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Magnesium in PDB 1uzh: A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme

Enzymatic activity of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme

All present enzymatic activity of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme:
4.1.1.39;

Protein crystallography data

The structure of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme, PDB code: 1uzh 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) 30.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 220.820, 223.969, 111.752, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.3

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 1uzh

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Magnesium binding site 1 out of 8 in the A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg476

b:17.6
occ:1.00
OQ2 A:KCX201 2.0 15.0 1.0
OD1 A:ASP203 2.0 16.9 1.0
O3 A:CAP477 2.1 17.4 1.0
OE1 A:GLU204 2.1 16.8 1.0
O7 A:CAP477 2.3 16.5 1.0
O2 A:CAP477 2.3 23.9 1.0
CX A:KCX201 2.9 15.9 1.0
C2 A:CAP477 2.9 17.2 1.0
C A:CAP477 3.0 17.9 1.0
C3 A:CAP477 3.0 19.0 1.0
OQ1 A:KCX201 3.1 15.2 1.0
CD A:GLU204 3.2 15.8 1.0
CG A:ASP203 3.2 17.4 1.0
OE2 A:GLU204 3.6 18.0 1.0
N A:GLU204 3.7 15.2 1.0
CG2 A:THR173 3.9 11.9 1.0
OD2 A:ASP203 3.9 20.4 1.0
NZ A:LYS177 3.9 15.1 1.0
ND2 B:ASN123 4.0 18.2 1.0
NE2 A:HIS294 4.0 14.5 1.0
NZ A:LYS175 4.0 14.4 1.0
CA A:ASP203 4.1 14.9 1.0
NZ A:KCX201 4.1 13.7 1.0
CB A:ASP203 4.2 14.5 1.0
OG1 A:THR173 4.2 17.6 1.0
C4 A:CAP477 4.3 22.1 1.0
O6 A:CAP477 4.3 19.3 1.0
C1 A:CAP477 4.4 14.1 1.0
CG A:GLU204 4.4 13.3 1.0
C A:ASP203 4.4 15.8 1.0
CB A:GLU204 4.5 15.0 1.0
CD2 A:HIS294 4.6 12.1 1.0
CB A:THR173 4.6 17.2 1.0
C5 A:CAP477 4.7 15.0 1.0
CA A:GLU204 4.7 14.9 1.0
O1 A:CAP477 4.8 20.5 1.0
CE1 A:HIS294 5.0 15.6 1.0

Magnesium binding site 2 out of 8 in 1uzh

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Magnesium binding site 2 out of 8 in the A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg476

b:13.0
occ:1.00
OQ2 B:KCX201 2.1 15.1 1.0
OD1 B:ASP203 2.1 17.3 1.0
OE1 B:GLU204 2.1 16.6 1.0
O7 B:CAP477 2.1 18.1 1.0
O3 B:CAP477 2.1 14.3 1.0
O2 B:CAP477 2.2 22.0 1.0
C2 B:CAP477 2.8 18.7 1.0
C B:CAP477 2.9 19.4 1.0
C3 B:CAP477 3.0 15.2 1.0
CX B:KCX201 3.1 16.1 1.0
CD B:GLU204 3.1 16.1 1.0
CG B:ASP203 3.2 17.4 1.0
OQ1 B:KCX201 3.3 15.1 1.0
OE2 B:GLU204 3.6 17.7 1.0
NZ B:LYS177 3.7 14.8 1.0
ND2 A:ASN123 3.8 18.4 1.0
N B:GLU204 3.8 15.2 1.0
OD2 B:ASP203 3.8 20.2 1.0
NZ B:LYS175 3.9 14.3 1.0
CG2 B:THR173 3.9 12.0 1.0
NE2 B:HIS294 4.0 13.9 1.0
O6 B:CAP477 4.1 20.1 1.0
CA B:ASP203 4.2 14.8 1.0
C4 B:CAP477 4.2 16.5 1.0
OG1 B:THR173 4.2 17.5 1.0
CB B:ASP203 4.3 14.6 1.0
NZ B:KCX201 4.3 13.1 1.0
C1 B:CAP477 4.3 18.1 1.0
CG B:GLU204 4.4 13.4 1.0
C B:ASP203 4.5 16.1 1.0
CB B:GLU204 4.6 14.8 1.0
CD2 B:HIS294 4.6 12.2 1.0
CB B:THR173 4.7 17.4 1.0
C5 B:CAP477 4.7 15.9 1.0
CA B:GLU204 4.8 15.4 1.0
O1 B:CAP477 4.8 19.2 1.0
O A:HOH2043 4.9 19.7 1.0
CE1 B:HIS294 4.9 15.3 1.0
CG A:ASN123 5.0 19.5 1.0

Magnesium binding site 3 out of 8 in 1uzh

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Magnesium binding site 3 out of 8 in the A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg476

b:13.6
occ:1.00
OD1 E:ASP203 2.0 16.9 1.0
OE1 E:GLU204 2.0 17.0 1.0
OQ2 E:KCX201 2.0 15.0 1.0
O7 E:CAP477 2.0 20.2 1.0
O3 E:CAP477 2.2 24.2 1.0
O2 E:CAP477 2.4 19.9 1.0
C E:CAP477 2.9 20.7 1.0
C2 E:CAP477 2.9 20.2 1.0
CD E:GLU204 3.0 16.0 1.0
CX E:KCX201 3.0 16.1 1.0
C3 E:CAP477 3.1 19.1 1.0
CG E:ASP203 3.1 17.8 1.0
OQ1 E:KCX201 3.3 15.2 1.0
OE2 E:GLU204 3.4 18.0 1.0
N E:GLU204 3.7 15.8 1.0
NZ E:LYS177 3.7 15.4 1.0
OD2 E:ASP203 3.8 20.5 1.0
ND2 K:ASN123 3.9 18.4 1.0
CG2 E:THR173 3.9 11.8 1.0
NE2 E:HIS294 4.0 13.3 1.0
NZ E:LYS175 4.0 14.5 1.0
CA E:ASP203 4.1 15.0 1.0
CB E:ASP203 4.1 14.1 1.0
O6 E:CAP477 4.2 23.7 1.0
NZ E:KCX201 4.2 13.4 1.0
CG E:GLU204 4.3 13.8 1.0
OG1 E:THR173 4.3 17.6 1.0
C4 E:CAP477 4.4 22.2 1.0
C E:ASP203 4.4 15.9 1.0
C1 E:CAP477 4.4 19.1 1.0
CB E:GLU204 4.5 15.1 1.0
CD2 E:HIS294 4.6 12.1 1.0
CB E:THR173 4.7 17.3 1.0
CA E:GLU204 4.7 15.1 1.0
C5 E:CAP477 4.8 19.0 1.0
O1 E:CAP477 4.8 21.1 1.0
CE1 E:HIS294 5.0 15.6 1.0

Magnesium binding site 4 out of 8 in 1uzh

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Magnesium binding site 4 out of 8 in the A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg476

b:16.5
occ:1.00
O7 H:CAP477 2.0 18.4 1.0
OD1 H:ASP203 2.0 17.3 1.0
OQ2 H:KCX201 2.1 15.0 1.0
OE1 H:GLU204 2.1 16.6 1.0
O3 H:CAP477 2.2 21.1 1.0
O2 H:CAP477 2.4 23.7 1.0
C H:CAP477 2.8 20.0 1.0
C2 H:CAP477 2.9 22.0 1.0
CX H:KCX201 3.1 15.8 1.0
C3 H:CAP477 3.1 18.9 1.0
CD H:GLU204 3.1 15.9 1.0
CG H:ASP203 3.2 17.6 1.0
OQ1 H:KCX201 3.3 15.4 1.0
OE2 H:GLU204 3.5 17.6 1.0
NZ H:LYS177 3.7 15.4 1.0
OD2 H:ASP203 3.8 20.5 1.0
N H:GLU204 3.8 15.5 1.0
ND2 R:ASN123 3.9 18.0 1.0
NZ H:LYS175 3.9 14.6 1.0
CG2 H:THR173 4.0 12.1 1.0
NE2 H:HIS294 4.0 14.3 1.0
O6 H:CAP477 4.1 17.0 1.0
CA H:ASP203 4.2 15.1 1.0
OG1 H:THR173 4.2 17.6 1.0
C4 H:CAP477 4.2 18.9 1.0
CB H:ASP203 4.2 14.5 1.0
NZ H:KCX201 4.3 13.5 1.0
C1 H:CAP477 4.4 23.3 1.0
CG H:GLU204 4.4 13.6 1.0
C H:ASP203 4.5 16.2 1.0
CB H:GLU204 4.6 15.0 1.0
C5 H:CAP477 4.6 22.5 1.0
CB H:THR173 4.6 17.2 1.0
CD2 H:HIS294 4.7 12.2 1.0
O1 H:CAP477 4.8 21.5 1.0
CA H:GLU204 4.8 15.4 1.0
CE1 H:HIS294 5.0 15.6 1.0
O R:HOH2042 5.0 21.6 1.0

Magnesium binding site 5 out of 8 in 1uzh

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Magnesium binding site 5 out of 8 in the A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg476

b:19.3
occ:1.00
OD1 K:ASP203 2.0 16.9 1.0
OE1 K:GLU204 2.0 16.8 1.0
OQ2 K:KCX201 2.1 15.0 1.0
O7 K:CAP477 2.2 15.2 1.0
O3 K:CAP477 2.2 20.2 1.0
O2 K:CAP477 2.4 21.6 1.0
C K:CAP477 3.0 18.1 1.0
C2 K:CAP477 3.0 16.2 1.0
CD K:GLU204 3.0 15.7 1.0
C3 K:CAP477 3.1 17.2 1.0
CX K:KCX201 3.1 15.8 1.0
CG K:ASP203 3.2 17.5 1.0
OQ1 K:KCX201 3.3 15.5 1.0
OE2 K:GLU204 3.3 17.7 1.0
N K:GLU204 3.7 15.6 1.0
NZ K:LYS177 3.7 15.0 1.0
ND2 E:ASN123 3.8 17.9 1.0
OD2 K:ASP203 3.8 20.2 1.0
NE2 K:HIS294 4.0 14.1 1.0
CG2 K:THR173 4.0 11.7 1.0
NZ K:LYS175 4.1 14.4 1.0
CA K:ASP203 4.1 14.9 1.0
CB K:ASP203 4.2 14.5 1.0
O6 K:CAP477 4.2 17.7 1.0
NZ K:KCX201 4.3 13.7 1.0
C4 K:CAP477 4.3 20.8 1.0
CG K:GLU204 4.3 13.7 1.0
C1 K:CAP477 4.4 20.1 1.0
C K:ASP203 4.4 16.0 1.0
OG1 K:THR173 4.4 17.5 1.0
CB K:GLU204 4.5 14.9 1.0
CD2 K:HIS294 4.6 12.2 1.0
CA K:GLU204 4.7 15.0 1.0
C5 K:CAP477 4.7 13.7 1.0
CB K:THR173 4.8 17.2 1.0
O1 K:CAP477 4.9 18.9 1.0
CE1 K:HIS294 4.9 15.5 1.0
CG E:ASN123 4.9 19.6 1.0

Magnesium binding site 6 out of 8 in 1uzh

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Magnesium binding site 6 out of 8 in the A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg476

b:15.4
occ:1.00
OD1 O:ASP203 1.9 17.3 1.0
OE1 O:GLU204 2.0 16.8 1.0
OQ2 O:KCX201 2.1 14.9 1.0
O7 O:CAP477 2.2 12.2 1.0
O3 O:CAP477 2.2 19.4 1.0
O2 O:CAP477 2.3 23.3 1.0
C2 O:CAP477 3.0 18.9 1.0
C O:CAP477 3.0 16.9 1.0
CX O:KCX201 3.1 15.8 1.0
CD O:GLU204 3.1 16.1 1.0
CG O:ASP203 3.1 17.7 1.0
C3 O:CAP477 3.1 20.7 1.0
OQ1 O:KCX201 3.3 15.3 1.0
OE2 O:GLU204 3.5 17.8 1.0
NZ O:LYS177 3.7 14.8 1.0
OD2 O:ASP203 3.7 20.5 1.0
N O:GLU204 3.7 15.6 1.0
ND2 V:ASN123 3.8 17.8 1.0
CG2 O:THR173 3.9 11.7 1.0
NZ O:LYS175 4.0 14.4 1.0
NE2 O:HIS294 4.0 13.8 1.0
CA O:ASP203 4.1 14.9 1.0
CB O:ASP203 4.1 14.3 1.0
NZ O:KCX201 4.2 13.4 1.0
O6 O:CAP477 4.2 17.9 1.0
OG1 O:THR173 4.3 17.5 1.0
C4 O:CAP477 4.3 15.6 1.0
CG O:GLU204 4.3 13.8 1.0
C1 O:CAP477 4.4 19.8 1.0
C O:ASP203 4.5 15.8 1.0
CB O:GLU204 4.5 14.7 1.0
CD2 O:HIS294 4.7 12.0 1.0
CB O:THR173 4.7 17.3 1.0
CA O:GLU204 4.7 15.1 1.0
C5 O:CAP477 4.7 14.1 1.0
O1 O:CAP477 4.8 19.4 1.0
CE1 O:HIS294 5.0 15.4 1.0

Magnesium binding site 7 out of 8 in 1uzh

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Magnesium binding site 7 out of 8 in the A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg476

b:12.0
occ:1.00
OD1 R:ASP203 2.0 17.2 1.0
OQ2 R:KCX201 2.0 15.2 1.0
OE1 R:GLU204 2.0 16.7 1.0
O3 R:CAP477 2.3 17.9 1.0
O7 R:CAP477 2.3 16.6 1.0
O2 R:CAP477 2.3 17.7 1.0
C2 R:CAP477 3.0 16.4 1.0
C R:CAP477 3.0 17.1 1.0
CX R:KCX201 3.1 15.9 1.0
CD R:GLU204 3.1 15.7 1.0
CG R:ASP203 3.1 17.7 1.0
C3 R:CAP477 3.2 16.7 1.0
OQ1 R:KCX201 3.3 14.8 1.0
OE2 R:GLU204 3.5 18.0 1.0
NZ R:LYS177 3.7 15.2 1.0
N R:GLU204 3.7 15.5 1.0
OD2 R:ASP203 3.8 20.4 1.0
ND2 H:ASN123 3.8 17.6 1.0
CG2 R:THR173 4.0 11.7 1.0
NZ R:LYS175 4.0 14.2 1.0
NE2 R:HIS294 4.0 13.6 1.0
CA R:ASP203 4.1 14.8 1.0
CB R:ASP203 4.2 14.3 1.0
NZ R:KCX201 4.2 13.3 1.0
O6 R:CAP477 4.3 19.0 1.0
OG1 R:THR173 4.3 17.4 1.0
CG R:GLU204 4.3 13.4 1.0
C4 R:CAP477 4.3 22.4 1.0
C1 R:CAP477 4.4 15.5 1.0
C R:ASP203 4.4 15.8 1.0
CB R:GLU204 4.5 15.0 1.0
CD2 R:HIS294 4.6 12.4 1.0
CB R:THR173 4.7 17.3 1.0
CA R:GLU204 4.7 15.2 1.0
C5 R:CAP477 4.8 20.1 1.0
O1 R:CAP477 4.8 15.9 1.0
CE1 R:HIS294 4.9 15.7 1.0

Magnesium binding site 8 out of 8 in 1uzh

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Magnesium binding site 8 out of 8 in the A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg476

b:16.3
occ:1.00
OQ2 V:KCX201 2.0 14.8 1.0
OD1 V:ASP203 2.0 17.3 1.0
O3 V:CAP477 2.1 17.0 1.0
O2 V:CAP477 2.1 21.2 1.0
O7 V:CAP477 2.1 20.4 1.0
OE1 V:GLU204 2.1 16.8 1.0
C2 V:CAP477 2.7 23.7 1.0
C V:CAP477 2.8 21.0 1.0
C3 V:CAP477 2.9 17.9 1.0
CX V:KCX201 3.0 16.2 1.0
CD V:GLU204 3.2 16.0 1.0
CG V:ASP203 3.2 17.6 1.0
OQ1 V:KCX201 3.2 14.9 1.0
OE2 V:GLU204 3.6 17.9 1.0
NZ V:LYS177 3.8 15.1 1.0
OD2 V:ASP203 3.8 20.6 1.0
N V:GLU204 3.8 15.6 1.0
ND2 O:ASN123 3.9 17.9 1.0
CG2 V:THR173 3.9 12.0 1.0
NZ V:LYS175 4.0 14.3 1.0
NE2 V:HIS294 4.0 14.2 1.0
O6 V:CAP477 4.1 18.7 1.0
C4 V:CAP477 4.1 23.2 1.0
NZ V:KCX201 4.2 13.6 1.0
CA V:ASP203 4.2 14.9 1.0
C1 V:CAP477 4.2 20.2 1.0
OG1 V:THR173 4.2 17.4 1.0
CB V:ASP203 4.2 14.5 1.0
CG V:GLU204 4.4 13.7 1.0
C V:ASP203 4.6 16.1 1.0
CB V:THR173 4.6 17.2 1.0
CB V:GLU204 4.6 14.8 1.0
C5 V:CAP477 4.6 18.0 1.0
CD2 V:HIS294 4.6 12.2 1.0
O1 V:CAP477 4.7 17.8 1.0
CA V:GLU204 4.8 14.8 1.0
CE1 V:HIS294 5.0 15.3 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 06:53:50 2020

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