Atomistry » Magnesium » PDB 1iah-1iru » 1ir1
Atomistry »
  Magnesium »
    PDB 1iah-1iru »
      1ir1 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy