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Magnesium in PDB 3axm: Structure of Rice Rubisco in Complex with 6PG

Enzymatic activity of Structure of Rice Rubisco in Complex with 6PG

All present enzymatic activity of Structure of Rice Rubisco in Complex with 6PG:
4.1.1.39;

Protein crystallography data

The structure of Structure of Rice Rubisco in Complex with 6PG, PDB code: 3axm was solved by H.Matsumura, E.Mizohata, H.Ishida, A.Kogami, T.Ueno, A.Makino, T.Inoue, A.Yokota, T.Mae, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.26 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 110.408, 199.624, 111.169, 90.00, 91.45, 90.00
R / Rfree (%) 17.1 / 19

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Rice Rubisco in Complex with 6PG (pdb code 3axm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Rice Rubisco in Complex with 6PG, PDB code: 3axm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3axm

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Magnesium binding site 1 out of 8 in the Structure of Rice Rubisco in Complex with 6PG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg478

b:11.7
occ:1.00
 OD2 A:ASP203 2.0 10.4 1.0
O1 A:6PG479 2.1 12.5 1.0
OQ1 A:KCX201 2.1 10.4 1.0
OE1 A:GLU204 2.1 9.0 1.0
O2 A:6PG479 2.1 14.2 1.0
O A:HOH2934 2.1 11.9 1.0
C1 A:6PG479 2.9 16.1 1.0
CG A:ASP203 3.0 10.9 1.0
C2 A:6PG479 3.0 15.1 1.0
CD A:GLU204 3.1 11.1 1.0
CX A:KCX201 3.2 11.5 1.0
OQ2 A:KCX201 3.4 10.1 1.0
OE2 A:GLU204 3.5 12.0 1.0
OD1 A:ASP203 3.6 11.3 1.0
O3 A:6PG479 3.8 15.3 1.0
NZ A:LYS177 3.9 13.1 1.0
N A:GLU204 4.0 9.3 1.0
C3 A:6PG479 4.0 16.5 1.0
O1A A:6PG479 4.0 13.7 1.0
CB A:ASP203 4.0 8.7 1.0
O A:HOH2223 4.0 32.7 1.0
O A:HOH3555 4.1 15.6 1.0
CA A:ASP203 4.2 8.7 1.0
NE2 A:HIS294 4.3 10.7 1.0
NZ A:KCX201 4.3 10.3 1.0
CG A:GLU204 4.5 8.4 1.0
CG2 A:THR173 4.5 14.8 1.0
CE A:LYS177 4.6 13.8 1.0
C A:ASP203 4.6 9.2 1.0
O B:HOH696 4.8 18.6 1.0
NZ A:LYS175 4.8 20.3 1.0
CB A:GLU204 4.8 9.9 1.0
C4 A:6PG479 5.0 19.1 1.0
CD2 A:HIS294 5.0 9.7 1.0

Magnesium binding site 2 out of 8 in 3axm

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Magnesium binding site 2 out of 8 in the Structure of Rice Rubisco in Complex with 6PG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg478

b:11.0
occ:1.00
 O1A B:6PG479 2.0 12.6 1.0
OQ1 B:KCX201 2.1 10.0 1.0
OD2 B:ASP203 2.1 11.8 1.0
OE1 B:GLU204 2.1 10.0 1.0
O2 B:6PG479 2.1 14.7 1.0
O B:HOH2967 2.2 11.9 1.0
C1 B:6PG479 2.9 15.1 1.0
CG B:ASP203 3.0 11.2 1.0
CX B:KCX201 3.1 11.0 1.0
CD B:GLU204 3.1 11.2 1.0
C2 B:6PG479 3.1 15.7 1.0
OQ2 B:KCX201 3.3 11.4 1.0
OE2 B:GLU204 3.4 12.8 1.0
O B:HOH3597 3.6 36.4 1.0
OD1 B:ASP203 3.6 9.8 1.0
O3 B:6PG479 3.8 16.6 1.0
N B:GLU204 4.0 8.5 1.0
O1 B:6PG479 4.0 15.7 1.0
CB B:ASP203 4.1 10.9 1.0
NZ B:LYS177 4.1 14.2 1.0
C3 B:6PG479 4.1 17.6 1.0
O B:HOH3213 4.1 12.7 1.0
CA B:ASP203 4.1 9.7 1.0
NE2 B:HIS294 4.2 12.4 1.0
NZ B:KCX201 4.3 10.0 1.0
O B:HOH1425 4.4 57.9 1.0
CG B:GLU204 4.4 9.1 1.0
CG2 B:THR173 4.4 14.3 1.0
C B:ASP203 4.6 9.2 1.0
NZ B:LYS175 4.8 19.8 1.0
CB B:GLU204 4.8 9.4 1.0
CE B:LYS177 4.8 15.8 1.0
CD2 B:HIS294 4.8 11.6 1.0

Magnesium binding site 3 out of 8 in 3axm

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Magnesium binding site 3 out of 8 in the Structure of Rice Rubisco in Complex with 6PG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg478

b:10.3
occ:1.00
 O C:HOH481 2.0 11.9 1.0
O1A C:6PG479 2.1 11.9 1.0
O2 C:6PG479 2.1 11.7 1.0
OD2 C:ASP203 2.1 10.7 1.0
OE1 C:GLU204 2.1 9.1 1.0
OQ1 C:KCX201 2.2 11.2 1.0
C1 C:6PG479 2.8 13.5 1.0
C2 C:6PG479 3.0 14.0 1.0
CG C:ASP203 3.0 11.1 1.0
CD C:GLU204 3.1 11.9 1.0
CX C:KCX201 3.2 12.1 1.0
OE2 C:GLU204 3.4 12.6 1.0
OQ2 C:KCX201 3.5 11.5 1.0
OD1 C:ASP203 3.6 9.5 1.0
O3 C:6PG479 3.7 15.2 1.0
C3 C:6PG479 3.9 14.3 1.0
NZ C:LYS177 4.0 11.2 1.0
O1 C:6PG479 4.0 13.5 1.0
O C:HOH1962 4.0 33.1 1.0
N C:GLU204 4.1 8.5 1.0
CB C:ASP203 4.1 9.9 1.0
O C:HOH508 4.2 14.2 1.0
NE2 C:HIS294 4.2 10.1 1.0
CA C:ASP203 4.3 8.9 1.0
NZ C:KCX201 4.4 10.8 1.0
CG C:GLU204 4.4 9.2 1.0
CG2 C:THR173 4.6 12.5 1.0
CE C:LYS177 4.6 12.3 1.0
C C:ASP203 4.7 9.6 1.0
O D:HOH1142 4.7 21.6 1.0
C4 C:6PG479 4.8 17.9 1.0
CB C:GLU204 4.8 8.6 1.0
NZ C:LYS175 4.8 17.2 1.0
CD2 C:HIS294 4.9 9.9 1.0

Magnesium binding site 4 out of 8 in 3axm

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Magnesium binding site 4 out of 8 in the Structure of Rice Rubisco in Complex with 6PG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg478

b:10.3
occ:1.00
 O1A D:6PG479 2.0 10.9 1.0
OD2 D:ASP203 2.0 9.9 1.0
OQ1 D:KCX201 2.1 10.0 1.0
OE1 D:GLU204 2.1 10.3 1.0
O2 D:6PG479 2.1 11.1 1.0
O D:HOH3132 2.2 13.5 1.0
C1 D:6PG479 2.9 14.8 1.0
CG D:ASP203 3.0 10.0 1.0
C2 D:6PG479 3.0 15.2 1.0
CD D:GLU204 3.1 11.1 1.0
CX D:KCX201 3.1 10.9 1.0
OQ2 D:KCX201 3.4 11.1 1.0
OE2 D:GLU204 3.5 12.1 1.0
OD1 D:ASP203 3.6 9.5 1.0
O3 D:6PG479 3.7 14.6 1.0
C3 D:6PG479 3.9 16.6 1.0
O1 D:6PG479 4.0 14.5 1.0
N D:GLU204 4.0 7.6 1.0
CB D:ASP203 4.1 9.1 1.0
NZ D:LYS177 4.1 11.1 1.0
O D:HOH504 4.1 14.3 1.0
CA D:ASP203 4.2 8.3 1.0
NE2 D:HIS294 4.2 10.9 1.0
NZ D:KCX201 4.3 10.6 1.0
CG D:GLU204 4.4 8.8 1.0
CG2 D:THR173 4.5 13.7 1.0
C D:ASP203 4.6 8.8 1.0
CE D:LYS177 4.7 13.6 1.0
O C:HOH564 4.8 18.9 1.0
CB D:GLU204 4.8 8.3 1.0
CD2 D:HIS294 4.9 10.6 1.0
C4 D:6PG479 4.9 20.6 1.0
NZ D:LYS175 5.0 16.0 1.0

Magnesium binding site 5 out of 8 in 3axm

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Magnesium binding site 5 out of 8 in the Structure of Rice Rubisco in Complex with 6PG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg478

b:11.9
occ:1.00
 OD1 E:ASP203 2.0 9.6 1.0
O1A E:6PG479 2.1 12.5 1.0
OQ1 E:KCX201 2.1 10.9 1.0
OE1 E:GLU204 2.1 10.2 1.0
O E:HOH1908 2.1 11.0 1.0
O2 E:6PG479 2.1 13.9 1.0
C1 E:6PG479 2.9 15.3 1.0
CG E:ASP203 3.0 9.6 1.0
C2 E:6PG479 3.0 15.6 1.0
CX E:KCX201 3.1 12.5 1.0
CD E:GLU204 3.1 10.2 1.0
OQ2 E:KCX201 3.4 10.4 1.0
OE2 E:GLU204 3.5 11.7 1.0
OD2 E:ASP203 3.6 10.6 1.0
O3 E:6PG479 3.8 16.3 1.0
C3 E:6PG479 4.0 17.2 1.0
N E:GLU204 4.0 7.9 1.0
O1 E:6PG479 4.0 15.2 1.0
CB E:ASP203 4.1 9.6 1.0
NZ E:LYS177 4.1 11.1 1.0
O E:HOH504 4.1 16.5 1.0
CA E:ASP203 4.2 8.1 1.0
NE2 E:HIS294 4.2 11.3 1.0
NZ E:KCX201 4.3 10.4 1.0
CG2 E:THR173 4.4 13.5 1.0
CG E:GLU204 4.4 7.6 1.0
C E:ASP203 4.6 8.2 1.0
NZ E:LYS175 4.7 20.7 1.0
CE E:LYS177 4.7 13.5 1.0
CB E:GLU204 4.8 7.9 1.0
O F:HOH1019 4.8 20.8 1.0
CD2 E:HIS294 4.9 11.5 1.0
C4 E:6PG479 5.0 20.5 1.0

Magnesium binding site 6 out of 8 in 3axm

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Magnesium binding site 6 out of 8 in the Structure of Rice Rubisco in Complex with 6PG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg478

b:9.1
occ:1.00
 OE1 F:GLU204 2.0 8.7 1.0
OQ1 F:KCX201 2.1 9.9 1.0
O2 F:6PG479 2.1 14.0 1.0
OD2 F:ASP203 2.1 11.7 1.0
O1A F:6PG479 2.1 12.6 1.0
O F:HOH2817 2.1 12.4 1.0
C1 F:6PG479 2.9 14.1 1.0
C2 F:6PG479 3.0 15.2 1.0
CD F:GLU204 3.0 11.5 1.0
CG F:ASP203 3.1 11.1 1.0
CX F:KCX201 3.1 10.8 1.0
OQ2 F:KCX201 3.4 11.5 1.0
OE2 F:GLU204 3.4 13.0 1.0
OD1 F:ASP203 3.7 8.8 1.0
O3 F:6PG479 3.7 14.5 1.0
N F:GLU204 3.9 8.3 1.0
C3 F:6PG479 4.0 17.4 1.0
O1 F:6PG479 4.1 14.0 1.0
CB F:ASP203 4.1 10.2 1.0
O F:HOH3508 4.1 13.9 1.0
NE2 F:HIS294 4.1 10.2 1.0
NZ F:LYS177 4.1 11.7 1.0
CA F:ASP203 4.2 9.9 1.0
NZ F:KCX201 4.3 9.7 1.0
O F:HOH2487 4.3 33.9 1.0
CG F:GLU204 4.4 9.6 1.0
CG2 F:THR173 4.4 13.0 1.0
C F:ASP203 4.6 9.8 1.0
CE F:LYS177 4.7 14.0 1.0
CB F:GLU204 4.7 8.8 1.0
CD2 F:HIS294 4.8 10.4 1.0
C4 F:6PG479 4.8 21.6 1.0
O E:HOH647 4.9 19.4 1.0
NZ F:LYS175 4.9 18.9 1.0
CE1 F:HIS294 5.0 10.6 1.0
CA F:GLU204 5.0 9.7 1.0

Magnesium binding site 7 out of 8 in 3axm

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Magnesium binding site 7 out of 8 in the Structure of Rice Rubisco in Complex with 6PG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg478

b:10.8
occ:1.00
 OD1 G:ASP203 2.0 10.5 1.0
O1A G:6PG479 2.1 11.7 1.0
OQ1 G:KCX201 2.1 9.8 1.0
O G:HOH1909 2.1 12.6 1.0
OE1 G:GLU204 2.2 9.2 1.0
O2 G:6PG479 2.2 12.9 1.0
C1 G:6PG479 2.9 14.5 1.0
CG G:ASP203 3.0 11.6 1.0
C2 G:6PG479 3.0 15.5 1.0
CX G:KCX201 3.1 10.3 1.0
CD G:GLU204 3.1 11.5 1.0
OQ2 G:KCX201 3.4 11.5 1.0
OE2 G:GLU204 3.5 13.8 1.0
OD2 G:ASP203 3.6 10.6 1.0
O3 G:6PG479 3.8 16.6 1.0
C3 G:6PG479 4.0 17.0 1.0
O1 G:6PG479 4.0 12.4 1.0
O G:HOH2334 4.0 31.8 1.0
N G:GLU204 4.0 9.1 1.0
CB G:ASP203 4.0 10.7 1.0
NZ G:LYS177 4.0 14.0 1.0
O G:HOH3170 4.1 14.6 1.0
CA G:ASP203 4.2 10.4 1.0
NE2 G:HIS294 4.2 11.5 1.0
NZ G:KCX201 4.3 11.3 1.0
CG2 G:THR173 4.4 12.5 1.0
CG G:GLU204 4.5 10.1 1.0
C G:ASP203 4.6 9.8 1.0
CE G:LYS177 4.7 15.1 1.0
NZ G:LYS175 4.7 22.8 1.0
CB G:GLU204 4.9 9.6 1.0
CD2 G:HIS294 4.9 10.4 1.0
C4 G:6PG479 4.9 19.4 1.0
O H:HOH1295 5.0 24.0 1.0

Magnesium binding site 8 out of 8 in 3axm

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Magnesium binding site 8 out of 8 in the Structure of Rice Rubisco in Complex with 6PG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg478

b:11.3
occ:1.00
 OQ1 H:KCX201 2.0 10.7 1.0
OD2 H:ASP203 2.1 10.0 1.0
O1A H:6PG479 2.1 11.9 1.0
O2 H:6PG479 2.1 14.7 1.0
OE2 H:GLU204 2.1 9.8 1.0
O H:HOH3197 2.2 11.4 1.0
C1 H:6PG479 2.9 16.9 1.0
C2 H:6PG479 3.0 16.5 1.0
CG H:ASP203 3.0 9.6 1.0
CX H:KCX201 3.1 9.9 1.0
CD H:GLU204 3.1 9.7 1.0
OQ2 H:KCX201 3.3 12.9 1.0
OE1 H:GLU204 3.4 11.8 1.0
OD1 H:ASP203 3.6 9.8 1.0
O3 H:6PG479 3.8 17.9 1.0
C3 H:6PG479 3.9 18.7 1.0
O1 H:6PG479 4.0 16.0 1.0
N H:GLU204 4.0 8.0 1.0
CB H:ASP203 4.1 9.2 1.0
NZ H:LYS177 4.1 13.0 1.0
O H:HOH3542 4.1 12.6 1.0
NE2 H:HIS294 4.2 11.6 1.0
CA H:ASP203 4.2 8.6 1.0
NZ H:KCX201 4.2 11.3 1.0
CG2 H:THR173 4.5 15.0 1.0
CG H:GLU204 4.5 8.0 1.0
C H:ASP203 4.6 9.2 1.0
CE H:LYS177 4.7 13.0 1.0
NZ H:LYS175 4.8 18.1 1.0
CB H:GLU204 4.8 8.1 1.0
C4 H:6PG479 4.8 22.0 1.0
CD2 H:HIS294 4.9 10.7 1.0
O G:HOH491 4.9 17.9 1.0

Reference:

H.Matsumura, E.Mizohata, H.Ishida, A.Kogami, T.Ueno, A.Makino, T.Inoue, A.Yokota, T.Mae, Y.Kai. Crystal Structure of Rice Rubisco and Implications For Activation Induced By Positive Effectors Nadph and 6-Phosphogluconate J.Mol.Biol. V. 422 75 2012.
ISSN: ISSN 0022-2836
PubMed: 22609438
DOI: 10.1016/J.JMB.2012.05.014
Page generated: Wed Aug 14 08:47:38 2024

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