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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

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