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Calcium in PDB 1upm: Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.

Enzymatic activity of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.

All present enzymatic activity of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.:
4.1.1.39;

Protein crystallography data

The structure of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+., PDB code: 1upm was solved by S.Karkehabadi, T.C.Taylor, I.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 2.3
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 219.600, 220.942, 116.984, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. (pdb code 1upm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+., PDB code: 1upm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1upm

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Calcium binding site 1 out of 8 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.


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 Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca476

b:42.5
occ:1.00
 OE1 B:GLU204 2.6 19.7 1.0
OQ2 B:KCX201 2.6 22.6 1.0
OD1 B:ASP203 2.7 25.5 1.0
O6 B:CAP477 2.7 27.0 1.0
O2 B:CAP477 2.8 24.9 1.0
O3 B:CAP477 2.8 24.5 1.0
C B:CAP477 3.3 26.3 1.0
CG B:ASP203 3.3 25.2 1.0
C2 B:CAP477 3.3 25.0 1.0
CD B:GLU204 3.4 21.7 1.0
OQ1 B:KCX201 3.5 24.2 1.0
CX B:KCX201 3.5 24.0 1.0
NZ B:LYS177 3.5 22.8 1.0
C3 B:CAP477 3.6 24.1 1.0
N B:GLU204 3.7 19.2 1.0
OE2 B:GLU204 3.7 23.7 1.0
OD2 B:ASP203 3.7 25.8 1.0
ND2 L:ASN123 3.9 22.7 1.0
NE2 B:HIS294 4.1 12.8 1.0
NZ B:LYS175 4.1 14.8 1.0
CA B:ASP203 4.2 21.1 1.0
CG2 B:THR173 4.3 25.4 1.0
CB B:ASP203 4.3 23.5 1.0
C B:ASP203 4.4 21.3 1.0
O7 B:CAP477 4.5 26.9 1.0
CB B:GLU204 4.5 19.5 1.0
CG B:GLU204 4.6 20.4 1.0
CA B:GLU204 4.7 18.9 1.0
C4 B:CAP477 4.7 23.8 1.0
OG1 B:THR173 4.8 26.9 1.0
NZ B:KCX201 4.8 21.1 1.0
C1 B:CAP477 4.8 22.9 1.0
CE1 B:HIS294 4.8 13.2 1.0
CD2 B:HIS294 4.9 14.1 1.0

Calcium binding site 2 out of 8 in 1upm

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Calcium binding site 2 out of 8 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.


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 Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca476

b:42.2
occ:1.00
 OE1 E:GLU204 2.5 19.6 1.0
OD1 E:ASP203 2.7 25.2 1.0
OQ2 E:KCX201 2.7 22.9 1.0
O6 E:CAP477 2.7 26.6 1.0
O2 E:CAP477 2.7 24.2 1.0
O3 E:CAP477 2.8 23.5 1.0
CG E:ASP203 3.3 25.0 1.0
C2 E:CAP477 3.3 24.9 1.0
C E:CAP477 3.3 26.1 1.0
CD E:GLU204 3.4 21.8 1.0
OQ1 E:KCX201 3.5 23.8 1.0
CX E:KCX201 3.5 23.8 1.0
OD2 E:ASP203 3.5 25.7 1.0
C3 E:CAP477 3.6 24.0 1.0
NZ E:LYS177 3.6 23.1 1.0
OE2 E:GLU204 3.7 23.5 1.0
N E:GLU204 3.7 18.9 1.0
ND2 H:ASN123 3.9 22.5 1.0
NZ E:LYS175 4.0 14.3 1.0
CA E:ASP203 4.1 21.1 1.0
NE2 E:HIS294 4.2 12.2 1.0
CG2 E:THR173 4.2 25.1 1.0
CB E:ASP203 4.3 23.4 1.0
C E:ASP203 4.4 21.3 1.0
O7 E:CAP477 4.5 26.9 1.0
CB E:GLU204 4.6 19.8 1.0
CG E:GLU204 4.6 20.4 1.0
OG1 E:THR173 4.7 26.7 1.0
C4 E:CAP477 4.7 23.7 1.0
CA E:GLU204 4.7 19.2 1.0
C1 E:CAP477 4.7 22.9 1.0
NZ E:KCX201 4.8 21.2 1.0
CE1 E:HIS294 4.9 12.9 1.0
CD2 E:HIS294 4.9 13.9 1.0
CB E:THR173 4.9 25.8 1.0

Calcium binding site 3 out of 8 in 1upm

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Calcium binding site 3 out of 8 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.


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 Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca476

b:43.0
occ:1.00
 OE1 H:GLU204 2.5 19.9 1.0
OD1 H:ASP203 2.7 25.4 1.0
OQ2 H:KCX201 2.7 23.0 1.0
O6 H:CAP477 2.7 26.9 1.0
O3 H:CAP477 2.7 23.8 1.0
O2 H:CAP477 2.8 24.6 1.0
C H:CAP477 3.3 26.1 1.0
CG H:ASP203 3.3 25.1 1.0
C2 H:CAP477 3.3 24.9 1.0
CD H:GLU204 3.4 22.0 1.0
OQ1 H:KCX201 3.5 24.5 1.0
C3 H:CAP477 3.5 24.2 1.0
NZ H:LYS177 3.5 23.0 1.0
CX H:KCX201 3.6 24.1 1.0
OE2 H:GLU204 3.6 23.9 1.0
OD2 H:ASP203 3.7 26.0 1.0
N H:GLU204 3.7 19.3 1.0
ND2 E:ASN123 3.9 22.7 1.0
NZ H:LYS175 3.9 14.9 1.0
CA H:ASP203 4.1 21.0 1.0
NE2 H:HIS294 4.2 12.5 1.0
CG2 H:THR173 4.2 25.4 1.0
CB H:ASP203 4.3 23.4 1.0
C H:ASP203 4.4 21.5 1.0
O7 H:CAP477 4.5 26.9 1.0
CB H:GLU204 4.6 19.6 1.0
CG H:GLU204 4.6 20.7 1.0
C4 H:CAP477 4.7 23.7 1.0
CA H:GLU204 4.7 19.3 1.0
NZ H:KCX201 4.8 21.3 1.0
C1 H:CAP477 4.8 22.9 1.0
OG1 H:THR173 4.8 26.6 1.0
CE1 H:HIS294 4.9 13.1 1.0
CD2 H:HIS294 5.0 14.0 1.0
CB H:THR173 5.0 25.6 1.0

Calcium binding site 4 out of 8 in 1upm

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Calcium binding site 4 out of 8 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.


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 Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca476

b:42.0
occ:1.00
 OE1 K:GLU204 2.5 19.3 1.0
OQ2 K:KCX201 2.7 22.7 1.0
O3 K:CAP477 2.7 24.0 1.0
O6 K:CAP477 2.7 26.8 1.0
O2 K:CAP477 2.8 24.4 1.0
OD1 K:ASP203 2.8 25.1 1.0
CG K:ASP203 3.3 25.2 1.0
C2 K:CAP477 3.3 24.8 1.0
C K:CAP477 3.3 26.5 1.0
CD K:GLU204 3.4 21.8 1.0
OQ1 K:KCX201 3.4 24.3 1.0
CX K:KCX201 3.5 23.8 1.0
C3 K:CAP477 3.5 24.1 1.0
OD2 K:ASP203 3.6 25.6 1.0
N K:GLU204 3.6 19.2 1.0
NZ K:LYS177 3.7 23.1 1.0
OE2 K:GLU204 3.7 23.8 1.0
ND2 O:ASN123 3.9 22.6 1.0
NE2 K:HIS294 4.0 12.0 1.0
NZ K:LYS175 4.1 14.6 1.0
CA K:ASP203 4.2 21.0 1.0
CG2 K:THR173 4.3 25.2 1.0
CB K:ASP203 4.3 23.4 1.0
C K:ASP203 4.4 21.2 1.0
CB K:GLU204 4.4 19.5 1.0
O7 K:CAP477 4.5 27.1 1.0
CG K:GLU204 4.5 20.4 1.0
CA K:GLU204 4.6 19.1 1.0
C4 K:CAP477 4.7 23.7 1.0
NZ K:KCX201 4.7 21.0 1.0
OG1 K:THR173 4.7 26.9 1.0
CE1 K:HIS294 4.8 12.6 1.0
C1 K:CAP477 4.8 22.9 1.0
CD2 K:HIS294 4.8 14.0 1.0
CB K:THR173 5.0 25.6 1.0

Calcium binding site 5 out of 8 in 1upm

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Calcium binding site 5 out of 8 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca476

b:42.0
occ:1.00
 OE1 L:GLU204 2.5 19.2 1.0
OQ2 L:KCX201 2.6 22.3 1.0
O6 L:CAP477 2.7 26.8 1.0
OD1 L:ASP203 2.7 25.2 1.0
O2 L:CAP477 2.7 24.5 1.0
O3 L:CAP477 2.8 23.9 1.0
C2 L:CAP477 3.3 24.9 1.0
C L:CAP477 3.3 26.3 1.0
CG L:ASP203 3.3 25.0 1.0
CD L:GLU204 3.4 21.5 1.0
CX L:KCX201 3.5 23.8 1.0
OQ1 L:KCX201 3.5 24.2 1.0
C3 L:CAP477 3.6 24.1 1.0
NZ L:LYS177 3.6 22.4 1.0
OE2 L:GLU204 3.7 23.3 1.0
OD2 L:ASP203 3.7 25.6 1.0
N L:GLU204 3.7 19.1 1.0
ND2 B:ASN123 3.9 22.4 1.0
NZ L:LYS175 4.0 14.6 1.0
NE2 L:HIS294 4.1 12.2 1.0
CA L:ASP203 4.1 21.0 1.0
CG2 L:THR173 4.2 25.0 1.0
CB L:ASP203 4.3 23.3 1.0
C L:ASP203 4.4 21.3 1.0
O7 L:CAP477 4.5 26.7 1.0
CB L:GLU204 4.5 19.6 1.0
CG L:GLU204 4.6 20.2 1.0
C4 L:CAP477 4.7 23.6 1.0
OG1 L:THR173 4.7 26.6 1.0
CA L:GLU204 4.7 18.9 1.0
C1 L:CAP477 4.7 22.6 1.0
NZ L:KCX201 4.7 20.9 1.0
CE1 L:HIS294 4.9 12.7 1.0
CD2 L:HIS294 4.9 13.9 1.0
CB L:THR173 4.9 25.7 1.0

Calcium binding site 6 out of 8 in 1upm

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Calcium binding site 6 out of 8 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca476

b:43.0
occ:1.00
 OE1 O:GLU204 2.5 19.8 1.0
OQ2 O:KCX201 2.7 23.0 1.0
OD1 O:ASP203 2.7 25.6 1.0
O3 O:CAP477 2.7 24.3 1.0
O6 O:CAP477 2.8 27.0 1.0
O2 O:CAP477 2.8 24.9 1.0
CG O:ASP203 3.3 25.5 1.0
CD O:GLU204 3.4 21.9 1.0
C2 O:CAP477 3.4 25.1 1.0
C O:CAP477 3.4 26.6 1.0
OQ1 O:KCX201 3.5 24.4 1.0
CX O:KCX201 3.5 24.0 1.0
OE2 O:GLU204 3.5 23.5 1.0
NZ O:LYS177 3.6 23.0 1.0
C3 O:CAP477 3.6 24.1 1.0
OD2 O:ASP203 3.6 26.3 1.0
N O:GLU204 3.6 19.2 1.0
ND2 K:ASN123 3.9 22.9 1.0
NZ O:LYS175 4.1 15.3 1.0
NE2 O:HIS294 4.1 12.4 1.0
CA O:ASP203 4.1 21.3 1.0
CB O:ASP203 4.3 23.5 1.0
CG2 O:THR173 4.3 25.3 1.0
C O:ASP203 4.3 21.6 1.0
CB O:GLU204 4.5 19.9 1.0
O7 O:CAP477 4.5 27.0 1.0
CG O:GLU204 4.6 20.4 1.0
CA O:GLU204 4.6 18.9 1.0
C4 O:CAP477 4.7 23.8 1.0
NZ O:KCX201 4.7 21.1 1.0
OG1 O:THR173 4.8 27.0 1.0
C1 O:CAP477 4.8 22.9 1.0
CE1 O:HIS294 4.8 13.3 1.0
CD2 O:HIS294 4.9 13.9 1.0

Calcium binding site 7 out of 8 in 1upm

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Calcium binding site 7 out of 8 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca476

b:41.9
occ:1.00
 OE1 R:GLU204 2.5 19.6 1.0
OD1 R:ASP203 2.7 25.2 1.0
OQ2 R:KCX201 2.7 22.6 1.0
O6 R:CAP477 2.7 26.5 1.0
O3 R:CAP477 2.8 23.8 1.0
O2 R:CAP477 2.8 24.4 1.0
CD R:GLU204 3.3 22.0 1.0
C R:CAP477 3.4 26.1 1.0
C2 R:CAP477 3.4 24.8 1.0
CG R:ASP203 3.4 25.0 1.0
OQ1 R:KCX201 3.5 24.3 1.0
CX R:KCX201 3.5 24.0 1.0
NZ R:LYS177 3.5 22.6 1.0
C3 R:CAP477 3.6 24.0 1.0
OE2 R:GLU204 3.6 24.0 1.0
N R:GLU204 3.6 18.8 1.0
OD2 R:ASP203 3.7 25.8 1.0
ND2 V:ASN123 3.8 22.4 1.0
NE2 R:HIS294 4.0 12.2 1.0
NZ R:LYS175 4.1 14.6 1.0
CA R:ASP203 4.1 20.9 1.0
CG2 R:THR173 4.3 25.1 1.0
CB R:ASP203 4.3 23.4 1.0
C R:ASP203 4.3 20.9 1.0
CB R:GLU204 4.4 19.4 1.0
O7 R:CAP477 4.5 26.9 1.0
CG R:GLU204 4.5 20.8 1.0
CA R:GLU204 4.6 19.0 1.0
C4 R:CAP477 4.7 23.6 1.0
CD2 R:HIS294 4.8 14.2 1.0
CE1 R:HIS294 4.8 12.4 1.0
NZ R:KCX201 4.8 21.2 1.0
C1 R:CAP477 4.8 22.8 1.0
OG1 R:THR173 4.9 26.9 1.0

Calcium binding site 8 out of 8 in 1upm

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Calcium binding site 8 out of 8 in the Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Activated Spinach Rubisco Complexed with 2-Carboxyarabinitol 2 Bisphosphat and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Ca476

b:42.0
occ:1.00
 OE1 V:GLU204 2.6 20.2 1.0
O6 V:CAP477 2.6 27.2 1.0
O2 V:CAP477 2.7 24.5 1.0
OQ2 V:KCX201 2.7 23.0 1.0
OD1 V:ASP203 2.8 25.3 1.0
O3 V:CAP477 2.8 24.1 1.0
C2 V:CAP477 3.2 24.9 1.0
C V:CAP477 3.2 26.3 1.0
CG V:ASP203 3.3 25.1 1.0
CD V:GLU204 3.5 22.3 1.0
NZ V:LYS177 3.5 23.0 1.0
C3 V:CAP477 3.5 24.2 1.0
OQ1 V:KCX201 3.5 24.3 1.0
OD2 V:ASP203 3.6 25.9 1.0
CX V:KCX201 3.6 23.9 1.0
OE2 V:GLU204 3.6 24.1 1.0
ND2 R:ASN123 3.8 22.8 1.0
N V:GLU204 3.8 19.3 1.0
NZ V:LYS175 4.0 15.4 1.0
NE2 V:HIS294 4.2 12.4 1.0
CA V:ASP203 4.2 21.1 1.0
CG2 V:THR173 4.3 25.3 1.0
CB V:ASP203 4.4 23.3 1.0
O7 V:CAP477 4.4 27.4 1.0
C V:ASP203 4.5 21.2 1.0
C4 V:CAP477 4.6 23.8 1.0
CB V:GLU204 4.6 19.6 1.0
CG V:GLU204 4.7 20.6 1.0
C1 V:CAP477 4.7 23.0 1.0
OG1 V:THR173 4.7 27.0 1.0
CA V:GLU204 4.8 19.2 1.0
NZ V:KCX201 4.9 21.4 1.0
CE1 V:HIS294 4.9 13.0 1.0
O R:HOH2044 5.0 36.8 1.0
CE V:LYS177 5.0 24.2 1.0
CB V:THR173 5.0 25.7 1.0

Reference:

S.Karkehabadi, T.C.Taylor, I.Andersson. Calcium Supports Loop Closure But Not Catalysis in Rubisco J.Mol.Biol. V. 334 65 2003.
ISSN: ISSN 0022-2836
PubMed: 14596800
DOI: 10.1016/J.JMB.2003.09.025
Page generated: Thu Jul 11 23:35:10 2024

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