Calcium in PDB 1rxo: Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium
Enzymatic activity of Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium
All present enzymatic activity of Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium:
4.1.1.39;
Protein crystallography data
The structure of Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium, PDB code: 1rxo
was solved by
T.C.Taylor,
I.Andersson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
7.00 /
2.20
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
157.600,
158.500,
202.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.5 /
22.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium
(pdb code 1rxo). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium, PDB code: 1rxo:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1rxo
Go back to
Calcium Binding Sites List in 1rxo
Calcium binding site 1 out
of 4 in the Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ca477
b:32.1
occ:1.00
|
OQ2
|
L:KCX201
|
2.3
|
25.2
|
1.0
|
OE1
|
L:GLU204
|
2.3
|
14.3
|
1.0
|
O2
|
L:RUB476
|
2.3
|
33.2
|
1.0
|
OD1
|
L:ASP203
|
2.4
|
21.1
|
1.0
|
O
|
L:HOH583
|
2.5
|
30.1
|
1.0
|
O3
|
L:RUB476
|
2.6
|
24.1
|
1.0
|
C2
|
L:RUB476
|
3.2
|
32.3
|
1.0
|
CD
|
L:GLU204
|
3.2
|
11.0
|
1.0
|
CX
|
L:KCX201
|
3.3
|
22.1
|
1.0
|
CG
|
L:ASP203
|
3.4
|
19.4
|
1.0
|
C3
|
L:RUB476
|
3.4
|
33.0
|
1.0
|
OE2
|
L:GLU204
|
3.5
|
17.5
|
1.0
|
OQ1
|
L:KCX201
|
3.6
|
19.9
|
1.0
|
OD2
|
L:ASP203
|
3.9
|
18.5
|
1.0
|
NZ
|
L:LYS177
|
4.1
|
15.9
|
1.0
|
NE2
|
L:HIS294
|
4.2
|
11.7
|
1.0
|
N
|
L:GLU204
|
4.3
|
9.3
|
1.0
|
C4
|
L:RUB476
|
4.3
|
36.1
|
1.0
|
CB
|
L:ASP203
|
4.4
|
12.7
|
1.0
|
CA
|
L:ASP203
|
4.4
|
10.3
|
1.0
|
CG2
|
L:THR173
|
4.5
|
19.1
|
1.0
|
NZ
|
L:KCX201
|
4.5
|
16.5
|
1.0
|
O
|
L:HOH534
|
4.5
|
34.5
|
1.0
|
O
|
L:HOH594
|
4.6
|
22.0
|
1.0
|
NZ
|
L:LYS175
|
4.6
|
34.7
|
1.0
|
CG
|
L:GLU204
|
4.6
|
11.4
|
1.0
|
C1
|
L:RUB476
|
4.6
|
31.2
|
1.0
|
CE
|
L:LYS177
|
4.7
|
17.9
|
1.0
|
C
|
L:ASP203
|
4.9
|
10.2
|
1.0
|
CE1
|
L:HIS294
|
5.0
|
10.7
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1rxo
Go back to
Calcium Binding Sites List in 1rxo
Calcium binding site 2 out
of 4 in the Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca477
b:32.1
occ:1.00
|
OQ2
|
B:KCX201
|
2.3
|
25.2
|
1.0
|
OE1
|
B:GLU204
|
2.3
|
14.3
|
1.0
|
O2
|
B:RUB476
|
2.3
|
33.2
|
1.0
|
OD1
|
B:ASP203
|
2.4
|
21.1
|
1.0
|
O
|
B:HOH584
|
2.5
|
30.1
|
1.0
|
O3
|
B:RUB476
|
2.6
|
24.1
|
1.0
|
C2
|
B:RUB476
|
3.2
|
32.3
|
1.0
|
CD
|
B:GLU204
|
3.2
|
11.0
|
1.0
|
CX
|
B:KCX201
|
3.3
|
22.1
|
1.0
|
CG
|
B:ASP203
|
3.4
|
19.4
|
1.0
|
C3
|
B:RUB476
|
3.4
|
33.0
|
1.0
|
OE2
|
B:GLU204
|
3.5
|
17.5
|
1.0
|
OQ1
|
B:KCX201
|
3.6
|
19.9
|
1.0
|
OD2
|
B:ASP203
|
3.9
|
18.5
|
1.0
|
NZ
|
B:LYS177
|
4.1
|
15.9
|
1.0
|
NE2
|
B:HIS294
|
4.2
|
11.7
|
1.0
|
N
|
B:GLU204
|
4.3
|
9.3
|
1.0
|
C4
|
B:RUB476
|
4.3
|
36.1
|
1.0
|
CB
|
B:ASP203
|
4.4
|
12.7
|
1.0
|
CA
|
B:ASP203
|
4.4
|
10.3
|
1.0
|
CG2
|
B:THR173
|
4.5
|
19.1
|
1.0
|
NZ
|
B:KCX201
|
4.5
|
16.5
|
1.0
|
O
|
B:HOH535
|
4.5
|
34.5
|
1.0
|
O
|
B:HOH595
|
4.6
|
22.0
|
1.0
|
NZ
|
B:LYS175
|
4.6
|
34.7
|
1.0
|
CG
|
B:GLU204
|
4.6
|
11.4
|
1.0
|
C1
|
B:RUB476
|
4.6
|
31.2
|
1.0
|
CE
|
B:LYS177
|
4.7
|
17.9
|
1.0
|
C
|
B:ASP203
|
4.9
|
10.2
|
1.0
|
CE1
|
B:HIS294
|
5.0
|
10.7
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1rxo
Go back to
Calcium Binding Sites List in 1rxo
Calcium binding site 3 out
of 4 in the Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca477
b:32.1
occ:1.00
|
OQ2
|
E:KCX201
|
2.3
|
25.2
|
1.0
|
OE1
|
E:GLU204
|
2.3
|
14.3
|
1.0
|
O2
|
E:RUB476
|
2.3
|
33.2
|
1.0
|
OD1
|
E:ASP203
|
2.4
|
21.1
|
1.0
|
O
|
E:HOH628
|
2.5
|
30.1
|
1.0
|
O3
|
E:RUB476
|
2.6
|
24.1
|
1.0
|
C2
|
E:RUB476
|
3.2
|
32.3
|
1.0
|
CD
|
E:GLU204
|
3.2
|
11.0
|
1.0
|
CX
|
E:KCX201
|
3.3
|
22.1
|
1.0
|
CG
|
E:ASP203
|
3.4
|
19.4
|
1.0
|
C3
|
E:RUB476
|
3.4
|
33.0
|
1.0
|
OE2
|
E:GLU204
|
3.5
|
17.5
|
1.0
|
OQ1
|
E:KCX201
|
3.6
|
19.9
|
1.0
|
OD2
|
E:ASP203
|
3.9
|
18.5
|
1.0
|
NZ
|
E:LYS177
|
4.1
|
15.9
|
1.0
|
NE2
|
E:HIS294
|
4.2
|
11.7
|
1.0
|
N
|
E:GLU204
|
4.3
|
9.3
|
1.0
|
C4
|
E:RUB476
|
4.3
|
36.1
|
1.0
|
CB
|
E:ASP203
|
4.4
|
12.7
|
1.0
|
CA
|
E:ASP203
|
4.4
|
10.3
|
1.0
|
CG2
|
E:THR173
|
4.5
|
19.1
|
1.0
|
NZ
|
E:KCX201
|
4.5
|
16.5
|
1.0
|
O
|
E:HOH576
|
4.5
|
34.5
|
1.0
|
O
|
E:HOH639
|
4.6
|
22.0
|
1.0
|
NZ
|
E:LYS175
|
4.6
|
34.7
|
1.0
|
CG
|
E:GLU204
|
4.6
|
11.4
|
1.0
|
C1
|
E:RUB476
|
4.6
|
31.2
|
1.0
|
CE
|
E:LYS177
|
4.7
|
17.9
|
1.0
|
C
|
E:ASP203
|
4.9
|
10.2
|
1.0
|
CE1
|
E:HIS294
|
5.0
|
10.7
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1rxo
Go back to
Calcium Binding Sites List in 1rxo
Calcium binding site 4 out
of 4 in the Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Activated Spinach Rubisco in Complex with Its Substrate Ribulose-1,5- Bisphosphate and Calcium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca477
b:32.1
occ:1.00
|
OQ2
|
H:KCX201
|
2.3
|
25.2
|
1.0
|
OE1
|
H:GLU204
|
2.3
|
14.3
|
1.0
|
O2
|
H:RUB476
|
2.3
|
33.2
|
1.0
|
OD1
|
H:ASP203
|
2.4
|
21.1
|
1.0
|
O
|
H:HOH586
|
2.5
|
30.1
|
1.0
|
O3
|
H:RUB476
|
2.6
|
24.1
|
1.0
|
C2
|
H:RUB476
|
3.2
|
32.3
|
1.0
|
CD
|
H:GLU204
|
3.2
|
11.0
|
1.0
|
CX
|
H:KCX201
|
3.3
|
22.1
|
1.0
|
CG
|
H:ASP203
|
3.4
|
19.4
|
1.0
|
C3
|
H:RUB476
|
3.4
|
33.0
|
1.0
|
OE2
|
H:GLU204
|
3.5
|
17.5
|
1.0
|
OQ1
|
H:KCX201
|
3.6
|
19.9
|
1.0
|
OD2
|
H:ASP203
|
3.9
|
18.5
|
1.0
|
NZ
|
H:LYS177
|
4.1
|
15.9
|
1.0
|
NE2
|
H:HIS294
|
4.2
|
11.7
|
1.0
|
N
|
H:GLU204
|
4.3
|
9.3
|
1.0
|
C4
|
H:RUB476
|
4.3
|
36.1
|
1.0
|
CB
|
H:ASP203
|
4.4
|
12.7
|
1.0
|
CA
|
H:ASP203
|
4.4
|
10.3
|
1.0
|
CG2
|
H:THR173
|
4.5
|
19.1
|
1.0
|
NZ
|
H:KCX201
|
4.5
|
16.5
|
1.0
|
O
|
H:HOH537
|
4.5
|
34.5
|
1.0
|
O
|
H:HOH597
|
4.6
|
22.0
|
1.0
|
NZ
|
H:LYS175
|
4.6
|
34.7
|
1.0
|
CG
|
H:GLU204
|
4.6
|
11.4
|
1.0
|
C1
|
H:RUB476
|
4.6
|
31.2
|
1.0
|
CE
|
H:LYS177
|
4.7
|
17.9
|
1.0
|
C
|
H:ASP203
|
4.9
|
10.2
|
1.0
|
CE1
|
H:HIS294
|
5.0
|
10.7
|
1.0
|
|
Reference:
T.C.Taylor,
I.Andersson.
The Structure of the Complex Between Rubisco and Its Natural Substrate Ribulose 1,5-Bisphosphate. J.Mol.Biol. V. 265 432 1997.
ISSN: ISSN 0022-2836
PubMed: 9034362
DOI: 10.1006/JMBI.1996.0738
Page generated: Thu Jul 11 22:19:00 2024
|