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Magnesium in PDB 1ir1: Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate

Enzymatic activity of Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate

All present enzymatic activity of Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate:
4.1.1.39;

Protein crystallography data

The structure of Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate, PDB code: 1ir1 was solved by E.Mizohata, H.Matsumura, Y.Okano, M.Kumei, H.Takuma, J.Onodera, K.Kato, N.Shibata, T.Inoue, A.Yokota, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 157.800, 157.800, 200.900, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 17.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate (pdb code 1ir1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate, PDB code: 1ir1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ir1

Go back to Magnesium Binding Sites List in 1ir1
Magnesium binding site 1 out of 4 in the Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 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 Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg476

b:6.9
occ:1.00
 OE1 A:GLU204 2.0 6.1 1.0
OD1 A:ASP203 2.0 10.6 1.0
OQ2 A:KCX201 2.1 7.9 1.0
O3 A:CAP501 2.2 6.5 1.0
O6 A:CAP501 2.3 11.0 1.0
O2 A:CAP501 2.3 8.7 1.0
C2 A:CAP501 2.8 9.5 1.0
C A:CAP501 2.9 9.6 1.0
C3 A:CAP501 3.0 6.9 1.0
CX A:KCX201 3.1 9.5 1.0
CD A:GLU204 3.1 7.9 1.0
CG A:ASP203 3.2 7.3 1.0
OQ1 A:KCX201 3.3 8.8 1.0
OE2 A:GLU204 3.7 7.6 1.0
N A:GLU204 3.8 7.0 1.0
NZ A:LYS177 3.9 7.5 1.0
NE2 A:HIS294 4.0 7.8 1.0
OD2 A:ASP203 4.0 10.4 1.0
CG2 A:THR173 4.0 8.4 1.0
O7 A:CAP501 4.1 9.1 1.0
NZ A:LYS175 4.1 7.6 1.0
CA A:ASP203 4.2 8.5 1.0
CB A:ASP203 4.3 7.8 1.0
NZ A:KCX201 4.3 7.6 1.0
C4 A:CAP501 4.3 7.8 1.0
C1 A:CAP501 4.3 8.6 1.0
CG A:GLU204 4.3 5.3 1.0
OG1 A:THR173 4.5 7.8 1.0
CB A:GLU204 4.5 6.1 1.0
C A:ASP203 4.5 8.1 1.0
CD2 A:HIS294 4.6 6.8 1.0
CB A:THR173 4.8 9.0 1.0
CA A:GLU204 4.8 5.7 1.0
C5 A:CAP501 4.8 7.2 1.0
O1 A:CAP501 4.9 11.5 1.0
CE1 A:HIS294 4.9 7.7 1.0

Magnesium binding site 2 out of 4 in 1ir1

Go back to Magnesium Binding Sites List in 1ir1
Magnesium binding site 2 out of 4 in the Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 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 Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg476

b:8.4
occ:1.00
 OE1 B:GLU204 2.0 6.7 1.0
OD1 B:ASP203 2.0 9.3 1.0
O6 B:CAP501 2.1 7.1 1.0
OQ2 B:KCX201 2.2 6.2 1.0
O3 B:CAP501 2.3 9.5 1.0
O2 B:CAP501 2.4 11.1 1.0
C B:CAP501 2.8 9.2 1.0
C2 B:CAP501 2.8 9.9 1.0
C3 B:CAP501 3.1 10.5 1.0
CD B:GLU204 3.1 8.5 1.0
CX B:KCX201 3.2 6.9 1.0
CG B:ASP203 3.2 7.3 1.0
OQ1 B:KCX201 3.4 5.1 1.0
OE2 B:GLU204 3.5 8.7 1.0
NZ B:LYS177 3.8 8.9 1.0
N B:GLU204 3.8 5.5 1.0
OD2 B:ASP203 3.9 9.5 1.0
NE2 B:HIS294 4.0 8.3 1.0
O7 B:CAP501 4.0 9.9 1.0
NZ B:LYS175 4.0 5.9 1.0
CG2 B:THR173 4.1 5.9 1.0
CA B:ASP203 4.2 6.6 1.0
CB B:ASP203 4.3 5.7 1.0
C4 B:CAP501 4.3 9.6 1.0
CG B:GLU204 4.3 6.4 1.0
C1 B:CAP501 4.3 9.8 1.0
NZ B:KCX201 4.4 7.3 1.0
CB B:GLU204 4.5 7.2 1.0
C B:ASP203 4.5 7.0 1.0
OG1 B:THR173 4.5 8.6 1.0
CD2 B:HIS294 4.7 7.3 1.0
CA B:GLU204 4.8 6.2 1.0
C5 B:CAP501 4.8 9.0 1.0
CB B:THR173 4.9 6.9 1.0
CE1 B:HIS294 4.9 8.7 1.0
O1 B:CAP501 4.9 9.3 1.0

Magnesium binding site 3 out of 4 in 1ir1

Go back to Magnesium Binding Sites List in 1ir1
Magnesium binding site 3 out of 4 in the Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 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 Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg476

b:7.0
occ:1.00
 OD1 C:ASP203 2.0 8.1 1.0
OE1 C:GLU204 2.1 8.9 1.0
OQ2 C:KCX201 2.1 5.8 1.0
O3 C:CAP501 2.2 10.3 1.0
O6 C:CAP501 2.2 7.9 1.0
O2 C:CAP501 2.3 9.4 1.0
C2 C:CAP501 2.8 9.9 1.0
C C:CAP501 2.9 10.4 1.0
C3 C:CAP501 3.0 10.2 1.0
CX C:KCX201 3.1 6.5 1.0
CD C:GLU204 3.1 9.3 1.0
CG C:ASP203 3.2 7.4 1.0
OQ1 C:KCX201 3.3 7.1 1.0
OE2 C:GLU204 3.6 9.1 1.0
N C:GLU204 3.8 7.5 1.0
NZ C:LYS177 3.8 4.0 1.0
OD2 C:ASP203 3.9 8.2 1.0
NE2 C:HIS294 4.0 5.8 1.0
NZ C:LYS175 4.0 7.7 1.0
CG2 C:THR173 4.0 6.8 1.0
O7 C:CAP501 4.1 9.1 1.0
CA C:ASP203 4.2 7.8 1.0
CB C:ASP203 4.3 6.6 1.0
NZ C:KCX201 4.3 6.6 1.0
C4 C:CAP501 4.3 10.0 1.0
C1 C:CAP501 4.3 10.1 1.0
CG C:GLU204 4.3 6.2 1.0
OG1 C:THR173 4.5 9.8 1.0
CB C:GLU204 4.5 5.7 1.0
C C:ASP203 4.5 7.4 1.0
CD2 C:HIS294 4.7 5.5 1.0
CB C:THR173 4.8 8.6 1.0
C5 C:CAP501 4.8 9.1 1.0
CA C:GLU204 4.8 7.8 1.0
O1 C:CAP501 4.9 9.7 1.0
CE1 C:HIS294 4.9 6.1 1.0

Magnesium binding site 4 out of 4 in 1ir1

Go back to Magnesium Binding Sites List in 1ir1
Magnesium binding site 4 out of 4 in the Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 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 Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, MG2+ and 2- Carboxyarabinitol-1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg476

b:7.7
occ:1.00
 OD1 D:ASP203 2.1 9.0 1.0
OE1 D:GLU204 2.1 6.7 1.0
OQ2 D:KCX201 2.1 5.6 1.0
O6 D:CAP501 2.2 8.9 1.0
O3 D:CAP501 2.2 9.7 1.0
O2 D:CAP501 2.3 8.2 1.0
C2 D:CAP501 2.8 8.9 1.0
C D:CAP501 2.8 9.1 1.0
C3 D:CAP501 3.0 9.1 1.0
CX D:KCX201 3.1 7.9 1.0
CD D:GLU204 3.1 6.5 1.0
CG D:ASP203 3.2 9.3 1.0
OQ1 D:KCX201 3.3 7.7 1.0
OE2 D:GLU204 3.6 7.9 1.0
NZ D:LYS177 3.8 8.9 1.0
N D:GLU204 3.9 8.3 1.0
OD2 D:ASP203 3.9 8.8 1.0
NZ D:LYS175 4.0 6.0 1.0
O7 D:CAP501 4.0 8.4 1.0
NE2 D:HIS294 4.0 7.5 1.0
CG2 D:THR173 4.1 4.7 1.0
CA D:ASP203 4.2 7.8 1.0
C4 D:CAP501 4.3 9.8 1.0
CB D:ASP203 4.3 8.6 1.0
NZ D:KCX201 4.3 7.3 1.0
C1 D:CAP501 4.3 9.1 1.0
CG D:GLU204 4.4 5.7 1.0
OG1 D:THR173 4.5 9.0 1.0
CB D:GLU204 4.5 6.7 1.0
C D:ASP203 4.6 8.8 1.0
CD2 D:HIS294 4.7 7.8 1.0
C5 D:CAP501 4.7 7.2 1.0
CB D:THR173 4.8 6.2 1.0
CA D:GLU204 4.8 7.0 1.0
O1 D:CAP501 4.9 9.3 1.0
CE1 D:HIS294 4.9 7.1 1.0

Reference:

E.Mizohata, H.Matsumura, Y.Okano, M.Kumei, H.Takuma, J.Onodera, K.Kato, N.Shibata, T.Inoue, A.Yokota, Y.Kai. Crystal Structure of Activated Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Green Alga Chlamydomonas Reinhardtii Complexed with 2-Carboxyarabinitol-1,5-Bisphosphate. J.Mol.Biol. V. 316 679 2002.
ISSN: ISSN 0022-2836
PubMed: 11866526
DOI: 10.1006/JMBI.2001.5381
Page generated: Tue Aug 13 05:08:12 2024

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