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Magnesium in PDB 2v63: Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation

Enzymatic activity of Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation

All present enzymatic activity of Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation:
4.1.1.39;

Protein crystallography data

The structure of Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation, PDB code: 2v63 was solved by S.Karkehabadi, S.Satagopan, T.C.Taylor, R.J.Spreitzer, I.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 121.377, 177.446, 122.568, 90.00, 117.65, 90.00
R / Rfree (%) 19.1 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation (pdb code 2v63). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation, PDB code: 2v63:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2v63

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Magnesium binding site 1 out of 8 in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation


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 Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg477

b:9.4
occ:1.00
OD1 A:ASP203 2.0 12.0 1.0
OQ1 A:KCX201 2.0 9.5 1.0
OE1 A:GLU204 2.0 10.8 1.0
O7 A:CAP476 2.1 13.4 1.0
O3 A:CAP476 2.1 11.9 1.0
O2 A:CAP476 2.3 12.0 1.0
C A:CAP476 2.8 13.2 1.0
C2 A:CAP476 2.8 13.0 1.0
C3 A:CAP476 3.0 13.5 1.0
CX A:KCX201 3.1 10.7 1.0
CD A:GLU204 3.1 13.4 1.0
CG A:ASP203 3.2 12.7 1.0
OQ2 A:KCX201 3.4 11.2 1.0
OE2 A:GLU204 3.6 15.3 1.0
NZ A:LYS177 3.6 14.9 1.0
ND2 B:ASN123 3.8 14.5 1.0
N A:GLU204 3.9 8.9 1.0
OD2 A:ASP203 3.9 16.2 1.0
NZ A:LYS175 3.9 12.5 1.0
NE2 A:HIS294 4.0 7.8 1.0
O6 A:CAP476 4.0 13.6 1.0
CG2 A:THR173 4.1 12.7 1.0
CA A:ASP203 4.2 9.4 1.0
CB A:ASP203 4.2 10.0 1.0
C4 A:CAP476 4.2 14.8 1.0
NZ A:KCX201 4.2 9.8 1.0
C1 A:CAP476 4.3 12.8 1.0
CG A:GLU204 4.4 10.6 1.0
C A:ASP203 4.6 9.0 1.0
CB A:GLU204 4.6 9.7 1.0
OG1 A:THR173 4.6 14.7 1.0
CD2 A:HIS294 4.7 8.1 1.0
C5 A:CAP476 4.7 14.5 1.0
O1 A:CAP476 4.8 12.6 1.0
CE1 A:HIS294 4.8 8.3 1.0
CB A:THR173 4.9 12.7 1.0
CA A:GLU204 4.9 9.3 1.0

Magnesium binding site 2 out of 8 in 2v63

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Magnesium binding site 2 out of 8 in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation


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 Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg476

b:9.1
occ:1.00
OQ1 B:KCX201 2.0 9.6 1.0
OE1 B:GLU204 2.0 10.4 1.0
OD1 B:ASP203 2.0 12.3 1.0
O3 B:CAP477 2.1 11.9 1.0
O7 B:CAP477 2.2 13.4 1.0
O2 B:CAP477 2.3 11.7 1.0
C2 B:CAP477 2.9 12.8 1.0
C B:CAP477 2.9 13.1 1.0
CX B:KCX201 3.0 10.6 1.0
C3 B:CAP477 3.0 13.2 1.0
CD B:GLU204 3.1 13.2 1.0
CG B:ASP203 3.2 12.7 1.0
OQ2 B:KCX201 3.3 11.4 1.0
OE2 B:GLU204 3.6 14.8 1.0
NZ B:LYS177 3.7 14.9 1.0
ND2 A:ASN123 3.9 14.4 1.0
N B:GLU204 3.9 8.8 1.0
NE2 B:HIS294 3.9 7.8 1.0
OD2 B:ASP203 4.0 16.1 1.0
NZ B:LYS175 4.0 12.4 1.0
CG2 B:THR173 4.1 12.8 1.0
O6 B:CAP477 4.1 13.8 1.0
NZ B:KCX201 4.2 9.8 1.0
CA B:ASP203 4.2 9.2 1.0
C4 B:CAP477 4.2 14.6 1.0
CB B:ASP203 4.2 10.0 1.0
C1 B:CAP477 4.3 12.5 1.0
CG B:GLU204 4.4 10.4 1.0
CB B:GLU204 4.5 9.4 1.0
OG1 B:THR173 4.6 14.6 1.0
C B:ASP203 4.6 9.1 1.0
CD2 B:HIS294 4.6 8.3 1.0
C5 B:CAP477 4.7 14.4 1.0
CE1 B:HIS294 4.8 8.4 1.0
O1 B:CAP477 4.8 12.3 1.0
CB B:THR173 4.8 12.5 1.0
CA B:GLU204 4.8 9.2 1.0
O A:HOH2092 4.9 19.6 1.0

Magnesium binding site 3 out of 8 in 2v63

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Magnesium binding site 3 out of 8 in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation


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 Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg476

b:9.4
occ:1.00
OQ1 C:KCX201 1.9 9.3 1.0
OD1 C:ASP203 2.0 11.9 1.0
OE1 C:GLU204 2.0 11.1 1.0
O3 C:CAP477 2.1 11.4 1.0
O7 C:CAP477 2.2 13.4 1.0
O2 C:CAP477 2.3 11.7 1.0
C2 C:CAP477 2.9 12.8 1.0
C C:CAP477 2.9 13.0 1.0
CX C:KCX201 3.0 10.6 1.0
C3 C:CAP477 3.0 13.4 1.0
CD C:GLU204 3.1 13.3 1.0
CG C:ASP203 3.2 12.5 1.0
OQ2 C:KCX201 3.3 10.9 1.0
OE2 C:GLU204 3.5 15.2 1.0
NZ C:LYS177 3.8 14.7 1.0
N C:GLU204 3.8 8.8 1.0
ND2 D:ASN123 3.8 14.5 1.0
OD2 C:ASP203 3.9 16.3 1.0
NE2 C:HIS294 3.9 7.7 1.0
NZ C:LYS175 4.0 12.2 1.0
CG2 C:THR173 4.1 12.8 1.0
O6 C:CAP477 4.1 13.4 1.0
CA C:ASP203 4.1 9.3 1.0
NZ C:KCX201 4.2 9.7 1.0
CB C:ASP203 4.2 9.8 1.0
C4 C:CAP477 4.2 15.0 1.0
CG C:GLU204 4.3 10.6 1.0
C1 C:CAP477 4.4 12.7 1.0
C C:ASP203 4.5 8.8 1.0
CB C:GLU204 4.6 9.5 1.0
CD2 C:HIS294 4.6 8.4 1.0
OG1 C:THR173 4.6 14.8 1.0
C5 C:CAP477 4.7 14.4 1.0
CA C:GLU204 4.8 9.0 1.0
CE1 C:HIS294 4.8 8.0 1.0
O1 C:CAP477 4.8 12.8 1.0
CB C:THR173 4.9 12.7 1.0

Magnesium binding site 4 out of 8 in 2v63

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Magnesium binding site 4 out of 8 in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation


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 Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg476

b:9.5
occ:1.00
OD1 D:ASP203 2.0 11.3 1.0
OQ1 D:KCX201 2.0 10.3 1.0
OE1 D:GLU204 2.1 10.8 1.0
O3 D:CAP477 2.1 11.7 1.0
O7 D:CAP477 2.1 13.3 1.0
O2 D:CAP477 2.2 12.1 1.0
C D:CAP477 2.9 13.2 1.0
C2 D:CAP477 2.9 13.1 1.0
CX D:KCX201 3.0 10.3 1.0
C3 D:CAP477 3.0 13.6 1.0
CD D:GLU204 3.1 13.6 1.0
CG D:ASP203 3.2 12.5 1.0
OQ2 D:KCX201 3.3 11.6 1.0
OE2 D:GLU204 3.6 15.6 1.0
NZ D:LYS177 3.6 14.4 1.0
ND2 C:ASN123 3.8 14.0 1.0
N D:GLU204 3.9 9.3 1.0
NZ D:LYS175 3.9 12.9 1.0
OD2 D:ASP203 4.0 15.8 1.0
NE2 D:HIS294 4.0 7.9 1.0
O6 D:CAP477 4.1 13.7 1.0
CG2 D:THR173 4.1 12.6 1.0
CA D:ASP203 4.2 9.5 1.0
NZ D:KCX201 4.2 10.1 1.0
CB D:ASP203 4.2 9.9 1.0
C4 D:CAP477 4.2 14.5 1.0
C1 D:CAP477 4.3 12.8 1.0
CG D:GLU204 4.4 10.7 1.0
C D:ASP203 4.6 9.1 1.0
CB D:GLU204 4.6 9.7 1.0
OG1 D:THR173 4.6 14.6 1.0
CD2 D:HIS294 4.7 7.7 1.0
C5 D:CAP477 4.7 14.6 1.0
O1 D:CAP477 4.8 12.6 1.0
CE1 D:HIS294 4.8 8.7 1.0
CB D:THR173 4.8 12.6 1.0
CA D:GLU204 4.9 9.4 1.0

Magnesium binding site 5 out of 8 in 2v63

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Magnesium binding site 5 out of 8 in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg476

b:10.2
occ:1.00
OD1 E:ASP203 2.0 12.0 1.0
OQ1 E:KCX201 2.0 9.6 1.0
OE1 E:GLU204 2.1 11.0 1.0
O3 E:CAP477 2.1 11.7 1.0
O7 E:CAP477 2.1 13.1 1.0
O2 E:CAP477 2.2 12.1 1.0
C2 E:CAP477 2.8 13.0 1.0
C E:CAP477 2.8 13.2 1.0
C3 E:CAP477 3.0 13.7 1.0
CX E:KCX201 3.0 10.5 1.0
CD E:GLU204 3.2 13.5 1.0
CG E:ASP203 3.2 12.5 1.0
OQ2 E:KCX201 3.4 10.9 1.0
OE2 E:GLU204 3.6 15.5 1.0
NZ E:LYS177 3.7 14.7 1.0
ND2 F:ASN123 3.8 14.2 1.0
NZ E:LYS175 3.9 12.6 1.0
N E:GLU204 3.9 9.2 1.0
OD2 E:ASP203 4.0 16.0 1.0
NE2 E:HIS294 4.0 8.3 1.0
O6 E:CAP477 4.1 13.7 1.0
CG2 E:THR173 4.1 13.0 1.0
CA E:ASP203 4.2 9.4 1.0
C4 E:CAP477 4.2 14.9 1.0
CB E:ASP203 4.2 10.1 1.0
NZ E:KCX201 4.2 10.5 1.0
C1 E:CAP477 4.3 12.8 1.0
CG E:GLU204 4.4 10.9 1.0
C E:ASP203 4.6 9.1 1.0
OG1 E:THR173 4.6 14.7 1.0
CB E:GLU204 4.6 9.7 1.0
CD2 E:HIS294 4.7 8.3 1.0
C5 E:CAP477 4.7 14.5 1.0
O1 E:CAP477 4.8 12.4 1.0
CB E:THR173 4.8 12.6 1.0
CE1 E:HIS294 4.9 8.7 1.0
CA E:GLU204 4.9 9.5 1.0

Magnesium binding site 6 out of 8 in 2v63

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Magnesium binding site 6 out of 8 in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg476

b:10.9
occ:1.00
OD1 F:ASP203 2.0 12.2 1.0
OQ1 F:KCX201 2.0 9.1 1.0
OE1 F:GLU204 2.0 11.2 1.0
O7 F:CAP477 2.1 13.8 1.0
O3 F:CAP477 2.2 12.8 1.0
O2 F:CAP477 2.3 12.6 1.0
C F:CAP477 2.9 13.6 1.0
C2 F:CAP477 2.9 13.4 1.0
CX F:KCX201 3.0 10.8 1.0
C3 F:CAP477 3.1 13.7 1.0
CD F:GLU204 3.1 13.1 1.0
CG F:ASP203 3.2 12.9 1.0
OQ2 F:KCX201 3.3 11.3 1.0
OE2 F:GLU204 3.6 15.4 1.0
NZ F:LYS177 3.7 14.9 1.0
ND2 E:ASN123 3.9 15.0 1.0
N F:GLU204 3.9 9.5 1.0
OD2 F:ASP203 3.9 16.6 1.0
NZ F:LYS175 3.9 12.8 1.0
NE2 F:HIS294 4.0 7.9 1.0
O6 F:CAP477 4.1 14.1 1.0
CG2 F:THR173 4.1 12.9 1.0
CA F:ASP203 4.2 9.8 1.0
NZ F:KCX201 4.2 9.8 1.0
CB F:ASP203 4.2 10.0 1.0
C4 F:CAP477 4.3 15.1 1.0
C1 F:CAP477 4.3 13.0 1.0
CG F:GLU204 4.4 10.9 1.0
C F:ASP203 4.6 9.4 1.0
CB F:GLU204 4.6 10.0 1.0
OG1 F:THR173 4.6 15.0 1.0
CD2 F:HIS294 4.7 8.2 1.0
C5 F:CAP477 4.8 14.9 1.0
O1 F:CAP477 4.8 13.3 1.0
CE1 F:HIS294 4.8 8.1 1.0
CA F:GLU204 4.9 9.6 1.0
CB F:THR173 4.9 13.0 1.0

Magnesium binding site 7 out of 8 in 2v63

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Magnesium binding site 7 out of 8 in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg476

b:8.9
occ:1.00
OD1 G:ASP203 2.0 11.6 1.0
OE1 G:GLU204 2.0 10.7 1.0
OQ1 G:KCX201 2.0 9.7 1.0
O3 G:CAP477 2.2 12.0 1.0
O7 G:CAP477 2.2 13.7 1.0
O2 G:CAP477 2.2 12.3 1.0
C2 G:CAP477 2.9 13.1 1.0
C G:CAP477 2.9 13.1 1.0
CX G:KCX201 3.0 10.9 1.0
CD G:GLU204 3.0 13.1 1.0
C3 G:CAP477 3.1 13.4 1.0
CG G:ASP203 3.2 12.8 1.0
OQ2 G:KCX201 3.3 11.2 1.0
OE2 G:GLU204 3.5 14.9 1.0
NZ G:LYS177 3.7 15.2 1.0
ND2 H:ASN123 3.8 14.4 1.0
N G:GLU204 3.8 9.0 1.0
NE2 G:HIS294 3.9 7.8 1.0
OD2 G:ASP203 3.9 16.2 1.0
NZ G:LYS175 4.0 12.6 1.0
O6 G:CAP477 4.1 13.2 1.0
CG2 G:THR173 4.1 12.6 1.0
NZ G:KCX201 4.2 10.3 1.0
CA G:ASP203 4.2 9.2 1.0
CB G:ASP203 4.2 9.9 1.0
C4 G:CAP477 4.3 14.7 1.0
CG G:GLU204 4.3 10.4 1.0
C1 G:CAP477 4.4 12.6 1.0
CB G:GLU204 4.5 9.8 1.0
C G:ASP203 4.5 8.8 1.0
OG1 G:THR173 4.7 14.7 1.0
CD2 G:HIS294 4.7 8.1 1.0
CE1 G:HIS294 4.8 8.5 1.0
C5 G:CAP477 4.8 14.4 1.0
CA G:GLU204 4.8 9.3 1.0
O1 G:CAP477 4.8 12.1 1.0
CB G:THR173 4.9 12.6 1.0
O H:HOH2038 5.0 15.3 1.0
CG H:ASN123 5.0 13.3 1.0

Magnesium binding site 8 out of 8 in 2v63

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Magnesium binding site 8 out of 8 in the Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Rubisco From Chlamydomonas Reinhardtii with A Large-Subunit V331A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg476

b:9.2
occ:1.00
OQ1 H:KCX201 2.0 9.1 1.0
OD1 H:ASP203 2.0 12.3 1.0
OE1 H:GLU204 2.0 10.4 1.0
O7 H:CAP477 2.1 13.1 1.0
O3 H:CAP477 2.2 12.0 1.0
O2 H:CAP477 2.3 11.9 1.0
C H:CAP477 2.8 13.2 1.0
C2 H:CAP477 2.8 12.8 1.0
CX H:KCX201 3.0 10.8 1.0
C3 H:CAP477 3.0 13.5 1.0
CD H:GLU204 3.1 13.8 1.0
CG H:ASP203 3.2 12.4 1.0
OQ2 H:KCX201 3.3 11.2 1.0
OE2 H:GLU204 3.6 15.3 1.0
NZ H:LYS177 3.7 14.9 1.0
ND2 G:ASN123 3.8 14.2 1.0
N H:GLU204 3.9 8.7 1.0
NE2 H:HIS294 3.9 7.5 1.0
OD2 H:ASP203 4.0 16.3 1.0
NZ H:LYS175 4.0 12.6 1.0
O6 H:CAP477 4.1 13.6 1.0
CG2 H:THR173 4.1 12.4 1.0
NZ H:KCX201 4.2 9.4 1.0
C4 H:CAP477 4.2 14.6 1.0
CA H:ASP203 4.2 9.3 1.0
CB H:ASP203 4.2 10.1 1.0
C1 H:CAP477 4.3 13.1 1.0
CG H:GLU204 4.4 10.5 1.0
C H:ASP203 4.6 8.9 1.0
CB H:GLU204 4.6 9.6 1.0
OG1 H:THR173 4.6 14.5 1.0
CD2 H:HIS294 4.6 8.1 1.0
C5 H:CAP477 4.7 14.5 1.0
CE1 H:HIS294 4.8 8.3 1.0
O1 H:CAP477 4.8 12.7 1.0
CA H:GLU204 4.9 9.1 1.0
CB H:THR173 4.9 12.7 1.0
CG G:ASN123 5.0 13.3 1.0

Reference:

S.Karkehabadi, S.Satagopan, T.C.Taylor, R.J.Spreitzer, I.Andersson. Structural Analysis of Altered Large-Subunit Loop- 6-Carboxy-Terminus Interactions That Influence Catalytic Efficiency and CO2 O2 Specificity of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase Biochemistry V. 46 11080 2007.
ISSN: ISSN 0006-2960
PubMed: 17824672
DOI: 10.1021/BI701063F
Page generated: Mon Dec 14 07:41:03 2020

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