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Magnesium in PDB 1bwv: Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate

Enzymatic activity of Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate

All present enzymatic activity of Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate:
4.1.1.39;

Protein crystallography data

The structure of Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate, PDB code: 1bwv was solved by H.Sugawara, H.Yamamoto, N.Shibata, T.Inoue, C.Miyake, A.Yokota, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 117.070, 117.070, 319.630, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 19.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate (pdb code 1bwv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate, PDB code: 1bwv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1bwv

Go back to Magnesium Binding Sites List in 1bwv
Magnesium binding site 1 out of 4 in the Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg490

b:27.4
occ:1.00
 O3 A:CAP491 2.1 22.4 1.0
OQ1 A:KCX201 2.2 22.0 1.0
O2 A:CAP491 2.2 22.1 1.0
O7 A:CAP491 2.3 23.8 1.0
OE1 A:GLU204 2.5 13.6 1.0
OD1 A:ASP203 2.5 36.8 1.0
C2 A:CAP491 2.8 27.7 1.0
C3 A:CAP491 2.9 20.9 1.0
C A:CAP491 3.0 29.3 1.0
OQ2 A:KCX201 3.0 15.3 1.0
CX A:KCX201 3.0 23.9 1.0
CG A:ASP203 3.4 21.3 1.0
CD A:GLU204 3.5 26.7 1.0
OG1 A:THR173 3.7 14.7 1.0
CG2 A:THR173 3.9 6.9 1.0
OD2 A:ASP203 4.0 30.9 1.0
OE2 A:GLU204 4.1 14.4 1.0
C4 A:CAP491 4.1 13.6 1.0
O6 A:CAP491 4.1 26.7 1.0
NE2 A:HIS294 4.1 15.8 1.0
N A:GLU204 4.2 5.7 1.0
NZ A:LYS175 4.2 10.3 1.0
NZ A:KCX201 4.2 10.9 1.0
C1 A:CAP491 4.3 28.8 1.0
NZ A:LYS177 4.3 18.1 1.0
CD2 A:HIS294 4.4 16.1 1.0
CB A:THR173 4.4 7.3 1.0
CA A:ASP203 4.4 14.8 1.0
CB A:ASP203 4.5 10.4 1.0
C5 A:CAP491 4.5 2.0 1.0
CG A:GLU204 4.7 16.3 1.0
O1 A:CAP491 4.8 18.3 1.0
CB A:GLU204 4.8 5.6 1.0
C A:ASP203 4.9 8.3 1.0

Magnesium binding site 2 out of 4 in 1bwv

Go back to Magnesium Binding Sites List in 1bwv
Magnesium binding site 2 out of 4 in the Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg490

b:29.8
occ:1.00
 O3 C:CAP491 2.1 25.7 1.0
O2 C:CAP491 2.2 21.7 1.0
OQ1 C:KCX201 2.2 15.6 1.0
O7 C:CAP491 2.3 20.0 1.0
OD1 C:ASP203 2.4 33.5 1.0
OE1 C:GLU204 2.5 24.2 1.0
C2 C:CAP491 2.9 22.6 1.0
C3 C:CAP491 2.9 27.1 1.0
OQ2 C:KCX201 3.0 13.9 1.0
CX C:KCX201 3.0 14.1 1.0
C C:CAP491 3.0 25.8 1.0
CG C:ASP203 3.3 23.1 1.0
CD C:GLU204 3.5 30.0 1.0
OG1 C:THR173 3.8 22.8 1.0
CG2 C:THR173 3.9 17.2 1.0
OD2 C:ASP203 4.0 19.7 1.0
OE2 C:GLU204 4.0 14.0 1.0
C4 C:CAP491 4.1 13.5 1.0
NZ C:LYS175 4.2 3.9 1.0
NE2 C:HIS294 4.2 15.8 1.0
N C:GLU204 4.2 15.0 1.0
O6 C:CAP491 4.2 27.1 1.0
NZ C:LYS177 4.2 20.2 1.0
NZ C:KCX201 4.2 3.2 1.0
C1 C:CAP491 4.3 22.5 1.0
CB C:ASP203 4.3 9.0 1.0
CA C:ASP203 4.4 12.0 1.0
CB C:THR173 4.4 18.9 1.0
CD2 C:HIS294 4.4 13.7 1.0
C5 C:CAP491 4.6 13.1 1.0
CG C:GLU204 4.6 19.2 1.0
O1 C:CAP491 4.8 13.9 1.0
CB C:GLU204 4.8 16.8 1.0
C C:ASP203 4.8 17.1 1.0

Magnesium binding site 3 out of 4 in 1bwv

Go back to Magnesium Binding Sites List in 1bwv
Magnesium binding site 3 out of 4 in the Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg490

b:25.2
occ:1.00
 O3 E:CAP491 2.2 20.2 1.0
O2 E:CAP491 2.3 19.3 1.0
OQ1 E:KCX201 2.3 25.5 1.0
O7 E:CAP491 2.3 27.1 1.0
OE1 E:GLU204 2.4 16.4 1.0
OD1 E:ASP203 2.7 37.8 1.0
OQ2 E:KCX201 2.8 13.9 1.0
C2 E:CAP491 2.9 25.7 1.0
C3 E:CAP491 2.9 19.6 1.0
CX E:KCX201 3.0 23.9 1.0
C E:CAP491 3.0 31.6 1.0
CD E:GLU204 3.5 27.0 1.0
CG E:ASP203 3.6 21.2 1.0
OG1 E:THR173 3.8 16.8 1.0
CG2 E:THR173 3.9 6.4 1.0
OE2 E:GLU204 4.1 15.0 1.0
OD2 E:ASP203 4.1 29.8 1.0
C4 E:CAP491 4.1 12.5 1.0
NE2 E:HIS294 4.1 15.7 1.0
N E:GLU204 4.2 7.5 1.0
O6 E:CAP491 4.2 26.8 1.0
NZ E:LYS175 4.2 12.7 1.0
NZ E:KCX201 4.3 9.4 1.0
C1 E:CAP491 4.3 26.5 1.0
NZ E:LYS177 4.3 20.9 1.0
CD2 E:HIS294 4.3 18.1 1.0
CB E:THR173 4.4 9.1 1.0
CA E:ASP203 4.4 15.2 1.0
CB E:ASP203 4.6 14.0 1.0
C5 E:CAP491 4.6 4.0 1.0
CG E:GLU204 4.6 13.4 1.0
CB E:GLU204 4.8 8.4 1.0
O1 E:CAP491 4.8 20.2 1.0
C E:ASP203 4.9 10.6 1.0

Magnesium binding site 4 out of 4 in 1bwv

Go back to Magnesium Binding Sites List in 1bwv
Magnesium binding site 4 out of 4 in the Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg490

b:29.5
occ:1.00
 O3 G:CAP491 2.1 27.5 1.0
O2 G:CAP491 2.1 22.5 1.0
OQ1 G:KCX201 2.2 16.0 1.0
O7 G:CAP491 2.3 19.3 1.0
OD1 G:ASP203 2.5 31.9 1.0
OE1 G:GLU204 2.6 27.1 1.0
C2 G:CAP491 2.8 24.5 1.0
C3 G:CAP491 2.8 27.3 1.0
OQ2 G:KCX201 3.0 9.7 1.0
C G:CAP491 3.0 26.1 1.0
CX G:KCX201 3.0 12.8 1.0
CG G:ASP203 3.4 22.9 1.0
CD G:GLU204 3.6 30.9 1.0
OG1 G:THR173 3.7 25.3 1.0
CG2 G:THR173 3.9 16.7 1.0
OD2 G:ASP203 4.0 20.3 1.0
C4 G:CAP491 4.1 13.6 1.0
OE2 G:GLU204 4.1 13.6 1.0
NZ G:LYS175 4.1 4.9 1.0
O6 G:CAP491 4.2 27.5 1.0
NE2 G:HIS294 4.2 15.9 1.0
C1 G:CAP491 4.2 20.8 1.0
NZ G:KCX201 4.3 5.5 1.0
N G:GLU204 4.3 13.7 1.0
NZ G:LYS177 4.3 20.1 1.0
CB G:THR173 4.3 19.6 1.0
CD2 G:HIS294 4.4 11.5 1.0
CB G:ASP203 4.4 9.4 1.0
CA G:ASP203 4.4 13.2 1.0
C5 G:CAP491 4.6 11.2 1.0
O1 G:CAP491 4.7 15.3 1.0
CG G:GLU204 4.7 21.6 1.0
CB G:GLU204 4.9 15.9 1.0
C G:ASP203 4.9 16.8 1.0

Reference:

H.Sugawara, H.Yamamoto, N.Shibata, T.Inoue, S.Okada, C.Miyake, A.Yokota, Y.Kai. Crystal Structure of Carboxylase Reaction-Oriented Ribulose 1, 5-Bisphosphate Carboxylase/Oxygenase From A Thermophilic Red Alga, Galdieria Partita. J.Biol.Chem. V. 274 15655 1999.
ISSN: ISSN 0021-9258
PubMed: 10336462
DOI: 10.1074/JBC.274.22.15655
Page generated: Tue Aug 13 02:15:45 2024

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