.1 1.0
O2 E:CAP477 2.3 35.3 1.0
OQ1 E:KCX201 2.5 27.0 1.0
OQ2 E:KCX201 3.0 38.2 1.0
C2 E:CAP477 3.0 65.0 1.0
C E:CAP477 3.0 50.2 1.0
CX E:KCX201 3.1 32.1 1.0
C3 E:CAP477 3.2 27.2 1.0
CG E:ASP203 3.2 31.8 1.0
CD E:GLU204 3.2 30.8 1.0
N E:GLU204 3.7 20.4 1.0
OE2 E:GLU204 3.8 33.2 1.0
NZ E:LYS177 3.8 29.1 1.0
NZ E:LYS175 4.0 31.5 1.0
NE2 E:HIS294 4.0 20.7 1.0
OD2 E:ASP203 4.0 35.6 1.0
CA E:ASP203 4.0 22.6 1.0
CG2 E:THR173 4.1 31.1 1.0
CB E:ASP203 4.2 20.3 1.0
O6 E:CAP477 4.2 29.2 1.0
C4 E:CAP477 4.4 27.2 1.0
CG E:GLU204 4.4 24.7 1.0
C E:ASP203 4.4 26.2 1.0
NZ E:KCX201 4.4 39.0 1.0
C1 E:CAP477 4.4 29.4 1.0
CB E:GLU204 4.4 19.9 1.0
CD2 E:HIS294 4.6 23.7 1.0
CA E:GLU204 4.7 18.1 1.0
OG1 E:THR173 4.8 35.3 1.0
O1 E:CAP477 4.8 42.1 1.0
C5 E:CAP477 4.9 27.0 1.0
CE1 E:HIS294 4.9 20.7 1.0
CB E:THR173 4.9 34.0 1.0

Magnesium binding site 4 out of 4 in 3zxw

Go back to Magnesium Binding Sites List in 3zxw
Magnesium binding site 4 out of 4 in the Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Activated Rubisco From Thermosynechococcus Elongatus Complexed with 2-Carboxyarabinitol-1,5-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg476

b:29.2
occ:1.00
 OD1 G:ASP203 2.0 27.7 1.0
OE1 G:GLU204 2.1 25.5 1.0
O2 G:CAP477 2.3 40.2 1.0
O3 G:CAP477 2.4 29.2 1.0
O7 G:CAP477 2.4 29.7 1.0
OQ1 G:KCX201 2.4 28.0 1.0
OQ2 G:KCX201 2.9 37.4 1.0
C2 G:CAP477 3.0 0.7 1.0
CX G:KCX201 3.0 30.6 1.0
C G:CAP477 3.1 50.9 1.0
CG G:ASP203 3.1 30.6 1.0
CD G:GLU204 3.2 30.6 1.0
C3 G:CAP477 3.3 30.9 1.0
N G:GLU204 3.6 19.8 1.0
OE2 G:GLU204 3.8 33.0 1.0
NZ G:LYS177 3.8 28.3 1.0
NE2 G:HIS294 3.9 20.1 1.0
OD2 G:ASP203 3.9 34.4 1.0
CA G:ASP203 4.0 23.7 1.0
NZ G:LYS175 4.0 31.6 1.0
CG2 G:THR173 4.1 29.7 1.0
CB G:ASP203 4.1 21.3 1.0
O6 G:CAP477 4.3 31.1 1.0
C G:ASP203 4.3 25.2 1.0
NZ G:KCX201 4.4 39.4 1.0
CG G:GLU204 4.4 24.8 1.0
CB G:GLU204 4.4 20.7 1.0
C4 G:CAP477 4.4 37.2 1.0
C1 G:CAP477 4.5 29.7 1.0
CD2 G:HIS294 4.6 22.5 1.0
CA G:GLU204 4.6 19.4 1.0
CE1 G:HIS294 4.8 20.1 1.0
OG1 G:THR173 4.8 35.6 1.0
O1 G:CAP477 4.9 33.3 1.0
C5 G:CAP477 4.9 22.8 1.0
CB G:THR173 5.0 33.8 1.0

Reference:

B.Terlecka, V.Wilhelmi, W.Bialek, B.Gubernator, A.Szczepaniak, E.Hofmann. Structure of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase From Thermosynechococcus Elongatus To Be Published.
Page generated: Thu Aug 15 14:10:07 2024

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