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Magnesium in PDB 1uzd: Chlamydomonas,Spinach Chimeric Rubisco

Enzymatic activity of Chlamydomonas,Spinach Chimeric Rubisco

All present enzymatic activity of Chlamydomonas,Spinach Chimeric Rubisco:
4.1.1.39;

Protein crystallography data

The structure of Chlamydomonas,Spinach Chimeric Rubisco, PDB code: 1uzd was solved by S.Karkehabadi, R.J.Spreitzer, I.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 220.014, 224.078, 111.725, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 1uzd

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Magnesium binding site 1 out of 8 in the Chlamydomonas,Spinach Chimeric Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Chlamydomonas,Spinach Chimeric Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1476

b:11.2
occ:1.00
OD1 A:ASP203 1.8 18.3 1.0
OQ2 A:KCX201 2.0 12.5 1.0
O3 A:CAP1477 2.2 21.1 1.0
OE1 A:GLU204 2.2 15.0 1.0
O6 A:CAP1477 2.2 9.2 1.0
O2 A:CAP1477 2.3 16.0 1.0
C2 A:CAP1477 2.9 18.5 1.0
C A:CAP1477 2.9 15.3 1.0
CG A:ASP203 3.0 16.8 1.0
CX A:KCX201 3.1 14.4 1.0
C3 A:CAP1477 3.1 17.8 1.0
CD A:GLU204 3.1 15.8 1.0
OQ1 A:KCX201 3.4 14.5 1.0
OE2 A:GLU204 3.5 17.8 1.0
OD2 A:ASP203 3.5 21.2 1.0
NZ A:LYS177 3.7 17.8 1.0
NZ A:LYS175 3.8 14.7 1.0
N A:GLU204 3.8 12.2 1.0
ND2 B:ASN123 4.0 20.4 1.0
CG2 A:THR173 4.0 15.2 1.0
CB A:ASP203 4.1 13.2 1.0
CA A:ASP203 4.1 12.2 1.0
C4 A:CAP1477 4.2 22.7 1.0
O7 A:CAP1477 4.2 15.9 1.0
NE2 A:HIS294 4.2 12.1 1.0
NZ A:KCX201 4.3 13.8 1.0
C1 A:CAP1477 4.4 15.7 1.0
OG1 A:THR173 4.4 16.9 1.0
CG A:GLU204 4.5 14.0 1.0
C A:ASP203 4.5 12.6 1.0
CB A:GLU204 4.7 12.6 1.0
CB A:THR173 4.8 15.6 1.0
C5 A:CAP1477 4.8 14.7 1.0
CD2 A:HIS294 4.8 13.5 1.0
O1 A:CAP1477 4.8 17.8 1.0
CA A:GLU204 4.9 12.4 1.0

Magnesium binding site 2 out of 8 in 1uzd

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Magnesium binding site 2 out of 8 in the Chlamydomonas,Spinach Chimeric Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Chlamydomonas,Spinach Chimeric Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1476

b:25.0
occ:1.00
O6 B:CAP1477 1.8 10.1 1.0
OD1 B:ASP203 1.8 18.3 1.0
OQ2 B:KCX201 1.9 12.8 1.0
O3 B:CAP1477 2.2 9.3 1.0
OE1 B:GLU204 2.3 15.0 1.0
O2 B:CAP1477 2.3 7.6 1.0
C B:CAP1477 2.7 12.1 1.0
C2 B:CAP1477 2.8 15.1 1.0
CX B:KCX201 2.9 14.3 1.0
CG B:ASP203 3.0 16.8 1.0
C3 B:CAP1477 3.1 14.9 1.0
OQ1 B:KCX201 3.2 14.4 1.0
CD B:GLU204 3.3 16.1 1.0
OD2 B:ASP203 3.6 20.9 1.0
OE2 B:GLU204 3.6 17.7 1.0
NZ B:LYS175 3.8 14.8 1.0
NZ B:LYS177 3.8 17.6 1.0
CG2 B:THR173 3.9 15.0 1.0
O7 B:CAP1477 3.9 12.6 1.0
N B:GLU204 3.9 12.2 1.0
NZ B:KCX201 4.1 13.6 1.0
ND2 A:ASN123 4.1 20.2 1.0
NE2 B:HIS294 4.1 11.3 1.0
CA B:ASP203 4.1 12.0 1.0
CB B:ASP203 4.2 13.3 1.0
C4 B:CAP1477 4.2 14.5 1.0
OG1 B:THR173 4.2 17.0 1.0
C1 B:CAP1477 4.3 8.2 1.0
C B:ASP203 4.6 12.7 1.0
CB B:THR173 4.6 15.7 1.0
CG B:GLU204 4.6 13.9 1.0
CD2 B:HIS294 4.7 13.0 1.0
CB B:GLU204 4.8 12.5 1.0
O1 B:CAP1477 4.8 11.1 1.0
C5 B:CAP1477 4.8 17.2 1.0
CA B:GLU204 4.9 12.4 1.0

Magnesium binding site 3 out of 8 in 1uzd

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Magnesium binding site 3 out of 8 in the Chlamydomonas,Spinach Chimeric Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Chlamydomonas,Spinach Chimeric Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1476

b:29.5
occ:1.00
OD1 E:ASP203 1.9 18.2 1.0
O6 E:CAP1477 2.0 18.0 1.0
O3 E:CAP1477 2.0 15.6 1.0
OE1 E:GLU204 2.1 15.3 1.0
OQ2 E:KCX201 2.1 12.2 1.0
O2 E:CAP1477 2.3 16.2 1.0
C E:CAP1477 2.8 18.0 1.0
C2 E:CAP1477 2.8 17.4 1.0
C3 E:CAP1477 3.0 17.6 1.0
CD E:GLU204 3.1 15.9 1.0
CG E:ASP203 3.1 16.7 1.0
CX E:KCX201 3.2 14.5 1.0
OE2 E:GLU204 3.4 17.5 1.0
OQ1 E:KCX201 3.5 15.0 1.0
NZ E:LYS177 3.5 17.9 1.0
OD2 E:ASP203 3.7 20.9 1.0
ND2 K:ASN123 3.8 20.5 1.0
N E:GLU204 3.9 12.2 1.0
NZ E:LYS175 3.9 15.2 1.0
O7 E:CAP1477 4.0 18.0 1.0
NE2 E:HIS294 4.1 11.6 1.0
C4 E:CAP1477 4.1 15.4 1.0
CG2 E:THR173 4.2 15.3 1.0
CB E:ASP203 4.2 13.5 1.0
CA E:ASP203 4.3 12.2 1.0
C1 E:CAP1477 4.3 17.6 1.0
NZ E:KCX201 4.4 13.8 1.0
CG E:GLU204 4.4 14.1 1.0
OG1 E:THR173 4.6 17.1 1.0
C E:ASP203 4.6 12.5 1.0
CB E:GLU204 4.6 12.6 1.0
C5 E:CAP1477 4.7 20.7 1.0
CD2 E:HIS294 4.7 13.0 1.0
O1 E:CAP1477 4.7 13.1 1.0
CA E:GLU204 4.9 12.7 1.0
CB E:THR173 4.9 15.5 1.0
CE1 E:HIS294 5.0 13.6 1.0
CG K:ASN123 5.0 20.4 1.0
O K:HOH2023 5.0 38.1 1.0
CE E:LYS177 5.0 18.6 1.0

Magnesium binding site 4 out of 8 in 1uzd

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Magnesium binding site 4 out of 8 in the Chlamydomonas,Spinach Chimeric Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Chlamydomonas,Spinach Chimeric Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1476

b:24.1
occ:1.00
O6 H:CAP1477 1.9 16.4 1.0
OQ2 H:KCX201 2.0 12.3 1.0
OD1 H:ASP203 2.0 18.3 1.0
OE1 H:GLU204 2.1 15.2 1.0
O3 H:CAP1477 2.2 18.7 1.0
O2 H:CAP1477 2.5 20.3 1.0
C H:CAP1477 2.8 18.2 1.0
C2 H:CAP1477 2.9 20.5 1.0
CX H:KCX201 3.1 14.5 1.0
CD H:GLU204 3.1 15.9 1.0
C3 H:CAP1477 3.1 17.1 1.0
CG H:ASP203 3.2 16.9 1.0
OQ1 H:KCX201 3.4 14.7 1.0
OE2 H:GLU204 3.5 17.5 1.0
NZ H:LYS177 3.7 17.9 1.0
OD2 H:ASP203 3.8 21.3 1.0
ND2 R:ASN123 3.8 20.2 1.0
N H:GLU204 3.9 12.3 1.0
NE2 H:HIS294 3.9 11.9 1.0
NZ H:LYS175 4.0 15.2 1.0
O7 H:CAP1477 4.0 15.9 1.0
CG2 H:THR173 4.2 15.4 1.0
C4 H:CAP1477 4.2 21.8 1.0
NZ H:KCX201 4.2 13.7 1.0
CA H:ASP203 4.3 12.1 1.0
CB H:ASP203 4.3 13.4 1.0
CG H:GLU204 4.4 14.2 1.0
C1 H:CAP1477 4.4 20.1 1.0
CB H:GLU204 4.5 12.7 1.0
OG1 H:THR173 4.6 16.9 1.0
C5 H:CAP1477 4.6 21.2 1.0
C H:ASP203 4.6 12.7 1.0
CD2 H:HIS294 4.6 12.8 1.0
CE1 H:HIS294 4.8 13.7 1.0
CA H:GLU204 4.8 12.5 1.0
O1 H:CAP1477 4.9 19.9 1.0
CB H:THR173 4.9 15.6 1.0
CG R:ASN123 5.0 20.2 1.0

Magnesium binding site 5 out of 8 in 1uzd

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Magnesium binding site 5 out of 8 in the Chlamydomonas,Spinach Chimeric Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Chlamydomonas,Spinach Chimeric Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1476

b:18.0
occ:1.00
O6 K:CAP1477 1.8 21.5 1.0
O3 K:CAP1477 1.8 13.7 1.0
OQ2 K:KCX201 2.0 12.4 1.0
OE1 K:GLU204 2.1 15.0 1.0
OD1 K:ASP203 2.2 17.9 1.0
O2 K:CAP1477 2.2 14.4 1.0
C K:CAP1477 2.7 19.1 1.0
C2 K:CAP1477 2.8 18.1 1.0
C3 K:CAP1477 2.8 18.7 1.0
CX K:KCX201 2.9 14.4 1.0
CD K:GLU204 3.1 15.9 1.0
OQ1 K:KCX201 3.1 14.9 1.0
CG K:ASP203 3.4 16.7 1.0
OE2 K:GLU204 3.6 18.3 1.0
NE2 K:HIS294 3.7 12.0 1.0
ND2 E:ASN123 3.8 20.7 1.0
O7 K:CAP1477 3.9 20.5 1.0
NZ K:LYS177 3.9 17.8 1.0
OD2 K:ASP203 4.0 20.9 1.0
N K:GLU204 4.0 12.3 1.0
C4 K:CAP1477 4.0 23.0 1.0
NZ K:KCX201 4.1 13.5 1.0
NZ K:LYS175 4.2 14.9 1.0
CG2 K:THR173 4.2 15.0 1.0
C1 K:CAP1477 4.2 18.1 1.0
CD2 K:HIS294 4.4 13.1 1.0
CG K:GLU204 4.4 14.1 1.0
CA K:ASP203 4.4 12.2 1.0
C5 K:CAP1477 4.4 16.3 1.0
CB K:ASP203 4.5 13.3 1.0
OG1 K:THR173 4.5 17.0 1.0
CB K:GLU204 4.6 12.4 1.0
CE1 K:HIS294 4.7 13.6 1.0
C K:ASP203 4.7 12.6 1.0
O1 K:CAP1477 4.8 8.4 1.0
CG E:ASN123 4.9 20.2 1.0
CA K:GLU204 4.9 12.3 1.0
CB K:THR173 4.9 15.3 1.0

Magnesium binding site 6 out of 8 in 1uzd

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Magnesium binding site 6 out of 8 in the Chlamydomonas,Spinach Chimeric Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Chlamydomonas,Spinach Chimeric Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg1476

b:13.6
occ:1.00
OD1 O:ASP203 1.8 18.4 1.0
O6 O:CAP1477 1.9 19.1 1.0
O2 O:CAP1477 2.1 20.9 1.0
OQ2 O:KCX201 2.1 12.7 1.0
OE1 O:GLU204 2.2 15.0 1.0
O3 O:CAP1477 2.2 8.0 1.0
C O:CAP1477 2.8 19.0 1.0
C2 O:CAP1477 2.8 17.8 1.0
CG O:ASP203 3.0 17.0 1.0
C3 O:CAP1477 3.1 18.3 1.0
CD O:GLU204 3.1 16.1 1.0
CX O:KCX201 3.2 14.3 1.0
OD2 O:ASP203 3.5 20.8 1.0
OE2 O:GLU204 3.5 18.1 1.0
NZ O:LYS177 3.6 18.0 1.0
OQ1 O:KCX201 3.6 14.4 1.0
NZ O:LYS175 3.8 14.9 1.0
ND2 V:ASN123 3.9 20.5 1.0
N O:GLU204 3.9 12.4 1.0
O7 O:CAP1477 4.0 17.9 1.0
CB O:ASP203 4.1 13.4 1.0
CG2 O:THR173 4.1 15.0 1.0
CA O:ASP203 4.2 12.2 1.0
NE2 O:HIS294 4.2 11.9 1.0
C4 O:CAP1477 4.2 16.0 1.0
C1 O:CAP1477 4.2 17.9 1.0
NZ O:KCX201 4.4 13.7 1.0
CG O:GLU204 4.5 14.3 1.0
OG1 O:THR173 4.5 16.8 1.0
C O:ASP203 4.6 12.4 1.0
O1 O:CAP1477 4.6 14.3 1.0
CB O:GLU204 4.7 12.7 1.0
CB O:THR173 4.8 15.8 1.0
C5 O:CAP1477 4.8 12.0 1.0
CD2 O:HIS294 4.9 12.8 1.0
O V:HOH2026 4.9 28.5 1.0
CA O:GLU204 5.0 12.4 1.0
CE O:LYS177 5.0 18.7 1.0

Magnesium binding site 7 out of 8 in 1uzd

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Magnesium binding site 7 out of 8 in the Chlamydomonas,Spinach Chimeric Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Chlamydomonas,Spinach Chimeric Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1476

b:12.4
occ:1.00
OD1 R:ASP203 1.9 18.6 1.0
OE1 R:GLU204 2.0 14.8 1.0
OQ2 R:KCX201 2.0 12.9 1.0
O2 R:CAP1477 2.2 12.7 1.0
O3 R:CAP1477 2.2 21.6 1.0
O6 R:CAP1477 2.3 16.2 1.0
C2 R:CAP1477 2.8 19.2 1.0
C R:CAP1477 2.9 15.6 1.0
C3 R:CAP1477 3.0 17.0 1.0
CD R:GLU204 3.0 15.8 1.0
CG R:ASP203 3.1 16.8 1.0
CX R:KCX201 3.1 14.2 1.0
OE2 R:GLU204 3.5 17.9 1.0
OQ1 R:KCX201 3.5 14.5 1.0
OD2 R:ASP203 3.6 21.2 1.0
NZ R:LYS177 3.7 17.7 1.0
N R:GLU204 3.7 12.2 1.0
ND2 H:ASN123 3.8 20.6 1.0
NE2 R:HIS294 4.0 11.6 1.0
NZ R:LYS175 4.1 15.2 1.0
C4 R:CAP1477 4.1 21.4 1.0
CA R:ASP203 4.1 12.0 1.0
CB R:ASP203 4.1 13.2 1.0
O7 R:CAP1477 4.1 15.5 1.0
CG2 R:THR173 4.2 15.1 1.0
NZ R:KCX201 4.3 13.6 1.0
C1 R:CAP1477 4.3 21.3 1.0
CG R:GLU204 4.3 14.1 1.0
C R:ASP203 4.5 12.7 1.0
CB R:GLU204 4.5 12.6 1.0
CD2 R:HIS294 4.6 13.5 1.0
OG1 R:THR173 4.7 16.8 1.0
C5 R:CAP1477 4.7 15.1 1.0
CA R:GLU204 4.7 12.4 1.0
O1 R:CAP1477 4.9 15.9 1.0
CE1 R:HIS294 4.9 13.3 1.0
O R:HOH2067 4.9 13.2 1.0
CB R:THR173 4.9 15.6 1.0

Magnesium binding site 8 out of 8 in 1uzd

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Magnesium binding site 8 out of 8 in the Chlamydomonas,Spinach Chimeric Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Chlamydomonas,Spinach Chimeric Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1476

b:18.0
occ:1.00
OD1 V:ASP203 1.7 18.1 1.0
O6 V:CAP1477 1.8 15.9 1.0
OE1 V:GLU204 2.1 15.1 1.0
OQ2 V:KCX201 2.2 12.1 1.0
O2 V:CAP1477 2.3 21.6 1.0
O3 V:CAP1477 2.4 12.5 1.0
C V:CAP1477 2.7 17.7 1.0
CG V:ASP203 2.9 16.7 1.0
C2 V:CAP1477 2.9 19.9 1.0
CD V:GLU204 3.0 15.8 1.0
C3 V:CAP1477 3.2 17.0 1.0
CX V:KCX201 3.3 14.4 1.0
OE2 V:GLU204 3.3 17.4 1.0
NZ V:LYS177 3.4 17.8 1.0
OD2 V:ASP203 3.4 21.0 1.0
OQ1 V:KCX201 3.7 14.9 1.0
NZ V:LYS175 3.7 14.9 1.0
ND2 O:ASN123 3.8 20.3 1.0
N V:GLU204 3.9 12.3 1.0
O7 V:CAP1477 3.9 15.6 1.0
CB V:ASP203 4.1 13.5 1.0
CG2 V:THR173 4.1 15.1 1.0
NE2 V:HIS294 4.2 12.0 1.0
CA V:ASP203 4.2 12.2 1.0
C4 V:CAP1477 4.3 17.5 1.0
C1 V:CAP1477 4.4 17.2 1.0
CG V:GLU204 4.4 14.3 1.0
NZ V:KCX201 4.4 13.4 1.0
C V:ASP203 4.6 12.3 1.0
CB V:GLU204 4.7 12.4 1.0
OG1 V:THR173 4.7 17.2 1.0
O1 V:CAP1477 4.8 16.2 1.0
CE V:LYS177 4.8 18.6 1.0
O O:HOH2051 4.9 16.5 1.0
O O:HOH2021 4.9 36.1 1.0
C5 V:CAP1477 4.9 19.1 1.0
CD2 V:HIS294 4.9 12.9 1.0
CB V:THR173 4.9 15.5 1.0
CA V:GLU204 4.9 12.6 1.0

Reference:

S.Karkehabadi, S.R.Peddi, M.Anwaruzzaman, T.C.Taylor, A.Cederlund, T.Genkov, I.Andersson, R.J.Spreitzer. Chimeric Small Subunits Influence Catalysis Without Causing Global Conformational Changes in the Crystal Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Biochemistry V. 44 9851 2005.
ISSN: ISSN 0006-2960
PubMed: 16026157
DOI: 10.1021/BI050537V
Page generated: Mon Dec 14 06:53:46 2020

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