Magnesium in PDB 8bdb: Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis

Enzymatic activity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis

All present enzymatic activity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis:
4.1.1.39;

Protein crystallography data

The structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis, PDB code: 8bdb was solved by I.Andersson, L.H.Gunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.60 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.328, 131.925, 196.319, 90, 94.75, 90
R / Rfree (%) 15.8 / 17.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis (pdb code 8bdb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis, PDB code: 8bdb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8bdb

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Magnesium binding site 1 out of 8 in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:16.7
occ:1.00
OD1 A:ASP207 1.9 14.4 1.0
OE1 A:GLU208 2.0 14.4 1.0
OQ1 A:KCX205 2.0 15.5 1.0
O6 A:CAP502 2.1 16.2 1.0
O3 A:CAP502 2.2 16.5 1.0
O2 A:CAP502 2.3 16.2 1.0
C A:CAP502 2.9 16.3 1.0
C2 A:CAP502 2.9 16.4 1.0
CD A:GLU208 3.1 14.3 1.0
C3 A:CAP502 3.1 16.4 1.0
CX A:KCX205 3.1 15.7 1.0
CG A:ASP207 3.1 15.0 1.0
OQ2 A:KCX205 3.4 16.0 1.0
OE2 A:GLU208 3.5 14.8 1.0
NZ A:LYS181 3.6 16.5 1.0
OD2 A:ASP207 3.8 15.3 1.0
N A:GLU208 3.8 13.6 1.0
NZ A:LYS179 3.9 16.4 1.0
NE2 A:HIS297 4.0 14.1 1.0
CG2 A:THR177 4.0 15.1 1.0
O7 A:CAP502 4.1 15.7 1.0
CA A:ASP207 4.2 14.0 1.0
CB A:ASP207 4.2 14.4 1.0
NZ A:KCX205 4.3 15.1 1.0
CG A:GLU208 4.3 14.0 1.0
C4 A:CAP502 4.4 16.4 1.0
C1 A:CAP502 4.4 16.7 1.0
OG1 A:THR177 4.4 15.7 1.0
CD2 A:HIS297 4.4 14.0 1.0
CB A:GLU208 4.5 13.7 1.0
C A:ASP207 4.6 13.8 1.0
CB A:THR177 4.7 15.2 1.0
CA A:GLU208 4.8 13.6 1.0
C5 A:CAP502 4.9 16.3 1.0
O1 A:CAP502 4.9 16.6 1.0
CE1 A:HIS297 4.9 14.1 1.0

Magnesium binding site 2 out of 8 in 8bdb

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Magnesium binding site 2 out of 8 in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:15.5
occ:1.00
OD1 C:ASP207 1.9 14.6 1.0
OQ2 C:KCX205 2.0 12.7 1.0
OE1 C:GLU208 2.1 14.5 1.0
O7 C:CAP502 2.1 14.9 1.0
O3 C:CAP502 2.2 15.7 1.0
O2 C:CAP502 2.4 15.8 1.0
C C:CAP502 2.9 15.5 1.0
C2 C:CAP502 2.9 15.4 1.0
CX C:KCX205 3.1 13.1 1.0
CD C:GLU208 3.1 14.5 1.0
C3 C:CAP502 3.1 15.7 1.0
CG C:ASP207 3.1 14.9 1.0
OQ1 C:KCX205 3.3 13.0 1.0
OE2 C:GLU208 3.5 15.9 1.0
NZ C:LYS181 3.7 16.1 1.0
N C:GLU208 3.8 13.7 1.0
OD2 C:ASP207 3.8 16.0 1.0
NZ C:LYS179 3.9 15.6 1.0
CG2 C:THR177 3.9 15.0 1.0
NE2 C:HIS297 4.0 13.3 1.0
O6 C:CAP502 4.1 14.8 1.0
CA C:ASP207 4.2 14.0 1.0
CB C:ASP207 4.2 14.3 1.0
NZ C:KCX205 4.2 12.9 1.0
OG1 C:THR177 4.3 14.4 1.0
CG C:GLU208 4.4 14.2 1.0
C4 C:CAP502 4.4 15.7 1.0
C1 C:CAP502 4.4 15.7 1.0
CD2 C:HIS297 4.5 13.4 1.0
C C:ASP207 4.5 13.6 1.0
CB C:GLU208 4.5 14.0 1.0
CB C:THR177 4.7 14.9 1.0
CA C:GLU208 4.8 13.8 1.0
C5 C:CAP502 4.9 15.7 1.0
O1 C:CAP502 4.9 15.5 1.0
CE1 C:HIS297 5.0 13.6 1.0

Magnesium binding site 3 out of 8 in 8bdb

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Magnesium binding site 3 out of 8 in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:15.0
occ:1.00
OD1 E:ASP207 2.0 14.9 1.0
OQ2 E:KCX205 2.0 13.2 1.0
OE1 E:GLU208 2.1 13.5 1.0
O6 E:CAP502 2.1 15.5 1.0
O3 E:CAP502 2.2 15.7 1.0
O2 E:CAP502 2.3 15.2 1.0
C E:CAP502 2.9 16.1 1.0
C2 E:CAP502 2.9 15.8 1.0
CX E:KCX205 3.1 13.5 1.0
C3 E:CAP502 3.1 15.8 1.0
CD E:GLU208 3.1 13.8 1.0
CG E:ASP207 3.1 14.8 1.0
OQ1 E:KCX205 3.3 13.6 1.0
OE2 E:GLU208 3.6 14.9 1.0
NZ E:LYS181 3.7 14.7 1.0
OD2 E:ASP207 3.8 15.0 1.0
N E:GLU208 3.8 13.3 1.0
CG2 E:THR177 4.0 14.4 1.0
NE2 E:HIS297 4.0 13.9 1.0
NZ E:LYS179 4.0 16.0 1.0
O7 E:CAP502 4.1 16.2 1.0
NZ E:KCX205 4.2 13.3 1.0
CA E:ASP207 4.2 13.2 1.0
CB E:ASP207 4.2 13.9 1.0
C4 E:CAP502 4.3 15.8 1.0
OG1 E:THR177 4.3 14.4 1.0
CG E:GLU208 4.4 13.8 1.0
C1 E:CAP502 4.4 15.6 1.0
CD2 E:HIS297 4.5 13.9 1.0
CB E:GLU208 4.5 13.6 1.0
C E:ASP207 4.6 13.2 1.0
CB E:THR177 4.7 14.5 1.0
CA E:GLU208 4.8 13.4 1.0
C5 E:CAP502 4.8 15.3 1.0
O1 E:CAP502 4.9 15.7 1.0

Magnesium binding site 4 out of 8 in 8bdb

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Magnesium binding site 4 out of 8 in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:14.1
occ:1.00
OD1 G:ASP207 1.9 12.6 1.0
OQ1 G:KCX205 2.0 12.8 1.0
OE1 G:GLU208 2.1 13.3 1.0
O7 G:CAP502 2.1 13.4 1.0
O3 G:CAP502 2.2 12.4 1.0
O2 G:CAP502 2.3 12.9 1.0
C G:CAP502 2.9 13.4 1.0
C2 G:CAP502 2.9 13.1 1.0
CX G:KCX205 3.1 12.8 1.0
C3 G:CAP502 3.1 12.9 1.0
CD G:GLU208 3.1 13.2 1.0
CG G:ASP207 3.2 12.7 1.0
OQ2 G:KCX205 3.3 13.2 1.0
OE2 G:GLU208 3.6 14.2 1.0
NZ G:LYS181 3.7 15.7 1.0
OD2 G:ASP207 3.8 13.4 1.0
N G:GLU208 3.9 12.1 1.0
NE2 G:HIS297 3.9 11.8 1.0
NZ G:LYS179 4.0 13.0 1.0
CG2 G:THR177 4.0 12.2 1.0
O6 G:CAP502 4.1 13.1 1.0
CA G:ASP207 4.2 11.9 1.0
NZ G:KCX205 4.2 12.9 1.0
CB G:ASP207 4.2 12.2 1.0
OG1 G:THR177 4.3 12.4 1.0
C4 G:CAP502 4.3 13.1 1.0
CG G:GLU208 4.4 12.9 1.0
C1 G:CAP502 4.4 13.1 1.0
CD2 G:HIS297 4.4 11.5 1.0
CB G:GLU208 4.6 12.4 1.0
C G:ASP207 4.6 11.9 1.0
CB G:THR177 4.7 12.4 1.0
C5 G:CAP502 4.8 12.9 1.0
CA G:GLU208 4.8 12.2 1.0
O1 G:CAP502 4.9 13.3 1.0
CE1 G:HIS297 4.9 11.9 1.0

Magnesium binding site 5 out of 8 in 8bdb

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Magnesium binding site 5 out of 8 in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg501

b:14.4
occ:1.00
OD1 I:ASP207 1.9 14.4 1.0
OQ2 I:KCX205 2.0 12.8 1.0
OE1 I:GLU208 2.0 14.7 1.0
O7 I:CAP502 2.2 15.5 1.0
O3 I:CAP502 2.2 15.3 1.0
O2 I:CAP502 2.4 15.7 1.0
C I:CAP502 3.0 15.7 1.0
C2 I:CAP502 3.0 15.4 1.0
CX I:KCX205 3.1 13.3 1.0
CD I:GLU208 3.1 14.8 1.0
CG I:ASP207 3.1 14.9 1.0
C3 I:CAP502 3.1 15.4 1.0
OQ1 I:KCX205 3.3 13.6 1.0
OE2 I:GLU208 3.5 16.0 1.0
NZ I:LYS181 3.7 16.2 1.0
N I:GLU208 3.8 13.8 1.0
OD2 I:ASP207 3.8 15.9 1.0
CG2 I:THR177 4.0 15.0 1.0
NE2 I:HIS297 4.0 14.6 1.0
NZ I:LYS179 4.0 15.8 1.0
CA I:ASP207 4.2 13.8 1.0
O6 I:CAP502 4.2 15.9 1.0
CB I:ASP207 4.2 14.4 1.0
NZ I:KCX205 4.2 13.0 1.0
CG I:GLU208 4.3 14.7 1.0
OG1 I:THR177 4.3 15.0 1.0
C4 I:CAP502 4.4 15.4 1.0
C1 I:CAP502 4.4 15.2 1.0
CD2 I:HIS297 4.4 14.3 1.0
C I:ASP207 4.5 13.9 1.0
CB I:GLU208 4.5 14.2 1.0
CB I:THR177 4.7 14.8 1.0
CA I:GLU208 4.7 13.9 1.0
C5 I:CAP502 4.9 15.2 1.0
O1 I:CAP502 4.9 14.9 1.0
CE1 I:HIS297 5.0 14.7 1.0

Magnesium binding site 6 out of 8 in 8bdb

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Magnesium binding site 6 out of 8 in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg501

b:13.7
occ:1.00
OE1 K:GLU208 2.0 12.7 1.0
OD1 K:ASP207 2.0 12.9 1.0
OQ1 K:KCX205 2.0 12.5 1.0
O6 K:CAP502 2.1 12.9 1.0
O3 K:CAP502 2.2 12.8 1.0
O2 K:CAP502 2.3 13.2 1.0
C K:CAP502 2.9 13.4 1.0
C2 K:CAP502 2.9 13.2 1.0
CD K:GLU208 3.1 12.5 1.0
C3 K:CAP502 3.1 13.1 1.0
CX K:KCX205 3.1 12.6 1.0
CG K:ASP207 3.2 12.8 1.0
OQ2 K:KCX205 3.3 12.9 1.0
OE2 K:GLU208 3.5 12.7 1.0
NZ K:LYS181 3.7 14.3 1.0
N K:GLU208 3.9 11.6 1.0
OD2 K:ASP207 3.9 13.7 1.0
NZ K:LYS179 3.9 12.5 1.0
NE2 K:HIS297 4.0 12.0 1.0
CG2 K:THR177 4.0 12.2 1.0
O7 K:CAP502 4.1 13.0 1.0
CA K:ASP207 4.3 11.7 1.0
CB K:ASP207 4.3 12.1 1.0
NZ K:KCX205 4.3 12.2 1.0
CG K:GLU208 4.3 12.1 1.0
C4 K:CAP502 4.3 13.3 1.0
OG1 K:THR177 4.4 12.4 1.0
C1 K:CAP502 4.4 13.4 1.0
CD2 K:HIS297 4.5 12.0 1.0
CB K:GLU208 4.5 11.9 1.0
C K:ASP207 4.6 11.7 1.0
CB K:THR177 4.7 12.1 1.0
CA K:GLU208 4.8 11.7 1.0
C5 K:CAP502 4.8 13.2 1.0
O1 K:CAP502 4.9 13.6 1.0
CE1 K:HIS297 5.0 12.3 1.0

Magnesium binding site 7 out of 8 in 8bdb

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Magnesium binding site 7 out of 8 in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg501

b:16.8
occ:1.00
OD1 M:ASP207 2.0 14.6 1.0
OQ2 M:KCX205 2.0 16.4 1.0
OE1 M:GLU208 2.0 16.2 1.0
O7 M:CAP502 2.2 18.5 1.0
O3 M:CAP502 2.2 18.9 1.0
O2 M:CAP502 2.4 18.0 1.0
C2 M:CAP502 2.9 18.4 1.0
C M:CAP502 2.9 18.4 1.0
CX M:KCX205 3.1 16.0 1.0
C3 M:CAP502 3.1 18.2 1.0
CD M:GLU208 3.1 16.7 1.0
CG M:ASP207 3.1 15.7 1.0
OQ1 M:KCX205 3.3 16.0 1.0
OE2 M:GLU208 3.6 17.2 1.0
NZ M:LYS181 3.7 16.8 1.0
N M:GLU208 3.8 15.5 1.0
OD2 M:ASP207 3.8 16.8 1.0
CG2 M:THR177 4.0 16.5 1.0
NZ M:LYS179 4.0 17.5 1.0
NE2 M:HIS297 4.0 15.8 1.0
O6 M:CAP502 4.2 19.0 1.0
CA M:ASP207 4.2 15.5 1.0
CB M:ASP207 4.2 15.5 1.0
NZ M:KCX205 4.2 15.4 1.0
OG1 M:THR177 4.3 16.4 1.0
CG M:GLU208 4.3 16.4 1.0
C4 M:CAP502 4.4 18.2 1.0
C1 M:CAP502 4.4 17.4 1.0
CD2 M:HIS297 4.4 15.7 1.0
CB M:GLU208 4.5 16.1 1.0
C M:ASP207 4.5 15.6 1.0
CB M:THR177 4.7 16.4 1.0
CA M:GLU208 4.8 15.6 1.0
C5 M:CAP502 4.9 17.9 1.0
O1 M:CAP502 4.9 17.2 1.0
CE1 M:HIS297 5.0 15.7 1.0

Magnesium binding site 8 out of 8 in 8bdb

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Magnesium binding site 8 out of 8 in the Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Griffithsia Monilis within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg501

b:15.3
occ:1.00
OD1 O:ASP207 2.0 13.2 1.0
OQ1 O:KCX205 2.0 13.0 1.0
OE1 O:GLU208 2.1 13.5 1.0
O6 O:CAP502 2.1 14.8 1.0
O3 O:CAP502 2.2 15.8 1.0
O2 O:CAP502 2.3 15.2 1.0
C O:CAP502 2.9 15.3 1.0
C2 O:CAP502 2.9 15.6 1.0
C3 O:CAP502 3.1 15.6 1.0
CX O:KCX205 3.1 13.9 1.0
CD O:GLU208 3.1 13.6 1.0
CG O:ASP207 3.2 13.3 1.0
OQ2 O:KCX205 3.3 14.0 1.0
OE2 O:GLU208 3.6 14.1 1.0
NZ O:LYS181 3.7 14.9 1.0
N O:GLU208 3.8 12.4 1.0
OD2 O:ASP207 3.9 13.7 1.0
NZ O:LYS179 3.9 14.8 1.0
NE2 O:HIS297 4.0 13.6 1.0
CG2 O:THR177 4.0 14.3 1.0
O7 O:CAP502 4.1 14.9 1.0
CA O:ASP207 4.2 12.7 1.0
CB O:ASP207 4.2 12.9 1.0
NZ O:KCX205 4.3 13.8 1.0
C4 O:CAP502 4.3 15.8 1.0
OG1 O:THR177 4.4 14.3 1.0
CG O:GLU208 4.4 13.3 1.0
C1 O:CAP502 4.4 15.4 1.0
CD2 O:HIS297 4.5 13.6 1.0
C O:ASP207 4.6 12.5 1.0
CB O:GLU208 4.6 12.9 1.0
CB O:THR177 4.7 14.4 1.0
CA O:GLU208 4.8 12.6 1.0
C5 O:CAP502 4.9 15.3 1.0
O1 O:CAP502 4.9 15.2 1.0
CE1 O:HIS297 5.0 13.7 1.0

Reference:

Y.Zhou, L.H.Gunn, R.Birch, I.Andersson, S.M.Whitney. Grafting Rhodobacter Sphaeroides with Red Algae Rubisco to Enhance Catalysis and Accelerate Plant Growth To Be Published.
DOI: 10.1038/S41477-023-01436-7
Page generated: Thu Jul 27 22:33:52 2023

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