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Magnesium in PDB 1uwa: L290F Mutant Rubisco From Chlamydomonas

Enzymatic activity of L290F Mutant Rubisco From Chlamydomonas

All present enzymatic activity of L290F Mutant Rubisco From Chlamydomonas:
4.1.1.39;

Protein crystallography data

The structure of L290F Mutant Rubisco From Chlamydomonas, PDB code: 1uwa was solved by S.Karkehabadi, 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 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 120.983, 177.709, 122.663, 90.00, 117.70, 90.00
R / Rfree (%) 17.1 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the L290F Mutant Rubisco From Chlamydomonas (pdb code 1uwa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the L290F Mutant Rubisco From Chlamydomonas, PDB code: 1uwa:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1uwa

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Magnesium binding site 1 out of 8 in the L290F Mutant Rubisco From Chlamydomonas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of L290F Mutant Rubisco From Chlamydomonas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:27.2
occ:1.00
OD1 A:ASP203 1.9 30.7 1.0
OQ2 A:KCX201 2.0 23.7 1.0
OE1 A:GLU204 2.1 30.5 1.0
O3 A:CAP502 2.1 32.2 1.0
O7 A:CAP502 2.2 32.4 1.0
O2 A:CAP502 2.2 32.9 1.0
C2 A:CAP502 2.8 32.7 1.0
C A:CAP502 2.9 32.8 1.0
C3 A:CAP502 3.0 31.9 1.0
CX A:KCX201 3.0 27.6 1.0
CG A:ASP203 3.1 30.5 1.0
CD A:GLU204 3.2 31.7 1.0
OQ1 A:KCX201 3.3 29.7 1.0
OE2 A:GLU204 3.6 33.2 1.0
NZ A:LYS177 3.7 30.0 1.0
OD2 A:ASP203 3.8 34.7 1.0
N A:GLU204 3.8 26.9 1.0
NZ A:LYS175 3.9 28.3 1.0
ND2 O:ASN123 3.9 31.1 1.0
CG2 A:THR173 4.0 27.9 1.0
NE2 A:HIS294 4.1 25.2 1.0
CA A:ASP203 4.1 26.6 1.0
CB A:ASP203 4.2 26.7 1.0
O6 A:CAP502 4.2 32.9 1.0
NZ A:KCX201 4.2 25.9 1.0
C4 A:CAP502 4.2 34.0 1.0
C1 A:CAP502 4.3 32.1 1.0
OG1 A:THR173 4.3 34.0 1.0
CG A:GLU204 4.4 25.6 1.0
C A:ASP203 4.5 27.6 1.0
CB A:GLU204 4.6 27.5 1.0
CD2 A:HIS294 4.7 21.6 1.0
CB A:THR173 4.7 31.6 1.0
C5 A:CAP502 4.8 30.7 1.0
O1 A:CAP502 4.8 31.1 1.0
CA A:GLU204 4.8 27.1 1.0

Magnesium binding site 2 out of 8 in 1uwa

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Magnesium binding site 2 out of 8 in the L290F Mutant Rubisco From Chlamydomonas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of L290F Mutant Rubisco From Chlamydomonas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:27.6
occ:1.00
OD1 B:ASP203 1.9 30.9 1.0
OE1 B:GLU204 2.1 30.5 1.0
O7 B:CAP502 2.1 32.2 1.0
OQ2 B:KCX201 2.1 24.0 1.0
O3 B:CAP502 2.1 32.2 1.0
O2 B:CAP502 2.2 32.7 1.0
C2 B:CAP502 2.8 32.6 1.0
C B:CAP502 2.9 32.6 1.0
C3 B:CAP502 3.0 32.0 1.0
CX B:KCX201 3.1 27.4 1.0
CD B:GLU204 3.2 31.7 1.0
CG B:ASP203 3.2 30.7 1.0
OQ1 B:KCX201 3.3 29.7 1.0
OE2 B:GLU204 3.6 33.0 1.0
NZ B:LYS177 3.7 30.2 1.0
OD2 B:ASP203 3.8 34.5 1.0
N B:GLU204 3.8 27.1 1.0
ND2 E:ASN123 3.9 31.0 1.0
NZ B:LYS175 4.0 27.9 1.0
CG2 B:THR173 4.0 28.1 1.0
NE2 B:HIS294 4.1 24.9 1.0
O6 B:CAP502 4.1 32.8 1.0
CA B:ASP203 4.1 26.7 1.0
CB B:ASP203 4.2 26.6 1.0
C4 B:CAP502 4.2 33.9 1.0
NZ B:KCX201 4.2 25.4 1.0
C1 B:CAP502 4.3 32.1 1.0
OG1 B:THR173 4.4 33.8 1.0
CG B:GLU204 4.4 25.6 1.0
C B:ASP203 4.5 27.4 1.0
CB B:GLU204 4.5 27.4 1.0
CD2 B:HIS294 4.7 21.6 1.0
CB B:THR173 4.7 31.7 1.0
C5 B:CAP502 4.7 30.6 1.0
CA B:GLU204 4.8 27.1 1.0
O1 B:CAP502 4.8 30.7 1.0
CE1 B:HIS294 5.0 24.8 1.0

Magnesium binding site 3 out of 8 in 1uwa

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Magnesium binding site 3 out of 8 in the L290F Mutant Rubisco From Chlamydomonas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of L290F Mutant Rubisco From Chlamydomonas within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:27.1
occ:1.00
OQ2 E:KCX201 2.0 24.1 1.0
OD1 E:ASP203 2.0 30.9 1.0
O3 E:CAP502 2.1 32.5 1.0
OE1 E:GLU204 2.1 30.6 1.0
O7 E:CAP502 2.1 32.2 1.0
O2 E:CAP502 2.2 32.9 1.0
C2 E:CAP502 2.8 32.6 1.0
C E:CAP502 2.9 32.9 1.0
C3 E:CAP502 3.0 31.8 1.0
CX E:KCX201 3.0 27.5 1.0
CD E:GLU204 3.2 31.4 1.0
CG E:ASP203 3.2 30.9 1.0
OQ1 E:KCX201 3.3 29.8 1.0
OE2 E:GLU204 3.6 32.4 1.0
NZ E:LYS177 3.7 30.2 1.0
N E:GLU204 3.8 26.8 1.0
OD2 E:ASP203 3.9 34.5 1.0
ND2 B:ASN123 3.9 31.0 1.0
NZ E:LYS175 3.9 28.1 1.0
CG2 E:THR173 4.0 27.8 1.0
NE2 E:HIS294 4.0 25.0 1.0
CA E:ASP203 4.1 26.5 1.0
O6 E:CAP502 4.1 33.3 1.0
NZ E:KCX201 4.2 26.1 1.0
C4 E:CAP502 4.2 34.0 1.0
CB E:ASP203 4.2 26.5 1.0
C1 E:CAP502 4.3 31.9 1.0
OG1 E:THR173 4.3 34.4 1.0
CG E:GLU204 4.4 25.8 1.0
C E:ASP203 4.5 27.4 1.0
CB E:GLU204 4.6 27.4 1.0
CD2 E:HIS294 4.6 21.7 1.0
C5 E:CAP502 4.7 30.5 1.0
CB E:THR173 4.7 31.8 1.0
O1 E:CAP502 4.8 30.8 1.0
CA E:GLU204 4.8 27.3 1.0
CE1 E:HIS294 5.0 25.1 1.0

Magnesium binding site 4 out of 8 in 1uwa

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Magnesium binding site 4 out of 8 in the L290F Mutant Rubisco From Chlamydomonas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of L290F Mutant Rubisco From Chlamydomonas within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:28.2
occ:1.00
OQ2 H:KCX201 1.9 23.9 1.0
OD1 H:ASP203 1.9 30.8 1.0
OE1 H:GLU204 2.0 30.5 1.0
O3 H:CAP502 2.1 32.3 1.0
O2 H:CAP502 2.2 32.9 1.0
O7 H:CAP502 2.2 32.4 1.0
C2 H:CAP502 2.9 32.8 1.0
C H:CAP502 2.9 32.9 1.0
CX H:KCX201 2.9 27.4 1.0
C3 H:CAP502 3.0 32.1 1.0
CD H:GLU204 3.1 31.8 1.0
CG H:ASP203 3.1 30.9 1.0
OQ1 H:KCX201 3.3 30.0 1.0
OE2 H:GLU204 3.6 33.1 1.0
N H:GLU204 3.7 27.2 1.0
NZ H:LYS177 3.8 30.4 1.0
OD2 H:ASP203 3.8 34.7 1.0
CG2 H:THR173 3.9 27.9 1.0
ND2 V:ASN123 4.0 31.4 1.0
NE2 H:HIS294 4.0 25.0 1.0
NZ H:LYS175 4.0 28.6 1.0
CA H:ASP203 4.1 26.8 1.0
NZ H:KCX201 4.1 25.7 1.0
CB H:ASP203 4.1 26.6 1.0
O6 H:CAP502 4.2 33.5 1.0
C4 H:CAP502 4.3 34.0 1.0
C1 H:CAP502 4.3 32.4 1.0
OG1 H:THR173 4.3 33.9 1.0
CG H:GLU204 4.4 25.9 1.0
C H:ASP203 4.4 27.7 1.0
CB H:GLU204 4.5 27.4 1.0
CD2 H:HIS294 4.6 21.6 1.0
CB H:THR173 4.7 31.8 1.0
CA H:GLU204 4.7 27.4 1.0
C5 H:CAP502 4.8 31.0 1.0
O1 H:CAP502 4.8 31.2 1.0
CE1 H:HIS294 5.0 25.0 1.0

Magnesium binding site 5 out of 8 in 1uwa

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Magnesium binding site 5 out of 8 in the L290F Mutant Rubisco From Chlamydomonas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of L290F Mutant Rubisco From Chlamydomonas within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg501

b:27.6
occ:1.00
OD1 K:ASP203 1.9 30.8 1.0
OQ2 K:KCX201 2.0 24.5 1.0
OE1 K:GLU204 2.1 30.4 1.0
O7 K:CAP502 2.2 32.3 1.0
O2 K:CAP502 2.2 32.8 1.0
O3 K:CAP502 2.2 32.1 1.0
C2 K:CAP502 2.8 33.0 1.0
C K:CAP502 2.9 32.7 1.0
C3 K:CAP502 3.0 31.7 1.0
CG K:ASP203 3.1 30.7 1.0
CX K:KCX201 3.1 27.3 1.0
CD K:GLU204 3.2 31.8 1.0
OQ1 K:KCX201 3.5 29.6 1.0
OE2 K:GLU204 3.6 33.0 1.0
NZ K:LYS177 3.7 30.1 1.0
OD2 K:ASP203 3.7 34.6 1.0
N K:GLU204 3.8 27.0 1.0
NZ K:LYS175 3.9 28.2 1.0
CG2 K:THR173 3.9 27.9 1.0
ND2 R:ASN123 4.0 31.3 1.0
CA K:ASP203 4.1 26.5 1.0
NE2 K:HIS294 4.1 25.0 1.0
CB K:ASP203 4.1 26.7 1.0
O6 K:CAP502 4.2 33.1 1.0
NZ K:KCX201 4.2 25.4 1.0
OG1 K:THR173 4.3 34.0 1.0
C1 K:CAP502 4.3 32.1 1.0
C4 K:CAP502 4.3 34.2 1.0
CG K:GLU204 4.5 25.6 1.0
C K:ASP203 4.5 27.4 1.0
CB K:GLU204 4.6 27.5 1.0
CB K:THR173 4.7 31.8 1.0
CD2 K:HIS294 4.7 21.6 1.0
O1 K:CAP502 4.8 30.9 1.0
CA K:GLU204 4.8 27.1 1.0
C5 K:CAP502 4.9 30.8 1.0

Magnesium binding site 6 out of 8 in 1uwa

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Magnesium binding site 6 out of 8 in the L290F Mutant Rubisco From Chlamydomonas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of L290F Mutant Rubisco From Chlamydomonas within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg501

b:27.5
occ:1.00
O3 O:CAP502 2.0 32.2 1.0
OQ2 O:KCX201 2.0 24.4 1.0
OD1 O:ASP203 2.0 31.0 1.0
OE1 O:GLU204 2.1 30.4 1.0
O7 O:CAP502 2.1 32.2 1.0
O2 O:CAP502 2.2 33.1 1.0
C2 O:CAP502 2.8 32.8 1.0
C O:CAP502 2.9 32.9 1.0
C3 O:CAP502 2.9 32.0 1.0
CX O:KCX201 3.0 27.5 1.0
CD O:GLU204 3.2 31.5 1.0
CG O:ASP203 3.3 30.7 1.0
OQ1 O:KCX201 3.3 29.6 1.0
OE2 O:GLU204 3.7 32.5 1.0
NZ O:LYS177 3.8 30.0 1.0
N O:GLU204 3.8 27.1 1.0
ND2 A:ASN123 3.9 31.2 1.0
OD2 O:ASP203 3.9 34.1 1.0
NE2 O:HIS294 3.9 25.3 1.0
NZ O:LYS175 4.0 28.2 1.0
CG2 O:THR173 4.0 27.9 1.0
C4 O:CAP502 4.1 34.0 1.0
O6 O:CAP502 4.2 33.3 1.0
CA O:ASP203 4.2 26.6 1.0
NZ O:KCX201 4.2 25.6 1.0
C1 O:CAP502 4.3 32.1 1.0
CB O:ASP203 4.3 26.3 1.0
OG1 O:THR173 4.3 34.4 1.0
CG O:GLU204 4.4 25.7 1.0
C O:ASP203 4.5 27.6 1.0
CD2 O:HIS294 4.6 21.6 1.0
CB O:GLU204 4.6 27.6 1.0
C5 O:CAP502 4.7 30.5 1.0
CB O:THR173 4.7 31.8 1.0
O1 O:CAP502 4.8 30.9 1.0
CA O:GLU204 4.8 27.3 1.0
CE1 O:HIS294 4.9 25.2 1.0

Magnesium binding site 7 out of 8 in 1uwa

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Magnesium binding site 7 out of 8 in the L290F Mutant Rubisco From Chlamydomonas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of L290F Mutant Rubisco From Chlamydomonas within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg501

b:28.1
occ:1.00
OD1 R:ASP203 1.9 31.2 1.0
OQ2 R:KCX201 2.0 24.1 1.0
O7 R:CAP502 2.1 32.6 1.0
OE1 R:GLU204 2.1 30.6 1.0
O2 R:CAP502 2.1 32.7 1.0
O3 R:CAP502 2.2 31.9 1.0
C2 R:CAP502 2.8 32.8 1.0
C R:CAP502 2.9 32.7 1.0
C3 R:CAP502 3.0 32.0 1.0
CX R:KCX201 3.1 27.4 1.0
CG R:ASP203 3.1 30.9 1.0
CD R:GLU204 3.2 31.8 1.0
OQ1 R:KCX201 3.4 29.8 1.0
OE2 R:GLU204 3.6 33.2 1.0
NZ R:LYS177 3.7 30.3 1.0
OD2 R:ASP203 3.8 34.6 1.0
N R:GLU204 3.8 27.0 1.0
NZ R:LYS175 3.9 28.2 1.0
ND2 K:ASN123 3.9 31.1 1.0
CG2 R:THR173 4.0 27.9 1.0
NE2 R:HIS294 4.1 25.4 1.0
O6 R:CAP502 4.1 33.1 1.0
CA R:ASP203 4.1 26.6 1.0
CB R:ASP203 4.2 26.6 1.0
NZ R:KCX201 4.2 25.8 1.0
C4 R:CAP502 4.3 33.9 1.0
C1 R:CAP502 4.3 32.3 1.0
OG1 R:THR173 4.3 34.3 1.0
CG R:GLU204 4.4 25.8 1.0
C R:ASP203 4.5 27.6 1.0
CB R:GLU204 4.6 27.5 1.0
CB R:THR173 4.7 31.7 1.0
CD2 R:HIS294 4.7 21.9 1.0
O1 R:CAP502 4.7 31.1 1.0
C5 R:CAP502 4.8 30.8 1.0
CA R:GLU204 4.9 27.1 1.0

Magnesium binding site 8 out of 8 in 1uwa

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Magnesium binding site 8 out of 8 in the L290F Mutant Rubisco From Chlamydomonas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of L290F Mutant Rubisco From Chlamydomonas within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg501

b:27.4
occ:1.00
OD1 V:ASP203 1.9 30.9 1.0
OQ2 V:KCX201 2.1 24.0 1.0
OE1 V:GLU204 2.1 30.7 1.0
O3 V:CAP502 2.1 32.1 1.0
O7 V:CAP502 2.1 32.5 1.0
O2 V:CAP502 2.2 33.1 1.0
C2 V:CAP502 2.9 32.7 1.0
C V:CAP502 2.9 32.9 1.0
C3 V:CAP502 3.0 32.0 1.0
CX V:KCX201 3.1 27.3 1.0
CG V:ASP203 3.1 30.8 1.0
CD V:GLU204 3.1 31.8 1.0
OQ1 V:KCX201 3.4 29.6 1.0
OE2 V:GLU204 3.6 33.2 1.0
NZ V:LYS177 3.7 30.3 1.0
OD2 V:ASP203 3.8 34.4 1.0
N V:GLU204 3.8 27.3 1.0
NZ V:LYS175 3.9 28.3 1.0
ND2 H:ASN123 3.9 31.1 1.0
CG2 V:THR173 4.0 27.8 1.0
NE2 V:HIS294 4.0 25.4 1.0
CA V:ASP203 4.1 26.8 1.0
O6 V:CAP502 4.2 33.1 1.0
CB V:ASP203 4.2 26.7 1.0
NZ V:KCX201 4.2 25.8 1.0
C4 V:CAP502 4.2 34.0 1.0
C1 V:CAP502 4.3 32.4 1.0
OG1 V:THR173 4.4 34.1 1.0
CG V:GLU204 4.4 25.6 1.0
C V:ASP203 4.5 27.8 1.0
CB V:GLU204 4.6 27.6 1.0
CD2 V:HIS294 4.6 22.1 1.0
CB V:THR173 4.7 31.7 1.0
C5 V:CAP502 4.8 30.7 1.0
CA V:GLU204 4.8 27.0 1.0
O1 V:CAP502 4.8 30.8 1.0
CE1 V:HIS294 5.0 25.0 1.0

Reference:

S.Karkehabadi, T.C.Taylor, R.J.Spreitzer, I.Andersson. Altered Intersubunit Interactions in Crystal Structures of Catalytically Compromised Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Biochemistry V. 44 113 2005.
ISSN: ISSN 0006-2960
PubMed: 15628851
DOI: 10.1021/BI047928E
Page generated: Mon Dec 14 06:53:42 2020

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