Magnesium in PDB 3axm: Structure of Rice Rubisco in Complex with 6PG
Enzymatic activity of Structure of Rice Rubisco in Complex with 6PG
All present enzymatic activity of Structure of Rice Rubisco in Complex with 6PG:
4.1.1.39;
Protein crystallography data
The structure of Structure of Rice Rubisco in Complex with 6PG, PDB code: 3axm
was solved by
H.Matsumura,
E.Mizohata,
H.Ishida,
A.Kogami,
T.Ueno,
A.Makino,
T.Inoue,
A.Yokota,
T.Mae,
Y.Kai,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
74.26 /
1.65
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.408,
199.624,
111.169,
90.00,
91.45,
90.00
|
|
R / Rfree (%)
|
17.1 /
19
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Rice Rubisco in Complex with 6PG
(pdb code 3axm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Structure of Rice Rubisco in Complex with 6PG, PDB code: 3axm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 3axm
Go back to
Magnesium Binding Sites List in 3axm
Magnesium binding site 1 out
of 8 in the Structure of Rice Rubisco in Complex with 6PG
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg478
b:11.7
occ:1.00
|
OD2
|
A:ASP203
|
2.0
|
10.4
|
1.0
|
|
O1
|
A:6PG479
|
2.1
|
12.5
|
1.0
|
|
OQ1
|
A:KCX201
|
2.1
|
10.4
|
1.0
|
|
OE1
|
A:GLU204
|
2.1
|
9.0
|
1.0
|
|
O2
|
A:6PG479
|
2.1
|
14.2
|
1.0
|
|
O
|
A:HOH2934
|
2.1
|
11.9
|
1.0
|
|
C1
|
A:6PG479
|
2.9
|
16.1
|
1.0
|
|
CG
|
A:ASP203
|
3.0
|
10.9
|
1.0
|
|
C2
|
A:6PG479
|
3.0
|
15.1
|
1.0
|
|
CD
|
A:GLU204
|
3.1
|
11.1
|
1.0
|
|
CX
|
A:KCX201
|
3.2
|
11.5
|
1.0
|
|
OQ2
|
A:KCX201
|
3.4
|
10.1
|
1.0
|
|
OE2
|
A:GLU204
|
3.5
|
12.0
|
1.0
|
|
OD1
|
A:ASP203
|
3.6
|
11.3
|
1.0
|
|
O3
|
A:6PG479
|
3.8
|
15.3
|
1.0
|
|
NZ
|
A:LYS177
|
3.9
|
13.1
|
1.0
|
|
N
|
A:GLU204
|
4.0
|
9.3
|
1.0
|
|
C3
|
A:6PG479
|
4.0
|
16.5
|
1.0
|
|
O1A
|
A:6PG479
|
4.0
|
13.7
|
1.0
|
|
CB
|
A:ASP203
|
4.0
|
8.7
|
1.0
|
|
O
|
A:HOH2223
|
4.0
|
32.7
|
1.0
|
|
O
|
A:HOH3555
|
4.1
|
15.6
|
1.0
|
|
CA
|
A:ASP203
|
4.2
|
8.7
|
1.0
|
|
NE2
|
A:HIS294
|
4.3
|
10.7
|
1.0
|
|
NZ
|
A:KCX201
|
4.3
|
10.3
|
1.0
|
|
CG
|
A:GLU204
|
4.5
|
8.4
|
1.0
|
|
CG2
|
A:THR173
|
4.5
|
14.8
|
1.0
|
|
CE
|
A:LYS177
|
4.6
|
13.8
|
1.0
|
|
C
|
A:ASP203
|
4.6
|
9.2
|
1.0
|
|
O
|
B:HOH696
|
4.8
|
18.6
|
1.0
|
|
NZ
|
A:LYS175
|
4.8
|
20.3
|
1.0
|
|
CB
|
A:GLU204
|
4.8
|
9.9
|
1.0
|
|
C4
|
A:6PG479
|
5.0
|
19.1
|
1.0
|
|
CD2
|
A:HIS294
|
5.0
|
9.7
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 3axm
Go back to
Magnesium Binding Sites List in 3axm
Magnesium binding site 2 out
of 8 in the Structure of Rice Rubisco in Complex with 6PG
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg478
b:11.0
occ:1.00
|
O1A
|
B:6PG479
|
2.0
|
12.6
|
1.0
|
|
OQ1
|
B:KCX201
|
2.1
|
10.0
|
1.0
|
|
OD2
|
B:ASP203
|
2.1
|
11.8
|
1.0
|
|
OE1
|
B:GLU204
|
2.1
|
10.0
|
1.0
|
|
O2
|
B:6PG479
|
2.1
|
14.7
|
1.0
|
|
O
|
B:HOH2967
|
2.2
|
11.9
|
1.0
|
|
C1
|
B:6PG479
|
2.9
|
15.1
|
1.0
|
|
CG
|
B:ASP203
|
3.0
|
11.2
|
1.0
|
|
CX
|
B:KCX201
|
3.1
|
11.0
|
1.0
|
|
CD
|
B:GLU204
|
3.1
|
11.2
|
1.0
|
|
C2
|
B:6PG479
|
3.1
|
15.7
|
1.0
|
|
OQ2
|
B:KCX201
|
3.3
|
11.4
|
1.0
|
|
OE2
|
B:GLU204
|
3.4
|
12.8
|
1.0
|
|
O
|
B:HOH3597
|
3.6
|
36.4
|
1.0
|
|
OD1
|
B:ASP203
|
3.6
|
9.8
|
1.0
|
|
O3
|
B:6PG479
|
3.8
|
16.6
|
1.0
|
|
N
|
B:GLU204
|
4.0
|
8.5
|
1.0
|
|
O1
|
B:6PG479
|
4.0
|
15.7
|
1.0
|
|
CB
|
B:ASP203
|
4.1
|
10.9
|
1.0
|
|
NZ
|
B:LYS177
|
4.1
|
14.2
|
1.0
|
|
C3
|
B:6PG479
|
4.1
|
17.6
|
1.0
|
|
O
|
B:HOH3213
|
4.1
|
12.7
|
1.0
|
|
CA
|
B:ASP203
|
4.1
|
9.7
|
1.0
|
|
NE2
|
B:HIS294
|
4.2
|
12.4
|
1.0
|
|
NZ
|
B:KCX201
|
4.3
|
10.0
|
1.0
|
|
O
|
B:HOH1425
|
4.4
|
57.9
|
1.0
|
|
CG
|
B:GLU204
|
4.4
|
9.1
|
1.0
|
|
CG2
|
B:THR173
|
4.4
|
14.3
|
1.0
|
|
C
|
B:ASP203
|
4.6
|
9.2
|
1.0
|
|
NZ
|
B:LYS175
|
4.8
|
19.8
|
1.0
|
|
CB
|
B:GLU204
|
4.8
|
9.4
|
1.0
|
|
CE
|
B:LYS177
|
4.8
|
15.8
|
1.0
|
|
CD2
|
B:HIS294
|
4.8
|
11.6
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 3axm
Go back to
Magnesium Binding Sites List in 3axm
Magnesium binding site 3 out
of 8 in the Structure of Rice Rubisco in Complex with 6PG
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg478
b:10.3
occ:1.00
|
O
|
C:HOH481
|
2.0
|
11.9
|
1.0
|
|
O1A
|
C:6PG479
|
2.1
|
11.9
|
1.0
|
|
O2
|
C:6PG479
|
2.1
|
11.7
|
1.0
|
|
OD2
|
C:ASP203
|
2.1
|
10.7
|
1.0
|
|
OE1
|
C:GLU204
|
2.1
|
9.1
|
1.0
|
|
OQ1
|
C:KCX201
|
2.2
|
11.2
|
1.0
|
|
C1
|
C:6PG479
|
2.8
|
13.5
|
1.0
|
|
C2
|
C:6PG479
|
3.0
|
14.0
|
1.0
|
|
CG
|
C:ASP203
|
3.0
|
11.1
|
1.0
|
|
CD
|
C:GLU204
|
3.1
|
11.9
|
1.0
|
|
CX
|
C:KCX201
|
3.2
|
12.1
|
1.0
|
|
OE2
|
C:GLU204
|
3.4
|
12.6
|
1.0
|
|
OQ2
|
C:KCX201
|
3.5
|
11.5
|
1.0
|
|
OD1
|
C:ASP203
|
3.6
|
9.5
|
1.0
|
|
O3
|
C:6PG479
|
3.7
|
15.2
|
1.0
|
|
C3
|
C:6PG479
|
3.9
|
14.3
|
1.0
|
|
NZ
|
C:LYS177
|
4.0
|
11.2
|
1.0
|
|
O1
|
C:6PG479
|
4.0
|
13.5
|
1.0
|
|
O
|
C:HOH1962
|
4.0
|
33.1
|
1.0
|
|
N
|
C:GLU204
|
4.1
|
8.5
|
1.0
|
|
CB
|
C:ASP203
|
4.1
|
9.9
|
1.0
|
|
O
|
C:HOH508
|
4.2
|
14.2
|
1.0
|
|
NE2
|
C:HIS294
|
4.2
|
10.1
|
1.0
|
|
CA
|
C:ASP203
|
4.3
|
8.9
|
1.0
|
|
NZ
|
C:KCX201
|
4.4
|
10.8
|
1.0
|
|
CG
|
C:GLU204
|
4.4
|
9.2
|
1.0
|
|
CG2
|
C:THR173
|
4.6
|
12.5
|
1.0
|
|
CE
|
C:LYS177
|
4.6
|
12.3
|
1.0
|
|
C
|
C:ASP203
|
4.7
|
9.6
|
1.0
|
|
O
|
D:HOH1142
|
4.7
|
21.6
|
1.0
|
|
C4
|
C:6PG479
|
4.8
|
17.9
|
1.0
|
|
CB
|
C:GLU204
|
4.8
|
8.6
|
1.0
|
|
NZ
|
C:LYS175
|
4.8
|
17.2
|
1.0
|
|
CD2
|
C:HIS294
|
4.9
|
9.9
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 3axm
Go back to
Magnesium Binding Sites List in 3axm
Magnesium binding site 4 out
of 8 in the Structure of Rice Rubisco in Complex with 6PG
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg478
b:10.3
occ:1.00
|
O1A
|
D:6PG479
|
2.0
|
10.9
|
1.0
|
|
OD2
|
D:ASP203
|
2.0
|
9.9
|
1.0
|
|
OQ1
|
D:KCX201
|
2.1
|
10.0
|
1.0
|
|
OE1
|
D:GLU204
|
2.1
|
10.3
|
1.0
|
|
O2
|
D:6PG479
|
2.1
|
11.1
|
1.0
|
|
O
|
D:HOH3132
|
2.2
|
13.5
|
1.0
|
|
C1
|
D:6PG479
|
2.9
|
14.8
|
1.0
|
|
CG
|
D:ASP203
|
3.0
|
10.0
|
1.0
|
|
C2
|
D:6PG479
|
3.0
|
15.2
|
1.0
|
|
CD
|
D:GLU204
|
3.1
|
11.1
|
1.0
|
|
CX
|
D:KCX201
|
3.1
|
10.9
|
1.0
|
|
OQ2
|
D:KCX201
|
3.4
|
11.1
|
1.0
|
|
OE2
|
D:GLU204
|
3.5
|
12.1
|
1.0
|
|
OD1
|
D:ASP203
|
3.6
|
9.5
|
1.0
|
|
O3
|
D:6PG479
|
3.7
|
14.6
|
1.0
|
|
C3
|
D:6PG479
|
3.9
|
16.6
|
1.0
|
|
O1
|
D:6PG479
|
4.0
|
14.5
|
1.0
|
|
N
|
D:GLU204
|
4.0
|
7.6
|
1.0
|
|
CB
|
D:ASP203
|
4.1
|
9.1
|
1.0
|
|
NZ
|
D:LYS177
|
4.1
|
11.1
|
1.0
|
|
O
|
D:HOH504
|
4.1
|
14.3
|
1.0
|
|
CA
|
D:ASP203
|
4.2
|
8.3
|
1.0
|
|
NE2
|
D:HIS294
|
4.2
|
10.9
|
1.0
|
|
NZ
|
D:KCX201
|
4.3
|
10.6
|
1.0
|
|
CG
|
D:GLU204
|
4.4
|
8.8
|
1.0
|
|
CG2
|
D:THR173
|
4.5
|
13.7
|
1.0
|
|
C
|
D:ASP203
|
4.6
|
8.8
|
1.0
|
|
CE
|
D:LYS177
|
4.7
|
13.6
|
1.0
|
|
O
|
C:HOH564
|
4.8
|
18.9
|
1.0
|
|
CB
|
D:GLU204
|
4.8
|
8.3
|
1.0
|
|
CD2
|
D:HIS294
|
4.9
|
10.6
|
1.0
|
|
C4
|
D:6PG479
|
4.9
|
20.6
|
1.0
|
|
NZ
|
D:LYS175
|
5.0
|
16.0
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 3axm
Go back to
Magnesium Binding Sites List in 3axm
Magnesium binding site 5 out
of 8 in the Structure of Rice Rubisco in Complex with 6PG
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg478
b:11.9
occ:1.00
|
OD1
|
E:ASP203
|
2.0
|
9.6
|
1.0
|
|
O1A
|
E:6PG479
|
2.1
|
12.5
|
1.0
|
|
OQ1
|
E:KCX201
|
2.1
|
10.9
|
1.0
|
|
OE1
|
E:GLU204
|
2.1
|
10.2
|
1.0
|
|
O
|
E:HOH1908
|
2.1
|
11.0
|
1.0
|
|
O2
|
E:6PG479
|
2.1
|
13.9
|
1.0
|
|
C1
|
E:6PG479
|
2.9
|
15.3
|
1.0
|
|
CG
|
E:ASP203
|
3.0
|
9.6
|
1.0
|
|
C2
|
E:6PG479
|
3.0
|
15.6
|
1.0
|
|
CX
|
E:KCX201
|
3.1
|
12.5
|
1.0
|
|
CD
|
E:GLU204
|
3.1
|
10.2
|
1.0
|
|
OQ2
|
E:KCX201
|
3.4
|
10.4
|
1.0
|
|
OE2
|
E:GLU204
|
3.5
|
11.7
|
1.0
|
|
OD2
|
E:ASP203
|
3.6
|
10.6
|
1.0
|
|
O3
|
E:6PG479
|
3.8
|
16.3
|
1.0
|
|
C3
|
E:6PG479
|
4.0
|
17.2
|
1.0
|
|
N
|
E:GLU204
|
4.0
|
7.9
|
1.0
|
|
O1
|
E:6PG479
|
4.0
|
15.2
|
1.0
|
|
CB
|
E:ASP203
|
4.1
|
9.6
|
1.0
|
|
NZ
|
E:LYS177
|
4.1
|
11.1
|
1.0
|
|
O
|
E:HOH504
|
4.1
|
16.5
|
1.0
|
|
CA
|
E:ASP203
|
4.2
|
8.1
|
1.0
|
|
NE2
|
E:HIS294
|
4.2
|
11.3
|
1.0
|
|
NZ
|
E:KCX201
|
4.3
|
10.4
|
1.0
|
|
CG2
|
E:THR173
|
4.4
|
13.5
|
1.0
|
|
CG
|
E:GLU204
|
4.4
|
7.6
|
1.0
|
|
C
|
E:ASP203
|
4.6
|
8.2
|
1.0
|
|
NZ
|
E:LYS175
|
4.7
|
20.7
|
1.0
|
|
CE
|
E:LYS177
|
4.7
|
13.5
|
1.0
|
|
CB
|
E:GLU204
|
4.8
|
7.9
|
1.0
|
|
O
|
F:HOH1019
|
4.8
|
20.8
|
1.0
|
|
CD2
|
E:HIS294
|
4.9
|
11.5
|
1.0
|
|
C4
|
E:6PG479
|
5.0
|
20.5
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 3axm
Go back to
Magnesium Binding Sites List in 3axm
Magnesium binding site 6 out
of 8 in the Structure of Rice Rubisco in Complex with 6PG
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg478
b:9.1
occ:1.00
|
OE1
|
F:GLU204
|
2.0
|
8.7
|
1.0
|
|
OQ1
|
F:KCX201
|
2.1
|
9.9
|
1.0
|
|
O2
|
F:6PG479
|
2.1
|
14.0
|
1.0
|
|
OD2
|
F:ASP203
|
2.1
|
11.7
|
1.0
|
|
O1A
|
F:6PG479
|
2.1
|
12.6
|
1.0
|
|
O
|
F:HOH2817
|
2.1
|
12.4
|
1.0
|
|
C1
|
F:6PG479
|
2.9
|
14.1
|
1.0
|
|
C2
|
F:6PG479
|
3.0
|
15.2
|
1.0
|
|
CD
|
F:GLU204
|
3.0
|
11.5
|
1.0
|
|
CG
|
F:ASP203
|
3.1
|
11.1
|
1.0
|
|
CX
|
F:KCX201
|
3.1
|
10.8
|
1.0
|
|
OQ2
|
F:KCX201
|
3.4
|
11.5
|
1.0
|
|
OE2
|
F:GLU204
|
3.4
|
13.0
|
1.0
|
|
OD1
|
F:ASP203
|
3.7
|
8.8
|
1.0
|
|
O3
|
F:6PG479
|
3.7
|
14.5
|
1.0
|
|
N
|
F:GLU204
|
3.9
|
8.3
|
1.0
|
|
C3
|
F:6PG479
|
4.0
|
17.4
|
1.0
|
|
O1
|
F:6PG479
|
4.1
|
14.0
|
1.0
|
|
CB
|
F:ASP203
|
4.1
|
10.2
|
1.0
|
|
O
|
F:HOH3508
|
4.1
|
13.9
|
1.0
|
|
NE2
|
F:HIS294
|
4.1
|
10.2
|
1.0
|
|
NZ
|
F:LYS177
|
4.1
|
11.7
|
1.0
|
|
CA
|
F:ASP203
|
4.2
|
9.9
|
1.0
|
|
NZ
|
F:KCX201
|
4.3
|
9.7
|
1.0
|
|
O
|
F:HOH2487
|
4.3
|
33.9
|
1.0
|
|
CG
|
F:GLU204
|
4.4
|
9.6
|
1.0
|
|
CG2
|
F:THR173
|
4.4
|
13.0
|
1.0
|
|
C
|
F:ASP203
|
4.6
|
9.8
|
1.0
|
|
CE
|
F:LYS177
|
4.7
|
14.0
|
1.0
|
|
CB
|
F:GLU204
|
4.7
|
8.8
|
1.0
|
|
CD2
|
F:HIS294
|
4.8
|
10.4
|
1.0
|
|
C4
|
F:6PG479
|
4.8
|
21.6
|
1.0
|
|
O
|
E:HOH647
|
4.9
|
19.4
|
1.0
|
|
NZ
|
F:LYS175
|
4.9
|
18.9
|
1.0
|
|
CE1
|
F:HIS294
|
5.0
|
10.6
|
1.0
|
|
CA
|
F:GLU204
|
5.0
|
9.7
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 3axm
Go back to
Magnesium Binding Sites List in 3axm
Magnesium binding site 7 out
of 8 in the Structure of Rice Rubisco in Complex with 6PG
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg478
b:10.8
occ:1.00
|
OD1
|
G:ASP203
|
2.0
|
10.5
|
1.0
|
|
O1A
|
G:6PG479
|
2.1
|
11.7
|
1.0
|
|
OQ1
|
G:KCX201
|
2.1
|
9.8
|
1.0
|
|
O
|
G:HOH1909
|
2.1
|
12.6
|
1.0
|
|
OE1
|
G:GLU204
|
2.2
|
9.2
|
1.0
|
|
O2
|
G:6PG479
|
2.2
|
12.9
|
1.0
|
|
C1
|
G:6PG479
|
2.9
|
14.5
|
1.0
|
|
CG
|
G:ASP203
|
3.0
|
11.6
|
1.0
|
|
C2
|
G:6PG479
|
3.0
|
15.5
|
1.0
|
|
CX
|
G:KCX201
|
3.1
|
10.3
|
1.0
|
|
CD
|
G:GLU204
|
3.1
|
11.5
|
1.0
|
|
OQ2
|
G:KCX201
|
3.4
|
11.5
|
1.0
|
|
OE2
|
G:GLU204
|
3.5
|
13.8
|
1.0
|
|
OD2
|
G:ASP203
|
3.6
|
10.6
|
1.0
|
|
O3
|
G:6PG479
|
3.8
|
16.6
|
1.0
|
|
C3
|
G:6PG479
|
4.0
|
17.0
|
1.0
|
|
O1
|
G:6PG479
|
4.0
|
12.4
|
1.0
|
|
O
|
G:HOH2334
|
4.0
|
31.8
|
1.0
|
|
N
|
G:GLU204
|
4.0
|
9.1
|
1.0
|
|
CB
|
G:ASP203
|
4.0
|
10.7
|
1.0
|
|
NZ
|
G:LYS177
|
4.0
|
14.0
|
1.0
|
|
O
|
G:HOH3170
|
4.1
|
14.6
|
1.0
|
|
CA
|
G:ASP203
|
4.2
|
10.4
|
1.0
|
|
NE2
|
G:HIS294
|
4.2
|
11.5
|
1.0
|
|
NZ
|
G:KCX201
|
4.3
|
11.3
|
1.0
|
|
CG2
|
G:THR173
|
4.4
|
12.5
|
1.0
|
|
CG
|
G:GLU204
|
4.5
|
10.1
|
1.0
|
|
C
|
G:ASP203
|
4.6
|
9.8
|
1.0
|
|
CE
|
G:LYS177
|
4.7
|
15.1
|
1.0
|
|
NZ
|
G:LYS175
|
4.7
|
22.8
|
1.0
|
|
CB
|
G:GLU204
|
4.9
|
9.6
|
1.0
|
|
CD2
|
G:HIS294
|
4.9
|
10.4
|
1.0
|
|
C4
|
G:6PG479
|
4.9
|
19.4
|
1.0
|
|
O
|
H:HOH1295
|
5.0
|
24.0
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 3axm
Go back to
Magnesium Binding Sites List in 3axm
Magnesium binding site 8 out
of 8 in the Structure of Rice Rubisco in Complex with 6PG
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structure of Rice Rubisco in Complex with 6PG within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg478
b:11.3
occ:1.00
|
OQ1
|
H:KCX201
|
2.0
|
10.7
|
1.0
|
|
OD2
|
H:ASP203
|
2.1
|
10.0
|
1.0
|
|
O1A
|
H:6PG479
|
2.1
|
11.9
|
1.0
|
|
O2
|
H:6PG479
|
2.1
|
14.7
|
1.0
|
|
OE2
|
H:GLU204
|
2.1
|
9.8
|
1.0
|
|
O
|
H:HOH3197
|
2.2
|
11.4
|
1.0
|
|
C1
|
H:6PG479
|
2.9
|
16.9
|
1.0
|
|
C2
|
H:6PG479
|
3.0
|
16.5
|
1.0
|
|
CG
|
H:ASP203
|
3.0
|
9.6
|
1.0
|
|
CX
|
H:KCX201
|
3.1
|
9.9
|
1.0
|
|
CD
|
H:GLU204
|
3.1
|
9.7
|
1.0
|
|
OQ2
|
H:KCX201
|
3.3
|
12.9
|
1.0
|
|
OE1
|
H:GLU204
|
3.4
|
11.8
|
1.0
|
|
OD1
|
H:ASP203
|
3.6
|
9.8
|
1.0
|
|
O3
|
H:6PG479
|
3.8
|
17.9
|
1.0
|
|
C3
|
H:6PG479
|
3.9
|
18.7
|
1.0
|
|
O1
|
H:6PG479
|
4.0
|
16.0
|
1.0
|
|
N
|
H:GLU204
|
4.0
|
8.0
|
1.0
|
|
CB
|
H:ASP203
|
4.1
|
9.2
|
1.0
|
|
NZ
|
H:LYS177
|
4.1
|
13.0
|
1.0
|
|
O
|
H:HOH3542
|
4.1
|
12.6
|
1.0
|
|
NE2
|
H:HIS294
|
4.2
|
11.6
|
1.0
|
|
CA
|
H:ASP203
|
4.2
|
8.6
|
1.0
|
|
NZ
|
H:KCX201
|
4.2
|
11.3
|
1.0
|
|
CG2
|
H:THR173
|
4.5
|
15.0
|
1.0
|
|
CG
|
H:GLU204
|
4.5
|
8.0
|
1.0
|
|
C
|
H:ASP203
|
4.6
|
9.2
|
1.0
|
|
CE
|
H:LYS177
|
4.7
|
13.0
|
1.0
|
|
NZ
|
H:LYS175
|
4.8
|
18.1
|
1.0
|
|
CB
|
H:GLU204
|
4.8
|
8.1
|
1.0
|
|
C4
|
H:6PG479
|
4.8
|
22.0
|
1.0
|
|
CD2
|
H:HIS294
|
4.9
|
10.7
|
1.0
|
|
O
|
G:HOH491
|
4.9
|
17.9
|
1.0
|
|
Reference:
H.Matsumura,
E.Mizohata,
H.Ishida,
A.Kogami,
T.Ueno,
A.Makino,
T.Inoue,
A.Yokota,
T.Mae,
Y.Kai.
Crystal Structure of Rice Rubisco and Implications For Activation Induced By Positive Effectors Nadph and 6-Phosphogluconate J.Mol.Biol. V. 422 75 2012.
ISSN: ISSN 0022-2836
PubMed: 22609438
DOI: 10.1016/J.JMB.2012.05.014
Page generated: Mon Dec 14 07:54:31 2020
|
