Magnesium in PDB 5n9z: Rubisco From Thalassiosira Hyalina
Enzymatic activity of Rubisco From Thalassiosira Hyalina
All present enzymatic activity of Rubisco From Thalassiosira Hyalina:
4.1.1.39;
Protein crystallography data
The structure of Rubisco From Thalassiosira Hyalina, PDB code: 5n9z
was solved by
I.Andersson,
K.Valegard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
62.03 /
1.90
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.992,
219.986,
124.274,
90.00,
118.34,
90.00
|
|
R / Rfree (%)
|
15.1 /
18.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Rubisco From Thalassiosira Hyalina
(pdb code 5n9z). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Rubisco From Thalassiosira Hyalina, PDB code: 5n9z:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 1 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:14.0
occ:1.00
|
OE2
|
A:GLU208
|
2.0
|
11.7
|
1.0
|
|
OD1
|
A:ASP207
|
2.0
|
16.0
|
1.0
|
|
OQ1
|
A:KCX205
|
2.1
|
14.8
|
1.0
|
|
O6
|
A:CAP502
|
2.1
|
16.7
|
1.0
|
|
O3
|
A:CAP502
|
2.2
|
13.9
|
1.0
|
|
O2
|
A:CAP502
|
2.3
|
13.9
|
1.0
|
|
C
|
A:CAP502
|
2.8
|
16.5
|
1.0
|
|
C2
|
A:CAP502
|
2.9
|
14.5
|
1.0
|
|
CD
|
A:GLU208
|
3.0
|
13.8
|
1.0
|
|
CX
|
A:KCX205
|
3.1
|
17.9
|
1.0
|
|
C3
|
A:CAP502
|
3.1
|
14.2
|
1.0
|
|
CG
|
A:ASP207
|
3.2
|
15.5
|
1.0
|
|
OQ2
|
A:KCX205
|
3.3
|
15.5
|
1.0
|
|
OE1
|
A:GLU208
|
3.5
|
16.5
|
1.0
|
|
NZ
|
A:LYS181
|
3.6
|
14.7
|
1.0
|
|
ND2
|
B:ASN127
|
3.7
|
14.2
|
1.0
|
|
N
|
A:GLU208
|
3.8
|
14.8
|
1.0
|
|
OD2
|
A:ASP207
|
3.9
|
16.5
|
1.0
|
|
NZ
|
A:LYS179
|
4.0
|
13.4
|
1.0
|
|
CG2
|
A:THR177
|
4.0
|
12.0
|
1.0
|
|
NE2
|
A:HIS297
|
4.0
|
13.5
|
1.0
|
|
O7
|
A:CAP502
|
4.1
|
16.9
|
1.0
|
|
CA
|
A:ASP207
|
4.2
|
12.2
|
1.0
|
|
NZ
|
A:KCX205
|
4.2
|
15.2
|
1.0
|
|
CB
|
A:ASP207
|
4.2
|
13.7
|
1.0
|
|
C4
|
A:CAP502
|
4.3
|
13.9
|
1.0
|
|
CG
|
A:GLU208
|
4.3
|
12.5
|
1.0
|
|
C1
|
A:CAP502
|
4.3
|
13.2
|
1.0
|
|
OG1
|
A:THR177
|
4.4
|
15.2
|
1.0
|
|
CD2
|
A:HIS297
|
4.4
|
13.2
|
1.0
|
|
CB
|
A:GLU208
|
4.5
|
12.2
|
1.0
|
|
C
|
A:ASP207
|
4.5
|
15.6
|
1.0
|
|
CB
|
A:THR177
|
4.7
|
13.8
|
1.0
|
|
CA
|
A:GLU208
|
4.8
|
13.9
|
1.0
|
|
C5
|
A:CAP502
|
4.8
|
15.7
|
1.0
|
|
CG
|
B:ASN127
|
4.8
|
18.8
|
1.0
|
|
O1
|
A:CAP502
|
4.9
|
15.3
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 2 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg201
b:21.3
occ:1.00
|
O
|
J:HOH396
|
2.2
|
30.6
|
1.0
|
|
O
|
I:HOH361
|
2.2
|
20.7
|
1.0
|
|
O
|
K:HOH388
|
2.2
|
21.9
|
1.0
|
|
O
|
J:HOH390
|
2.2
|
28.2
|
1.0
|
|
O
|
L:HOH391
|
2.2
|
23.0
|
1.0
|
|
O
|
J:HOH355
|
2.2
|
27.0
|
1.0
|
|
O
|
I:HOH339
|
4.1
|
22.3
|
1.0
|
|
O
|
L:HOH333
|
4.1
|
19.9
|
1.0
|
|
O
|
K:HOH334
|
4.1
|
21.5
|
1.0
|
|
O
|
J:HOH327
|
4.1
|
18.6
|
1.0
|
|
NZ
|
J:LYS126
|
4.4
|
26.0
|
1.0
|
|
NZ
|
I:LYS126
|
4.5
|
23.4
|
1.0
|
|
NZ
|
L:LYS126
|
4.7
|
20.9
|
1.0
|
|
NZ
|
K:LYS126
|
4.7
|
21.6
|
1.0
|
|
CE
|
I:LYS126
|
4.9
|
22.1
|
1.0
|
|
CE
|
K:LYS126
|
4.9
|
21.7
|
1.0
|
|
OD1
|
I:ASP112
|
4.9
|
31.5
|
1.0
|
|
CE
|
L:LYS126
|
5.0
|
22.2
|
1.0
|
|
OD1
|
K:ASP112
|
5.0
|
26.6
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 3 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg501
b:13.9
occ:1.00
|
OD2
|
H:ASP207
|
2.0
|
14.2
|
1.0
|
|
OQ2
|
H:KCX205
|
2.0
|
10.5
|
1.0
|
|
OE2
|
H:GLU208
|
2.0
|
12.5
|
1.0
|
|
O7
|
H:CAP502
|
2.1
|
12.4
|
1.0
|
|
O3
|
H:CAP502
|
2.2
|
13.3
|
1.0
|
|
O2
|
H:CAP502
|
2.3
|
11.7
|
1.0
|
|
C2
|
H:CAP502
|
2.8
|
12.9
|
1.0
|
|
C
|
H:CAP502
|
2.8
|
12.2
|
1.0
|
|
CX
|
H:KCX205
|
3.0
|
13.0
|
1.0
|
|
C3
|
H:CAP502
|
3.1
|
11.4
|
1.0
|
|
CD
|
H:GLU208
|
3.1
|
14.1
|
1.0
|
|
CG
|
H:ASP207
|
3.2
|
16.3
|
1.0
|
|
OQ1
|
H:KCX205
|
3.3
|
14.2
|
1.0
|
|
OE1
|
H:GLU208
|
3.5
|
14.3
|
1.0
|
|
NZ
|
H:LYS181
|
3.6
|
12.5
|
1.0
|
|
ND2
|
G:ASN127
|
3.8
|
11.7
|
1.0
|
|
N
|
H:GLU208
|
3.8
|
10.6
|
1.0
|
|
OD1
|
H:ASP207
|
3.9
|
15.8
|
1.0
|
|
NZ
|
H:LYS179
|
3.9
|
13.0
|
1.0
|
|
NE2
|
H:HIS297
|
4.0
|
12.5
|
1.0
|
|
CG2
|
H:THR177
|
4.0
|
9.1
|
1.0
|
|
O6
|
H:CAP502
|
4.1
|
12.1
|
1.0
|
|
NZ
|
H:KCX205
|
4.2
|
10.6
|
1.0
|
|
CA
|
H:ASP207
|
4.2
|
12.9
|
1.0
|
|
CB
|
H:ASP207
|
4.2
|
13.5
|
1.0
|
|
C4
|
H:CAP502
|
4.3
|
12.9
|
1.0
|
|
OG1
|
H:THR177
|
4.3
|
15.2
|
1.0
|
|
C1
|
H:CAP502
|
4.3
|
11.5
|
1.0
|
|
CG
|
H:GLU208
|
4.4
|
12.6
|
1.0
|
|
CD2
|
H:HIS297
|
4.4
|
10.7
|
1.0
|
|
CB
|
H:GLU208
|
4.5
|
10.3
|
1.0
|
|
C
|
H:ASP207
|
4.5
|
13.1
|
1.0
|
|
CB
|
H:THR177
|
4.7
|
13.3
|
1.0
|
|
C5
|
H:CAP502
|
4.8
|
12.1
|
1.0
|
|
CA
|
H:GLU208
|
4.8
|
9.9
|
1.0
|
|
O1
|
H:CAP502
|
4.8
|
13.4
|
1.0
|
|
CG
|
G:ASN127
|
4.9
|
14.0
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 4 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg501
b:13.1
occ:1.00
|
OD2
|
F:ASP207
|
2.0
|
12.4
|
1.0
|
|
OQ2
|
F:KCX205
|
2.0
|
11.6
|
1.0
|
|
OE2
|
F:GLU208
|
2.0
|
14.1
|
1.0
|
|
O7
|
F:CAP502
|
2.1
|
13.5
|
1.0
|
|
O3
|
F:CAP502
|
2.1
|
12.6
|
1.0
|
|
O2
|
F:CAP502
|
2.2
|
10.7
|
1.0
|
|
C2
|
F:CAP502
|
2.8
|
13.4
|
1.0
|
|
C
|
F:CAP502
|
2.8
|
14.5
|
1.0
|
|
CX
|
F:KCX205
|
3.0
|
13.7
|
1.0
|
|
C3
|
F:CAP502
|
3.0
|
10.7
|
1.0
|
|
CD
|
F:GLU208
|
3.1
|
12.8
|
1.0
|
|
CG
|
F:ASP207
|
3.2
|
13.9
|
1.0
|
|
OQ1
|
F:KCX205
|
3.3
|
11.4
|
1.0
|
|
OE1
|
F:GLU208
|
3.6
|
15.1
|
1.0
|
|
NZ
|
F:LYS181
|
3.7
|
12.2
|
1.0
|
|
ND2
|
E:ASN127
|
3.7
|
12.5
|
1.0
|
|
N
|
F:GLU208
|
3.8
|
9.5
|
1.0
|
|
OD1
|
F:ASP207
|
3.9
|
14.0
|
1.0
|
|
NZ
|
F:LYS179
|
4.0
|
11.9
|
1.0
|
|
NE2
|
F:HIS297
|
4.0
|
13.0
|
1.0
|
|
CG2
|
F:THR177
|
4.0
|
11.2
|
1.0
|
|
O6
|
F:CAP502
|
4.1
|
14.2
|
1.0
|
|
NZ
|
F:KCX205
|
4.2
|
11.7
|
1.0
|
|
CA
|
F:ASP207
|
4.2
|
10.8
|
1.0
|
|
CB
|
F:ASP207
|
4.2
|
12.4
|
1.0
|
|
C4
|
F:CAP502
|
4.3
|
13.3
|
1.0
|
|
C1
|
F:CAP502
|
4.3
|
10.4
|
1.0
|
|
OG1
|
F:THR177
|
4.3
|
15.4
|
1.0
|
|
CG
|
F:GLU208
|
4.4
|
12.4
|
1.0
|
|
CD2
|
F:HIS297
|
4.4
|
10.9
|
1.0
|
|
C
|
F:ASP207
|
4.5
|
12.8
|
1.0
|
|
CB
|
F:GLU208
|
4.6
|
9.6
|
1.0
|
|
CB
|
F:THR177
|
4.7
|
12.8
|
1.0
|
|
C5
|
F:CAP502
|
4.8
|
12.2
|
1.0
|
|
CA
|
F:GLU208
|
4.8
|
11.3
|
1.0
|
|
CG
|
E:ASN127
|
4.8
|
13.5
|
1.0
|
|
O1
|
F:CAP502
|
4.9
|
13.7
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 5 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg202
b:20.6
occ:1.00
|
O
|
O:HOH402
|
2.2
|
28.0
|
1.0
|
|
O
|
N:HOH387
|
2.2
|
22.8
|
1.0
|
|
O
|
O:HOH399
|
2.2
|
28.3
|
1.0
|
|
O
|
P:HOH372
|
2.2
|
22.1
|
1.0
|
|
O
|
O:HOH384
|
2.2
|
25.1
|
1.0
|
|
O
|
M:HOH394
|
2.2
|
21.1
|
1.0
|
|
O
|
M:HOH324
|
4.1
|
19.9
|
1.0
|
|
O
|
O:HOH318
|
4.1
|
18.6
|
1.0
|
|
O
|
P:HOH328
|
4.1
|
20.8
|
1.0
|
|
O
|
N:HOH335
|
4.1
|
21.7
|
1.0
|
|
NZ
|
P:LYS126
|
4.5
|
25.8
|
1.0
|
|
NZ
|
O:LYS126
|
4.5
|
23.0
|
1.0
|
|
NZ
|
N:LYS126
|
4.7
|
22.8
|
1.0
|
|
NZ
|
M:LYS126
|
4.7
|
21.8
|
1.0
|
|
OD1
|
N:ASP112
|
4.9
|
24.7
|
1.0
|
|
CE
|
N:LYS126
|
4.9
|
21.7
|
1.0
|
|
CE
|
M:LYS126
|
5.0
|
21.8
|
1.0
|
|
CE
|
P:LYS126
|
5.0
|
20.4
|
1.0
|
|
OD1
|
P:ASP112
|
5.0
|
31.0
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 6 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg501
b:13.2
occ:1.00
|
OD2
|
D:ASP207
|
2.0
|
12.2
|
1.0
|
|
OQ1
|
D:KCX205
|
2.0
|
9.8
|
1.0
|
|
O6
|
D:CAP502
|
2.1
|
12.5
|
1.0
|
|
OE2
|
D:GLU208
|
2.1
|
11.9
|
1.0
|
|
O3
|
D:CAP502
|
2.2
|
13.0
|
1.0
|
|
O2
|
D:CAP502
|
2.3
|
9.8
|
1.0
|
|
C
|
D:CAP502
|
2.8
|
13.1
|
1.0
|
|
C2
|
D:CAP502
|
2.9
|
10.9
|
1.0
|
|
CX
|
D:KCX205
|
3.0
|
13.3
|
1.0
|
|
C3
|
D:CAP502
|
3.1
|
10.3
|
1.0
|
|
CD
|
D:GLU208
|
3.1
|
12.8
|
1.0
|
|
CG
|
D:ASP207
|
3.1
|
12.2
|
1.0
|
|
OQ2
|
D:KCX205
|
3.4
|
12.3
|
1.0
|
|
OE1
|
D:GLU208
|
3.5
|
15.2
|
1.0
|
|
NZ
|
D:LYS181
|
3.7
|
12.9
|
1.0
|
|
ND2
|
C:ASN127
|
3.7
|
10.9
|
1.0
|
|
N
|
D:GLU208
|
3.8
|
9.0
|
1.0
|
|
OD1
|
D:ASP207
|
3.8
|
13.5
|
1.0
|
|
NZ
|
D:LYS179
|
3.9
|
9.9
|
1.0
|
|
CG2
|
D:THR177
|
4.0
|
11.0
|
1.0
|
|
O7
|
D:CAP502
|
4.1
|
12.1
|
1.0
|
|
NE2
|
D:HIS297
|
4.1
|
11.0
|
1.0
|
|
CA
|
D:ASP207
|
4.2
|
9.7
|
1.0
|
|
NZ
|
D:KCX205
|
4.2
|
10.3
|
1.0
|
|
CB
|
D:ASP207
|
4.2
|
9.6
|
1.0
|
|
C4
|
D:CAP502
|
4.3
|
13.5
|
1.0
|
|
OG1
|
D:THR177
|
4.4
|
12.0
|
1.0
|
|
C1
|
D:CAP502
|
4.4
|
11.2
|
1.0
|
|
CG
|
D:GLU208
|
4.4
|
9.8
|
1.0
|
|
CD2
|
D:HIS297
|
4.5
|
10.4
|
1.0
|
|
C
|
D:ASP207
|
4.5
|
10.0
|
1.0
|
|
CB
|
D:GLU208
|
4.5
|
8.6
|
1.0
|
|
CB
|
D:THR177
|
4.7
|
12.4
|
1.0
|
|
CA
|
D:GLU208
|
4.8
|
9.9
|
1.0
|
|
O1
|
D:CAP502
|
4.8
|
12.5
|
1.0
|
|
CG
|
C:ASN127
|
4.8
|
13.9
|
1.0
|
|
C5
|
D:CAP502
|
4.9
|
13.1
|
1.0
|
|
O
|
C:HOH706
|
4.9
|
15.6
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 7 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:14.6
occ:1.00
|
OE2
|
B:GLU208
|
2.0
|
12.1
|
1.0
|
|
OD2
|
B:ASP207
|
2.0
|
16.5
|
1.0
|
|
OQ1
|
B:KCX205
|
2.1
|
13.7
|
1.0
|
|
O6
|
B:CAP502
|
2.1
|
16.2
|
1.0
|
|
O3
|
B:CAP502
|
2.2
|
13.8
|
1.0
|
|
O2
|
B:CAP502
|
2.3
|
13.5
|
1.0
|
|
C
|
B:CAP502
|
2.8
|
18.1
|
1.0
|
|
C2
|
B:CAP502
|
2.9
|
15.6
|
1.0
|
|
CD
|
B:GLU208
|
3.0
|
15.1
|
1.0
|
|
CX
|
B:KCX205
|
3.1
|
18.2
|
1.0
|
|
C3
|
B:CAP502
|
3.1
|
15.2
|
1.0
|
|
CG
|
B:ASP207
|
3.2
|
15.3
|
1.0
|
|
OQ2
|
B:KCX205
|
3.4
|
15.5
|
1.0
|
|
OE1
|
B:GLU208
|
3.5
|
19.2
|
1.0
|
|
NZ
|
B:LYS181
|
3.6
|
15.5
|
1.0
|
|
ND2
|
A:ASN127
|
3.7
|
14.1
|
1.0
|
|
N
|
B:GLU208
|
3.8
|
14.0
|
1.0
|
|
OD1
|
B:ASP207
|
3.9
|
16.7
|
1.0
|
|
NZ
|
B:LYS179
|
4.0
|
15.1
|
1.0
|
|
NE2
|
B:HIS297
|
4.0
|
13.7
|
1.0
|
|
CG2
|
B:THR177
|
4.0
|
12.9
|
1.0
|
|
O7
|
B:CAP502
|
4.1
|
16.5
|
1.0
|
|
CA
|
B:ASP207
|
4.2
|
13.1
|
1.0
|
|
CB
|
B:ASP207
|
4.2
|
14.3
|
1.0
|
|
NZ
|
B:KCX205
|
4.3
|
15.0
|
1.0
|
|
C4
|
B:CAP502
|
4.3
|
14.7
|
1.0
|
|
CG
|
B:GLU208
|
4.3
|
13.1
|
1.0
|
|
C1
|
B:CAP502
|
4.4
|
13.6
|
1.0
|
|
OG1
|
B:THR177
|
4.4
|
15.6
|
1.0
|
|
CD2
|
B:HIS297
|
4.5
|
13.5
|
1.0
|
|
CB
|
B:GLU208
|
4.5
|
12.6
|
1.0
|
|
C
|
B:ASP207
|
4.5
|
15.4
|
1.0
|
|
CB
|
B:THR177
|
4.7
|
13.9
|
1.0
|
|
CA
|
B:GLU208
|
4.8
|
13.9
|
1.0
|
|
CG
|
A:ASN127
|
4.8
|
17.5
|
1.0
|
|
C5
|
B:CAP502
|
4.8
|
14.5
|
1.0
|
|
O1
|
B:CAP502
|
4.9
|
15.8
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 8 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg501
b:14.1
occ:1.00
|
OQ2
|
C:KCX205
|
2.0
|
11.2
|
1.0
|
|
OD2
|
C:ASP207
|
2.0
|
14.2
|
1.0
|
|
OE2
|
C:GLU208
|
2.0
|
12.1
|
1.0
|
|
O7
|
C:CAP502
|
2.1
|
12.4
|
1.0
|
|
O3
|
C:CAP502
|
2.2
|
12.8
|
1.0
|
|
O2
|
C:CAP502
|
2.3
|
11.2
|
1.0
|
|
C
|
C:CAP502
|
2.8
|
12.9
|
1.0
|
|
C2
|
C:CAP502
|
2.8
|
13.7
|
1.0
|
|
CX
|
C:KCX205
|
3.0
|
12.0
|
1.0
|
|
C3
|
C:CAP502
|
3.0
|
10.4
|
1.0
|
|
CD
|
C:GLU208
|
3.1
|
14.3
|
1.0
|
|
CG
|
C:ASP207
|
3.2
|
15.5
|
1.0
|
|
OQ1
|
C:KCX205
|
3.3
|
14.5
|
1.0
|
|
OE1
|
C:GLU208
|
3.5
|
15.4
|
1.0
|
|
NZ
|
C:LYS181
|
3.6
|
14.2
|
1.0
|
|
ND2
|
D:ASN127
|
3.8
|
12.6
|
1.0
|
|
N
|
C:GLU208
|
3.8
|
11.0
|
1.0
|
|
OD1
|
C:ASP207
|
3.9
|
16.1
|
1.0
|
|
NZ
|
C:LYS179
|
3.9
|
14.3
|
1.0
|
|
NE2
|
C:HIS297
|
4.0
|
12.5
|
1.0
|
|
CG2
|
C:THR177
|
4.0
|
9.9
|
1.0
|
|
O6
|
C:CAP502
|
4.1
|
12.1
|
1.0
|
|
NZ
|
C:KCX205
|
4.2
|
11.0
|
1.0
|
|
CA
|
C:ASP207
|
4.2
|
13.1
|
1.0
|
|
CB
|
C:ASP207
|
4.2
|
12.8
|
1.0
|
|
C4
|
C:CAP502
|
4.3
|
12.5
|
1.0
|
|
C1
|
C:CAP502
|
4.3
|
11.1
|
1.0
|
|
OG1
|
C:THR177
|
4.3
|
15.1
|
1.0
|
|
CG
|
C:GLU208
|
4.4
|
12.3
|
1.0
|
|
CD2
|
C:HIS297
|
4.4
|
11.0
|
1.0
|
|
CB
|
C:GLU208
|
4.5
|
10.0
|
1.0
|
|
C
|
C:ASP207
|
4.6
|
13.1
|
1.0
|
|
CB
|
C:THR177
|
4.7
|
15.0
|
1.0
|
|
C5
|
C:CAP502
|
4.8
|
10.8
|
1.0
|
|
CA
|
C:GLU208
|
4.8
|
10.0
|
1.0
|
|
O1
|
C:CAP502
|
4.8
|
13.8
|
1.0
|
|
CG
|
D:ASN127
|
4.9
|
16.1
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 9 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg501
b:13.7
occ:1.00
|
OD2
|
E:ASP207
|
2.0
|
13.3
|
1.0
|
|
OE2
|
E:GLU208
|
2.0
|
13.9
|
1.0
|
|
OQ2
|
E:KCX205
|
2.1
|
11.7
|
1.0
|
|
O7
|
E:CAP502
|
2.1
|
14.1
|
1.0
|
|
O3
|
E:CAP502
|
2.2
|
13.5
|
1.0
|
|
O2
|
E:CAP502
|
2.3
|
10.9
|
1.0
|
|
C
|
E:CAP502
|
2.8
|
13.6
|
1.0
|
|
C2
|
E:CAP502
|
2.8
|
13.8
|
1.0
|
|
C3
|
E:CAP502
|
3.0
|
10.8
|
1.0
|
|
CX
|
E:KCX205
|
3.0
|
13.7
|
1.0
|
|
CD
|
E:GLU208
|
3.1
|
13.3
|
1.0
|
|
CG
|
E:ASP207
|
3.1
|
13.2
|
1.0
|
|
OQ1
|
E:KCX205
|
3.3
|
11.9
|
1.0
|
|
OE1
|
E:GLU208
|
3.6
|
15.0
|
1.0
|
|
NZ
|
E:LYS181
|
3.6
|
11.8
|
1.0
|
|
ND2
|
F:ASN127
|
3.7
|
12.1
|
1.0
|
|
N
|
E:GLU208
|
3.8
|
9.2
|
1.0
|
|
OD1
|
E:ASP207
|
3.8
|
13.5
|
1.0
|
|
NZ
|
E:LYS179
|
4.0
|
11.4
|
1.0
|
|
NE2
|
E:HIS297
|
4.0
|
12.1
|
1.0
|
|
CG2
|
E:THR177
|
4.1
|
11.3
|
1.0
|
|
O6
|
E:CAP502
|
4.1
|
14.3
|
1.0
|
|
CA
|
E:ASP207
|
4.2
|
11.3
|
1.0
|
|
CB
|
E:ASP207
|
4.2
|
13.3
|
1.0
|
|
NZ
|
E:KCX205
|
4.2
|
11.3
|
1.0
|
|
C4
|
E:CAP502
|
4.3
|
14.1
|
1.0
|
|
C1
|
E:CAP502
|
4.3
|
11.7
|
1.0
|
|
OG1
|
E:THR177
|
4.3
|
14.4
|
1.0
|
|
CG
|
E:GLU208
|
4.4
|
13.2
|
1.0
|
|
CD2
|
E:HIS297
|
4.4
|
11.0
|
1.0
|
|
C
|
E:ASP207
|
4.5
|
12.5
|
1.0
|
|
CB
|
E:GLU208
|
4.5
|
10.5
|
1.0
|
|
CB
|
E:THR177
|
4.7
|
12.2
|
1.0
|
|
C5
|
E:CAP502
|
4.8
|
10.9
|
1.0
|
|
CA
|
E:GLU208
|
4.8
|
10.7
|
1.0
|
|
CG
|
F:ASN127
|
4.8
|
14.1
|
1.0
|
|
O1
|
E:CAP502
|
4.9
|
14.0
|
1.0
|
|
O
|
F:HOH651
|
5.0
|
14.6
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 5n9z
Go back to
Magnesium Binding Sites List in 5n9z
Magnesium binding site 10 out
of 10 in the Rubisco From Thalassiosira Hyalina
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Rubisco From Thalassiosira Hyalina within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg501
b:12.9
occ:1.00
|
OD2
|
G:ASP207
|
2.0
|
10.7
|
1.0
|
|
OQ1
|
G:KCX205
|
2.0
|
11.1
|
1.0
|
|
OE2
|
G:GLU208
|
2.1
|
11.2
|
1.0
|
|
O6
|
G:CAP502
|
2.1
|
14.2
|
1.0
|
|
O3
|
G:CAP502
|
2.2
|
12.8
|
1.0
|
|
O2
|
G:CAP502
|
2.3
|
10.1
|
1.0
|
|
C
|
G:CAP502
|
2.8
|
13.9
|
1.0
|
|
C2
|
G:CAP502
|
2.9
|
12.3
|
1.0
|
|
CX
|
G:KCX205
|
3.0
|
12.5
|
1.0
|
|
C3
|
G:CAP502
|
3.1
|
12.1
|
1.0
|
|
CD
|
G:GLU208
|
3.1
|
12.2
|
1.0
|
|
CG
|
G:ASP207
|
3.2
|
13.2
|
1.0
|
|
OQ2
|
G:KCX205
|
3.4
|
11.9
|
1.0
|
|
OE1
|
G:GLU208
|
3.5
|
14.1
|
1.0
|
|
NZ
|
G:LYS181
|
3.7
|
13.1
|
1.0
|
|
ND2
|
H:ASN127
|
3.7
|
12.3
|
1.0
|
|
N
|
G:GLU208
|
3.8
|
8.9
|
1.0
|
|
OD1
|
G:ASP207
|
3.8
|
14.0
|
1.0
|
|
NZ
|
G:LYS179
|
3.9
|
9.2
|
1.0
|
|
CG2
|
G:THR177
|
4.0
|
12.1
|
1.0
|
|
NE2
|
G:HIS297
|
4.1
|
10.0
|
1.0
|
|
O7
|
G:CAP502
|
4.1
|
12.9
|
1.0
|
|
CA
|
G:ASP207
|
4.2
|
11.3
|
1.0
|
|
NZ
|
G:KCX205
|
4.2
|
10.6
|
1.0
|
|
CB
|
G:ASP207
|
4.2
|
10.1
|
1.0
|
|
C4
|
G:CAP502
|
4.3
|
13.0
|
1.0
|
|
OG1
|
G:THR177
|
4.3
|
13.5
|
1.0
|
|
C1
|
G:CAP502
|
4.4
|
9.8
|
1.0
|
|
CG
|
G:GLU208
|
4.4
|
10.6
|
1.0
|
|
CD2
|
G:HIS297
|
4.5
|
9.8
|
1.0
|
|
C
|
G:ASP207
|
4.5
|
9.3
|
1.0
|
|
CB
|
G:GLU208
|
4.5
|
9.7
|
1.0
|
|
CB
|
G:THR177
|
4.7
|
13.2
|
1.0
|
|
CA
|
G:GLU208
|
4.8
|
9.4
|
1.0
|
|
O1
|
G:CAP502
|
4.8
|
11.3
|
1.0
|
|
CG
|
H:ASN127
|
4.8
|
13.7
|
1.0
|
|
C5
|
G:CAP502
|
4.9
|
13.1
|
1.0
|
|
O
|
H:HOH710
|
4.9
|
15.6
|
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: Sun Sep 29 23:14:28 2024
|
