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Magnesium in PDB 5oya: Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.

Protein crystallography data

The structure of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco., PDB code: 5oya was solved by K.Valegard, I.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.19 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.170, 219.110, 220.230, 90.00, 90.19, 90.00
R / Rfree (%) 16.7 / 19.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. (pdb code 5oya). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco., PDB code: 5oya:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5oya

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Magnesium binding site 1 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:21.4
occ:1.00
 OE2 A:GLU208 2.0 19.1 1.0
OD1 A:ASP207 2.0 19.6 1.0
OQ2 A:KCX205 2.0 20.9 1.0
O3 A:CAP502 2.2 23.0 1.0
O7 A:CAP502 2.3 22.5 1.0
O2 A:CAP502 2.4 22.7 1.0
C2 A:CAP502 3.0 23.6 1.0
C A:CAP502 3.0 24.3 1.0
CX A:KCX205 3.0 21.1 1.0
CD A:GLU208 3.0 19.0 1.0
C3 A:CAP502 3.1 23.9 1.0
CG A:ASP207 3.2 19.9 1.0
OQ1 A:KCX205 3.3 21.5 1.0
OE1 A:GLU208 3.6 19.4 1.0
NZ A:LYS181 3.7 21.1 1.0
N A:GLU208 3.7 18.2 1.0
OD2 A:ASP207 3.9 20.2 1.0
NE2 A:HIS297 3.9 18.6 1.0
CG2 A:THR177 4.0 21.3 1.0
NZ A:LYS179 4.1 21.0 1.0
CA A:ASP207 4.1 18.8 1.0
NZ A:KCX205 4.2 20.3 1.0
CB A:ASP207 4.2 19.3 1.0
O6 A:CAP502 4.2 23.8 1.0
CG A:GLU208 4.3 18.4 1.0
OG1 A:THR177 4.3 21.4 1.0
CD2 A:HIS297 4.3 18.2 1.0
C4 A:CAP502 4.4 23.1 1.0
CB A:GLU208 4.4 18.1 1.0
C A:ASP207 4.5 18.4 1.0
C1 A:CAP502 4.5 23.4 1.0
CA A:GLU208 4.7 17.8 1.0
CB A:THR177 4.7 21.6 1.0
C5 A:CAP502 4.8 22.9 1.0
CE1 A:HIS297 5.0 18.4 1.0
O1 A:CAP502 5.0 24.3 1.0

Magnesium binding site 2 out of 10 in 5oya

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Magnesium binding site 2 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:16.9
occ:1.00
 OD1 B:ASP207 2.0 17.3 1.0
OE2 B:GLU208 2.0 17.3 1.0
OQ2 B:KCX205 2.0 17.2 1.0
O7 B:CAP502 2.1 17.9 1.0
O3 B:CAP502 2.2 20.2 1.0
O2 B:CAP502 2.3 17.3 1.0
C2 B:CAP502 2.9 17.9 1.0
C B:CAP502 2.9 18.7 1.0
CX B:KCX205 3.0 17.4 1.0
C3 B:CAP502 3.1 18.8 1.0
CD B:GLU208 3.1 17.3 1.0
CG B:ASP207 3.2 17.4 1.0
OQ1 B:KCX205 3.3 17.6 1.0
OE1 B:GLU208 3.6 17.5 1.0
NZ B:LYS181 3.7 17.5 1.0
N B:GLU208 3.7 16.9 1.0
OD2 B:ASP207 3.9 17.6 1.0
CG2 B:THR177 3.9 17.6 1.0
NE2 B:HIS297 4.0 16.9 1.0
NZ B:LYS179 4.0 18.2 1.0
O6 B:CAP502 4.1 17.6 1.0
CA B:ASP207 4.2 16.8 1.0
NZ B:KCX205 4.2 16.9 1.0
CB B:ASP207 4.2 17.1 1.0
OG1 B:THR177 4.3 17.6 1.0
CG B:GLU208 4.3 17.0 1.0
C4 B:CAP502 4.4 18.9 1.0
CD2 B:HIS297 4.4 16.8 1.0
C1 B:CAP502 4.4 17.1 1.0
C B:ASP207 4.5 16.7 1.0
CB B:GLU208 4.5 16.8 1.0
CB B:THR177 4.7 17.8 1.0
CA B:GLU208 4.7 16.6 1.0
C5 B:CAP502 4.8 19.0 1.0
O1 B:CAP502 4.9 17.5 1.0

Magnesium binding site 3 out of 10 in 5oya

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Magnesium binding site 3 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:17.6
occ:1.00
 OD1 C:ASP207 2.0 16.8 1.0
OE2 C:GLU208 2.0 15.8 1.0
OQ2 C:KCX205 2.0 16.3 1.0
O7 C:CAP502 2.2 17.7 1.0
O2 C:CAP502 2.3 18.2 1.0
O3 C:CAP502 2.3 18.6 1.0
C2 C:CAP502 2.9 18.6 1.0
C C:CAP502 2.9 18.5 1.0
CX C:KCX205 3.1 16.8 1.0
CD C:GLU208 3.1 16.2 1.0
CG C:ASP207 3.1 16.8 1.0
C3 C:CAP502 3.2 18.6 1.0
OQ1 C:KCX205 3.3 16.9 1.0
OE1 C:GLU208 3.6 16.5 1.0
NZ C:LYS181 3.7 16.4 1.0
N C:GLU208 3.7 16.2 1.0
OD2 C:ASP207 3.8 17.2 1.0
CG2 C:THR177 3.9 16.8 1.0
NZ C:LYS179 4.0 17.5 1.0
NE2 C:HIS297 4.1 16.3 1.0
CA C:ASP207 4.1 16.2 1.0
O6 C:CAP502 4.2 17.9 1.0
CB C:ASP207 4.2 16.2 1.0
NZ C:KCX205 4.2 16.4 1.0
OG1 C:THR177 4.2 17.0 1.0
CG C:GLU208 4.3 16.0 1.0
C1 C:CAP502 4.4 18.3 1.0
C4 C:CAP502 4.4 19.0 1.0
C C:ASP207 4.5 16.1 1.0
CD2 C:HIS297 4.5 16.6 1.0
CB C:GLU208 4.5 16.0 1.0
CB C:THR177 4.6 17.0 1.0
CA C:GLU208 4.7 15.9 1.0
C5 C:CAP502 4.9 18.9 1.0
O1 C:CAP502 4.9 18.9 1.0

Magnesium binding site 4 out of 10 in 5oya

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Magnesium binding site 4 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:28.0
occ:1.00
 OE2 D:GLU208 2.0 26.3 1.0
OD1 D:ASP207 2.0 26.7 1.0
OQ1 D:KCX205 2.0 27.4 1.0
O2 D:CAP502 2.2 28.6 1.0
O3 D:CAP502 2.2 24.5 1.0
O6 D:CAP502 2.3 28.8 1.0
C2 D:CAP502 2.9 28.4 1.0
CX D:KCX205 3.0 28.4 1.0
C D:CAP502 3.0 29.6 1.0
CD D:GLU208 3.1 26.9 1.0
C3 D:CAP502 3.1 28.0 1.0
CG D:ASP207 3.2 27.1 1.0
OQ2 D:KCX205 3.3 29.2 1.0
OE1 D:GLU208 3.6 27.7 1.0
NZ D:LYS181 3.7 28.1 1.0
N D:GLU208 3.8 25.8 1.0
CG2 D:THR177 3.8 27.2 1.0
OD2 D:ASP207 3.9 27.4 1.0
NE2 D:HIS297 4.0 27.1 1.0
NZ D:LYS179 4.0 28.0 1.0
CA D:ASP207 4.1 25.8 1.0
NZ D:KCX205 4.2 27.3 1.0
OG1 D:THR177 4.2 27.5 1.0
CB D:ASP207 4.2 26.1 1.0
O7 D:CAP502 4.3 28.7 1.0
CG D:GLU208 4.3 26.2 1.0
C1 D:CAP502 4.4 28.6 1.0
CD2 D:HIS297 4.4 26.4 1.0
C4 D:CAP502 4.4 26.9 1.0
C D:ASP207 4.5 25.4 1.0
CB D:GLU208 4.5 25.7 1.0
CB D:THR177 4.5 27.6 1.0
CA D:GLU208 4.7 25.0 1.0
C5 D:CAP502 4.9 27.0 1.0
O1 D:CAP502 4.9 29.1 1.0

Magnesium binding site 5 out of 10 in 5oya

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Magnesium binding site 5 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:28.1
occ:1.00
 OE2 E:GLU208 2.0 26.3 1.0
OQ1 E:KCX205 2.0 26.7 1.0
OD1 E:ASP207 2.0 27.1 1.0
O2 E:CAP502 2.2 30.6 1.0
O3 E:CAP502 2.2 26.7 1.0
O6 E:CAP502 2.2 29.7 1.0
C2 E:CAP502 2.9 29.8 1.0
C E:CAP502 2.9 31.3 1.0
CX E:KCX205 3.0 26.7 1.0
C3 E:CAP502 3.1 29.1 1.0
CD E:GLU208 3.1 26.3 1.0
OQ2 E:KCX205 3.2 27.3 1.0
CG E:ASP207 3.2 26.9 1.0
OE1 E:GLU208 3.6 26.8 1.0
NZ E:LYS181 3.7 27.8 1.0
N E:GLU208 3.8 25.1 1.0
CG2 E:THR177 3.9 26.7 1.0
OD2 E:ASP207 3.9 27.4 1.0
NZ E:LYS179 4.0 28.6 1.0
NE2 E:HIS297 4.1 26.0 1.0
CA E:ASP207 4.2 25.5 1.0
O7 E:CAP502 4.2 30.7 1.0
NZ E:KCX205 4.2 25.9 1.0
CB E:ASP207 4.3 26.1 1.0
OG1 E:THR177 4.3 27.2 1.0
C1 E:CAP502 4.3 29.8 1.0
CG E:GLU208 4.4 25.7 1.0
C4 E:CAP502 4.4 28.0 1.0
CD2 E:HIS297 4.4 25.4 1.0
C E:ASP207 4.5 25.0 1.0
CB E:GLU208 4.5 25.1 1.0
CB E:THR177 4.6 27.2 1.0
CA E:GLU208 4.8 24.6 1.0
C5 E:CAP502 4.8 28.0 1.0
O1 E:CAP502 4.9 29.6 1.0

Magnesium binding site 6 out of 10 in 5oya

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Magnesium binding site 6 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:21.0
occ:1.00
 OD1 F:ASP207 1.9 20.1 1.0
OE2 F:GLU208 2.0 20.1 1.0
OQ1 F:KCX205 2.0 19.4 1.0
O6 F:CAP502 2.2 20.8 1.0
O3 F:CAP502 2.3 22.5 1.0
O2 F:CAP502 2.3 23.1 1.0
C2 F:CAP502 2.9 23.5 1.0
C F:CAP502 2.9 22.8 1.0
CX F:KCX205 3.0 19.7 1.0
CD F:GLU208 3.1 20.3 1.0
C3 F:CAP502 3.1 22.8 1.0
CG F:ASP207 3.1 20.6 1.0
OQ2 F:KCX205 3.3 19.4 1.0
OE1 F:GLU208 3.6 21.1 1.0
NZ F:LYS181 3.7 22.1 1.0
N F:GLU208 3.8 19.1 1.0
OD2 F:ASP207 3.9 21.0 1.0
NZ F:LYS179 3.9 23.3 1.0
CG2 F:THR177 4.0 21.6 1.0
NE2 F:HIS297 4.0 19.2 1.0
CA F:ASP207 4.1 19.7 1.0
O7 F:CAP502 4.2 22.2 1.0
CB F:ASP207 4.2 20.2 1.0
NZ F:KCX205 4.2 19.3 1.0
OG1 F:THR177 4.2 21.5 1.0
CG F:GLU208 4.3 19.4 1.0
CD2 F:HIS297 4.4 19.1 1.0
C1 F:CAP502 4.4 23.8 1.0
C4 F:CAP502 4.4 21.6 1.0
C F:ASP207 4.5 19.3 1.0
CB F:GLU208 4.5 19.1 1.0
CB F:THR177 4.6 22.0 1.0
CA F:GLU208 4.8 18.8 1.0
C5 F:CAP502 4.9 22.4 1.0
O1 F:CAP502 4.9 24.4 1.0

Magnesium binding site 7 out of 10 in 5oya

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Magnesium binding site 7 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:21.4
occ:1.00
 OE2 G:GLU208 2.0 20.4 1.0
OD1 G:ASP207 2.0 21.4 1.0
OQ1 G:KCX205 2.1 20.2 1.0
O3 G:CAP502 2.2 21.6 1.0
O6 G:CAP502 2.2 20.5 1.0
O2 G:CAP502 2.3 21.3 1.0
C2 G:CAP502 2.9 21.8 1.0
C G:CAP502 2.9 22.0 1.0
CD G:GLU208 3.0 20.5 1.0
CX G:KCX205 3.1 20.1 1.0
C3 G:CAP502 3.1 21.8 1.0
CG G:ASP207 3.2 21.6 1.0
OQ2 G:KCX205 3.3 20.2 1.0
OE1 G:GLU208 3.5 21.1 1.0
NZ G:LYS181 3.7 22.3 1.0
N G:GLU208 3.8 19.8 1.0
OD2 G:ASP207 3.9 22.2 1.0
NE2 G:HIS297 4.0 19.5 1.0
CG2 G:THR177 4.0 22.5 1.0
NZ G:LYS179 4.0 23.1 1.0
O7 G:CAP502 4.2 22.4 1.0
CA G:ASP207 4.2 20.6 1.0
NZ G:KCX205 4.3 19.7 1.0
CB G:ASP207 4.3 21.2 1.0
OG1 G:THR177 4.3 22.4 1.0
CG G:GLU208 4.3 19.8 1.0
C4 G:CAP502 4.3 20.9 1.0
C1 G:CAP502 4.4 21.4 1.0
CD2 G:HIS297 4.4 19.3 1.0
C G:ASP207 4.5 19.9 1.0
CB G:GLU208 4.5 19.4 1.0
CB G:THR177 4.7 22.8 1.0
CA G:GLU208 4.8 19.3 1.0
C5 G:CAP502 4.8 21.6 1.0
O1 G:CAP502 4.9 22.1 1.0
CE1 G:HIS297 5.0 19.2 1.0

Magnesium binding site 8 out of 10 in 5oya

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Magnesium binding site 8 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:22.7
occ:1.00
 OD1 H:ASP207 2.0 21.4 1.0
OQ2 H:KCX205 2.0 21.2 1.0
OE2 H:GLU208 2.0 20.4 1.0
O3 H:CAP502 2.2 23.5 1.0
O7 H:CAP502 2.2 22.0 1.0
O2 H:CAP502 2.4 24.1 1.0
C2 H:CAP502 3.0 24.5 1.0
C H:CAP502 3.0 24.7 1.0
CX H:KCX205 3.0 21.1 1.0
CD H:GLU208 3.1 20.4 1.0
C3 H:CAP502 3.1 24.4 1.0
CG H:ASP207 3.2 21.6 1.0
OQ1 H:KCX205 3.3 21.6 1.0
OE1 H:GLU208 3.5 20.8 1.0
N H:GLU208 3.7 19.7 1.0
NZ H:LYS181 3.7 22.7 1.0
NE2 H:HIS297 3.9 19.9 1.0
OD2 H:ASP207 3.9 22.1 1.0
CG2 H:THR177 4.0 21.9 1.0
NZ H:LYS179 4.1 23.6 1.0
CA H:ASP207 4.1 20.3 1.0
NZ H:KCX205 4.2 20.5 1.0
O6 H:CAP502 4.2 24.6 1.0
CB H:ASP207 4.2 20.9 1.0
CD2 H:HIS297 4.3 19.6 1.0
CG H:GLU208 4.3 19.8 1.0
OG1 H:THR177 4.4 22.0 1.0
C4 H:CAP502 4.4 23.8 1.0
C H:ASP207 4.4 19.8 1.0
C1 H:CAP502 4.5 24.2 1.0
CB H:GLU208 4.5 19.3 1.0
CA H:GLU208 4.7 19.2 1.0
CB H:THR177 4.7 22.2 1.0
C5 H:CAP502 4.8 23.6 1.0
CE1 H:HIS297 4.9 19.7 1.0
O1 H:CAP502 5.0 24.9 1.0

Magnesium binding site 9 out of 10 in 5oya

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Magnesium binding site 9 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:21.2
occ:1.00
 O K:HOH352 2.3 21.4 1.0
O K:HOH373 2.4 24.3 1.0
O K:HOH376 2.4 21.8 1.0
O I:HOH389 2.4 22.5 1.0
O J:HOH375 2.4 22.9 1.0
O L:HOH377 2.5 19.5 1.0
O K:HOH320 4.0 22.7 1.0
O L:HOH372 4.1 24.1 1.0
O I:HOH327 4.2 23.1 1.0
O J:HOH316 4.3 22.9 1.0
NZ K:LYS126 4.3 24.6 1.0
NZ J:LYS126 4.5 25.1 1.0
NZ I:LYS126 4.6 24.6 1.0
NZ L:LYS126 4.7 24.0 1.0
OD1 K:ASP112 4.9 24.2 1.0
CE J:LYS126 4.9 24.7 1.0
CE K:LYS126 5.0 25.0 1.0

Magnesium binding site 10 out of 10 in 5oya

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Magnesium binding site 10 out of 10 in the Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Unusual Posttranslational Modifications Revealed in Crystal Structures of Diatom Rubisco. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:23.3
occ:1.00
 O O:HOH405 2.3 21.6 1.0
O N:HOH348 2.3 22.1 1.0
O N:HOH374 2.4 27.9 1.0
O P:HOH383 2.4 23.2 1.0
O M:HOH385 2.5 21.0 1.0
O O:HOH392 2.5 19.8 1.0
O N:HOH335 4.1 22.7 1.0
O P:HOH345 4.2 23.2 1.0
O O:HOH324 4.2 23.6 1.0
O M:HOH308 4.2 21.8 1.0
NZ N:LYS126 4.4 27.3 1.0
NZ O:LYS126 4.5 27.0 1.0
NZ P:LYS126 4.5 23.3 1.0
NZ M:LYS126 4.6 23.0 1.0
OD1 N:ASP112 4.9 25.4 1.0

Reference:

K.Valegard, P.J.Andralojc, R.P.Haslam, F.G.Pearce, G.K.Eriksen, P.J.Madgwick, A.K.Kristoffersen, M.Van Lun, U.Klein, H.C.Eilertsen, M.A.J.Parry, I.Andersson. Structural and Functional Analyses of Rubisco From Arctic Diatom Species Reveal Unusual Posttranslational Modifications. J. Biol. Chem. V. 293 13033 2018.
ISSN: ESSN 1083-351X
PubMed: 29925588
DOI: 10.1074/JBC.RA118.003518
Page generated: Mon Sep 30 01:25:37 2024

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