Magnesium in PDB 8ruc: Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate

Enzymatic activity of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate

All present enzymatic activity of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate:
4.1.1.39;

Protein crystallography data

The structure of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate, PDB code: 8ruc was solved by I.Andersson, S.Knight, C.-I.Branden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 157.200, 157.200, 201.300, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate (pdb code 8ruc). 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 Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate, PDB code: 8ruc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8ruc

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Magnesium binding site 1 out of 4 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

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

b:15.1
occ:1.00
OE1 A:GLU204 2.3 8.8 1.0
OD1 A:ASP203 2.3 12.9 1.0
O6 A:CAP477 2.3 13.5 1.0
OQ2 A:KCX201 2.3 10.8 1.0
O2 A:CAP477 2.4 15.2 1.0
O3 A:CAP477 2.4 13.9 1.0
C2 A:CAP477 2.9 16.5 1.0
C A:CAP477 2.9 16.4 1.0
C3 A:CAP477 3.2 14.0 1.0
CD A:GLU204 3.3 12.4 1.0
CX A:KCX201 3.3 14.6 1.0
CG A:ASP203 3.3 11.8 1.0
OQ1 A:KCX201 3.5 12.3 1.0
OE2 A:GLU204 3.7 13.9 1.0
NZ A:LYS177 3.7 10.3 1.0
N A:GLU204 3.8 9.0 1.0
CG2 A:THR173 3.8 10.0 1.0
OD2 A:ASP203 3.9 9.9 1.0
NZ A:LYS175 4.0 6.3 1.0
NE2 A:HIS294 4.0 7.4 1.0
O7 A:CAP477 4.1 14.1 1.0
CA A:ASP203 4.2 10.6 1.0
CB A:ASP203 4.3 7.9 1.0
C1 A:CAP477 4.4 12.1 1.0
C4 A:CAP477 4.4 13.0 1.0
OG1 A:THR173 4.4 7.7 1.0
CG A:GLU204 4.5 12.4 1.0
NZ A:KCX201 4.5 6.8 1.0
C A:ASP203 4.5 9.9 1.0
CB A:GLU204 4.6 9.6 1.0
CB A:THR173 4.6 10.1 1.0
CD2 A:HIS294 4.6 5.8 1.0
O1 A:CAP477 4.8 12.2 1.0
CA A:GLU204 4.8 8.6 1.0
C5 A:CAP477 4.9 11.0 1.0

Magnesium binding site 2 out of 4 in 8ruc

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Magnesium binding site 2 out of 4 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg476

b:15.1
occ:1.00
OD1 C:ASP203 2.3 11.9 1.0
OE1 C:GLU204 2.3 11.9 1.0
OQ2 C:KCX201 2.3 11.3 1.0
O3 C:CAP477 2.3 11.2 1.0
O6 C:CAP477 2.4 14.5 1.0
O2 C:CAP477 2.4 13.0 1.0
C2 C:CAP477 2.8 15.2 1.0
C C:CAP477 2.9 13.6 1.0
C3 C:CAP477 3.1 13.3 1.0
CX C:KCX201 3.2 11.7 1.0
CD C:GLU204 3.2 13.5 1.0
OQ1 C:KCX201 3.3 11.1 1.0
CG C:ASP203 3.4 13.6 1.0
OE2 C:GLU204 3.6 12.6 1.0
NZ C:LYS177 3.8 8.2 1.0
N C:GLU204 3.9 6.1 1.0
NZ C:LYS175 4.0 5.9 1.0
CG2 C:THR173 4.0 5.6 1.0
NE2 C:HIS294 4.0 9.8 1.0
O7 C:CAP477 4.1 12.8 1.0
OD2 C:ASP203 4.1 18.3 1.0
CA C:ASP203 4.2 8.1 1.0
OG1 C:THR173 4.3 10.8 1.0
C4 C:CAP477 4.3 14.4 1.0
C1 C:CAP477 4.3 13.9 1.0
CB C:ASP203 4.4 10.1 1.0
NZ C:KCX201 4.4 8.9 1.0
CG C:GLU204 4.5 3.9 1.0
C C:ASP203 4.6 6.9 1.0
CB C:GLU204 4.6 5.9 1.0
CD2 C:HIS294 4.6 8.1 1.0
CB C:THR173 4.7 10.6 1.0
C5 C:CAP477 4.8 11.9 1.0
O1 C:CAP477 4.9 13.8 1.0
CA C:GLU204 4.9 7.2 1.0
CE1 C:HIS294 4.9 10.9 1.0

Magnesium binding site 3 out of 4 in 8ruc

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Magnesium binding site 3 out of 4 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg476

b:15.4
occ:1.00
OQ2 E:KCX201 2.3 10.9 1.0
OD1 E:ASP203 2.3 10.9 1.0
OE1 E:GLU204 2.3 12.4 1.0
O6 E:CAP477 2.3 14.6 1.0
O2 E:CAP477 2.4 12.7 1.0
O3 E:CAP477 2.4 15.4 1.0
C2 E:CAP477 3.0 14.4 1.0
C E:CAP477 3.0 14.3 1.0
C3 E:CAP477 3.2 13.9 1.0
CX E:KCX201 3.2 13.2 1.0
CD E:GLU204 3.3 12.6 1.0
CG E:ASP203 3.3 11.1 1.0
OQ1 E:KCX201 3.3 10.0 1.0
OE2 E:GLU204 3.6 9.2 1.0
NZ E:LYS177 3.9 11.3 1.0
N E:GLU204 3.9 5.6 1.0
OD2 E:ASP203 3.9 9.7 1.0
NE2 E:HIS294 4.0 6.0 1.0
CG2 E:THR173 4.0 8.7 1.0
NZ E:LYS175 4.1 5.5 1.0
CA E:ASP203 4.2 8.9 1.0
O7 E:CAP477 4.2 13.4 1.0
CB E:ASP203 4.3 7.5 1.0
OG1 E:THR173 4.4 10.9 1.0
C4 E:CAP477 4.4 14.1 1.0
C1 E:CAP477 4.4 10.7 1.0
NZ E:KCX201 4.4 8.2 1.0
CG E:GLU204 4.5 8.2 1.0
C E:ASP203 4.5 9.2 1.0
CB E:GLU204 4.6 9.4 1.0
CD2 E:HIS294 4.7 5.9 1.0
CB E:THR173 4.7 8.8 1.0
O1 E:CAP477 4.8 12.4 1.0
C5 E:CAP477 4.8 10.1 1.0
CE1 E:HIS294 4.8 5.8 1.0
CA E:GLU204 4.9 8.1 1.0

Magnesium binding site 4 out of 4 in 8ruc

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Magnesium binding site 4 out of 4 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg476

b:14.2
occ:1.00
OE1 G:GLU204 2.3 12.5 1.0
OD1 G:ASP203 2.3 15.3 1.0
OQ2 G:KCX201 2.3 14.6 1.0
O2 G:CAP477 2.3 13.8 1.0
O6 G:CAP477 2.4 10.9 1.0
O3 G:CAP477 2.4 9.5 1.0
C2 G:CAP477 2.8 12.9 1.0
C G:CAP477 2.9 11.5 1.0
C3 G:CAP477 3.1 13.6 1.0
CX G:KCX201 3.2 14.5 1.0
OQ1 G:KCX201 3.3 12.2 1.0
CD G:GLU204 3.3 13.6 1.0
CG G:ASP203 3.4 11.4 1.0
OE2 G:GLU204 3.8 13.8 1.0
N G:GLU204 3.8 5.1 1.0
NZ G:LYS177 4.0 12.0 1.0
NE2 G:HIS294 4.0 8.5 1.0
CG2 G:THR173 4.0 10.2 1.0
OD2 G:ASP203 4.0 11.1 1.0
O7 G:CAP477 4.1 10.7 1.0
NZ G:LYS175 4.1 14.0 1.0
CA G:ASP203 4.2 8.8 1.0
C4 G:CAP477 4.2 14.1 1.0
OG1 G:THR173 4.3 12.3 1.0
C1 G:CAP477 4.3 14.6 1.0
CB G:ASP203 4.4 9.0 1.0
NZ G:KCX201 4.5 11.7 1.0
CD2 G:HIS294 4.5 7.7 1.0
CG G:GLU204 4.5 6.3 1.0
C G:ASP203 4.5 8.2 1.0
CB G:GLU204 4.6 6.3 1.0
CB G:THR173 4.7 10.8 1.0
C5 G:CAP477 4.7 11.2 1.0
O1 G:CAP477 4.8 13.3 1.0
CA G:GLU204 4.8 6.7 1.0
CE1 G:HIS294 4.9 5.9 1.0

Reference:

I.Andersson, I.Andersson, S.Knight, C.-I.Branden. N/A N/A.
ISSN: ISSN 0022-2836
PubMed: 8648644
DOI: 10.1006/JMBI.1996.0310
Page generated: Tue Dec 15 03:45:45 2020

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