Calcium in PDB 1upp: Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium.

All present enzymatic activity of Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium.:
4.1.1.39;

The structure of Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium., PDB code: 1upp 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)	100 / 2.3
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	155.880, 156.250, 199.750, 90.00, 90.00, 90.00
R / Rfree (%)	25.598 / 30.71

The binding sites of Calcium atom in the Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium. (pdb code 1upp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium., PDB code: 1upp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 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 Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca476 b:38.2 occ:1.00 OE1 A:GLU204 2.5 19.6 1.0 O6 A:CAP477 2.5 23.2 1.0 OQ2 A:KCX201 2.5 17.1 1.0 OD1 A:ASP203 2.6 25.5 1.0 O3 A:CAP477 2.7 21.6 1.0 O2 A:CAP477 2.7 23.6 1.0 C A:CAP477 3.1 23.0 1.0 C2 A:CAP477 3.2 22.8 1.0 CG A:ASP203 3.4 24.7 1.0 C3 A:CAP477 3.4 22.9 1.0 CD A:GLU204 3.4 21.7 1.0 CX A:KCX201 3.5 18.0 1.0 OQ1 A:KCX201 3.6 18.6 1.0 NZ A:LYS177 3.6 22.3 1.0 NZ A:LYS175 3.6 16.4 1.0 OD2 A:ASP203 3.7 26.8 1.0 OE2 A:GLU204 3.8 24.4 1.0 N A:GLU204 3.9 15.1 1.0 CG2 A:THR173 4.2 27.0 1.0 CA A:ASP203 4.2 19.1 1.0 NE2 A:HIS294 4.2 9.1 1.0 O7 A:CAP477 4.3 20.3 1.0 CB A:ASP203 4.3 22.6 1.0 C A:ASP203 4.5 16.9 1.0 OG1 A:THR173 4.5 32.4 1.0 C4 A:CAP477 4.6 22.3 1.0 C1 A:CAP477 4.6 21.6 1.0 NZ A:KCX201 4.6 13.8 1.0 CG A:GLU204 4.6 18.4 1.0 CB A:GLU204 4.8 16.5 1.0 CE A:LYS177 4.8 22.9 1.0 O1 A:CAP477 4.8 17.9 1.0 CB A:THR173 4.8 28.8 1.0 CE A:LYS175 4.9 17.4 1.0 CD2 A:HIS294 4.9 9.4 1.0 CA A:GLU204 4.9 15.4 1.0

Calcium binding site 2 out of 4 in the Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 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 Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca476 b:38.1 occ:1.00 OQ2 C:KCX201 2.4 16.9 1.0 OE1 C:GLU204 2.4 19.7 1.0 OD1 C:ASP203 2.5 24.8 1.0 O6 C:CAP477 2.6 22.6 1.0 O2 C:CAP477 2.6 24.0 1.0 O3 C:CAP477 2.7 22.5 1.0 C C:CAP477 3.2 22.7 1.0 C2 C:CAP477 3.2 22.7 1.0 CG C:ASP203 3.4 24.5 1.0 CD C:GLU204 3.5 21.8 1.0 C3 C:CAP477 3.5 23.0 1.0 CX C:KCX201 3.5 18.2 1.0 NZ C:LYS177 3.5 22.1 1.0 NZ C:LYS175 3.6 16.9 1.0 N C:GLU204 3.8 14.6 1.0 OD2 C:ASP203 3.8 27.1 1.0 OQ1 C:KCX201 3.8 19.0 1.0 OE2 C:GLU204 3.8 24.3 1.0 CA C:ASP203 4.1 18.6 1.0 CG2 C:THR173 4.1 26.9 1.0 NE2 C:HIS294 4.3 9.1 1.0 O7 C:CAP477 4.3 20.2 1.0 CB C:ASP203 4.3 22.9 1.0 C C:ASP203 4.4 17.2 1.0 C4 C:CAP477 4.6 22.7 1.0 NZ C:KCX201 4.6 14.7 1.0 C1 C:CAP477 4.6 21.5 1.0 CB C:GLU204 4.7 17.1 1.0 CG C:GLU204 4.7 17.9 1.0 OG1 C:THR173 4.7 32.2 1.0 CA C:GLU204 4.8 15.4 1.0 CE C:LYS177 4.9 23.1 1.0 CB C:THR173 4.9 28.8 1.0 O1 C:CAP477 4.9 17.1 1.0 CD2 C:HIS294 5.0 10.6 1.0

Calcium binding site 3 out of 4 in the Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 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 Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium. within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca476 b:36.4 occ:1.00 OQ2 E:KCX201 2.5 17.2 1.0 OD1 E:ASP203 2.5 24.6 1.0 OE1 E:GLU204 2.6 20.5 1.0 O6 E:CAP477 2.6 22.7 1.0 O3 E:CAP477 2.7 22.8 1.0 O2 E:CAP477 2.7 23.3 1.0 C E:CAP477 3.2 22.9 1.0 C2 E:CAP477 3.2 22.8 1.0 CG E:ASP203 3.3 24.6 1.0 CX E:KCX201 3.4 18.1 1.0 C3 E:CAP477 3.5 22.8 1.0 CD E:GLU204 3.5 21.4 1.0 OQ1 E:KCX201 3.5 19.7 1.0 NZ E:LYS177 3.7 22.4 1.0 NZ E:LYS175 3.7 17.0 1.0 OD2 E:ASP203 3.7 27.0 1.0 N E:GLU204 3.7 14.7 1.0 OE2 E:GLU204 3.9 24.0 1.0 CG2 E:THR173 4.1 26.6 1.0 CA E:ASP203 4.1 19.2 1.0 NE2 E:HIS294 4.3 9.0 1.0 O7 E:CAP477 4.3 19.8 1.0 CB E:ASP203 4.4 22.8 1.0 OG1 E:THR173 4.4 32.2 1.0 C E:ASP203 4.4 17.4 1.0 NZ E:KCX201 4.5 14.5 1.0 C1 E:CAP477 4.7 21.2 1.0 CG E:GLU204 4.7 18.1 1.0 C4 E:CAP477 4.7 22.6 1.0 CB E:GLU204 4.7 16.6 1.0 CB E:THR173 4.8 28.9 1.0 CA E:GLU204 4.8 15.8 1.0 O1 E:CAP477 4.9 17.8 1.0 CE E:LYS175 4.9 17.0 1.0 O E:HOH2129 4.9 14.0 1.0 CD2 E:HIS294 4.9 9.4 1.0 CE E:LYS177 4.9 22.6 1.0

Calcium binding site 4 out of 4 in the Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 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 Spinach Rubisco in Complex with 2-Carboxyarabinitol 2 Bisphosphate and Calcium. within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca476 b:36.7 occ:1.00 OQ2 G:KCX201 2.5 16.6 1.0 OD1 G:ASP203 2.5 24.6 1.0 OE1 G:GLU204 2.6 20.2 1.0 O6 G:CAP477 2.6 23.5 1.0 O3 G:CAP477 2.6 22.4 1.0 O2 G:CAP477 2.7 24.2 1.0 C G:CAP477 3.1 22.8 1.0 C2 G:CAP477 3.1 22.7 1.0 CG G:ASP203 3.4 24.4 1.0 C3 G:CAP477 3.4 23.0 1.0 NZ G:LYS177 3.5 22.9 1.0 CX G:KCX201 3.5 18.0 1.0 OQ1 G:KCX201 3.5 18.8 1.0 CD G:GLU204 3.6 21.8 1.0 NZ G:LYS175 3.7 16.6 1.0 OD2 G:ASP203 3.8 27.2 1.0 N G:GLU204 3.9 14.5 1.0 OE2 G:GLU204 4.0 24.8 1.0 CG2 G:THR173 4.2 26.7 1.0 CA G:ASP203 4.2 18.7 1.0 O7 G:CAP477 4.2 19.9 1.0 NE2 G:HIS294 4.3 9.1 1.0 CB G:ASP203 4.4 22.4 1.0 O G:HOH2133 4.4 14.6 1.0 C G:ASP203 4.5 17.2 1.0 C4 G:CAP477 4.5 22.4 1.0 C1 G:CAP477 4.6 21.7 1.0 NZ G:KCX201 4.6 14.4 1.0 OG1 G:THR173 4.6 31.8 1.0 CG G:GLU204 4.8 18.3 1.0 O1 G:CAP477 4.8 17.2 1.0 CB G:GLU204 4.8 16.4 1.0 CB G:THR173 4.9 28.9 1.0 CE G:LYS177 4.9 23.0 1.0 CA G:GLU204 4.9 15.5 1.0 CD2 G:HIS294 5.0 9.5 1.0 CE G:LYS175 5.0 17.1 1.0

S.Karehabadi, 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