Magnesium in PDB 1wdd: Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate

All present enzymatic activity of Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate:
4.1.1.39;

The structure of Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate, PDB code: 1wdd was solved by E.Mizohata, H.Matsumura, T.Ueno, H.Ishida, T.Inoue, A.Makino, T.Mae, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.32 / 1.35
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	111.713, 111.713, 196.780, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 18.2

The binding sites of Magnesium atom in the Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate (pdb code 1wdd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate, PDB code: 1wdd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1476 b:13.3 occ:1.00 OD1 A:ASP203 2.0 14.2 1.0 OE1 A:GLU204 2.0 14.7 1.0 OQ2 A:KCX201 2.0 12.3 1.0 O6 A:CAP1001 2.1 14.4 1.0 O3 A:CAP1001 2.2 15.2 1.0 O2 A:CAP1001 2.2 14.9 1.0 C A:CAP1001 2.8 15.2 1.0 C2 A:CAP1001 2.8 14.8 1.0 CX A:KCX201 3.0 13.2 1.0 C3 A:CAP1001 3.0 15.0 1.0 CD A:GLU204 3.1 14.9 1.0 CG A:ASP203 3.2 14.9 1.0 OQ1 A:KCX201 3.3 13.9 1.0 OE2 A:GLU204 3.6 16.8 1.0 NZ A:LYS177 3.7 14.9 1.0 N A:GLU204 3.8 11.8 1.0 ND2 E:ASN123 3.8 13.3 1.0 OD2 A:ASP203 3.9 16.4 1.0 NZ A:LYS175 3.9 14.3 1.0 NE2 A:HIS294 3.9 11.9 1.0 CG2 A:THR173 4.0 14.2 1.0 O7 A:CAP1001 4.1 14.6 1.0 CA A:ASP203 4.2 11.1 1.0 NZ A:KCX201 4.2 12.1 1.0 CB A:ASP203 4.2 11.8 1.0 C4 A:CAP1001 4.3 16.4 1.0 C1 A:CAP1001 4.3 14.6 1.0 CG A:GLU204 4.3 13.7 1.0 OG1 A:THR173 4.3 14.9 1.0 CB A:GLU204 4.5 12.3 1.0 C A:ASP203 4.5 12.0 1.0 CD2 A:HIS294 4.5 12.0 1.0 CB A:THR173 4.7 14.6 1.0 C5 A:CAP1001 4.7 14.3 1.0 CA A:GLU204 4.8 12.2 1.0 O1 A:CAP1001 4.8 15.2 1.0 CE1 A:HIS294 4.9 12.2 1.0 O E:HOH3028 5.0 16.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Activated Rice Rubisco Complexed with 2- Carboxyarabinitol-1,5-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg2476 b:12.9 occ:1.00 OD1 E:ASP203 1.9 14.4 1.0 OQ2 E:KCX201 2.0 14.2 1.0 OE1 E:GLU204 2.0 14.6 1.0 O6 E:CAP2001 2.0 13.8 1.0 O3 E:CAP2001 2.1 13.4 1.0 O2 E:CAP2001 2.3 14.4 1.0 C E:CAP2001 2.8 14.9 1.0 C2 E:CAP2001 2.8 14.8 1.0 CX E:KCX201 3.0 13.7 1.0 C3 E:CAP2001 3.0 15.0 1.0 CD E:GLU204 3.1 16.1 1.0 CG E:ASP203 3.1 15.9 1.0 OQ1 E:KCX201 3.3 14.4 1.0 OE2 E:GLU204 3.6 16.4 1.0 NZ E:LYS177 3.6 16.0 1.0 N E:GLU204 3.8 11.6 1.0 ND2 A:ASN123 3.8 14.3 1.0 OD2 E:ASP203 3.9 16.6 1.0 NZ E:LYS175 3.9 14.5 1.0 NE2 E:HIS294 4.0 12.6 1.0 O7 E:CAP2001 4.0 15.3 1.0 CG2 E:THR173 4.0 14.6 1.0 CA E:ASP203 4.2 11.7 1.0 CB E:ASP203 4.2 12.3 1.0 NZ E:KCX201 4.2 12.9 1.0 C4 E:CAP2001 4.3 16.2 1.0 OG1 E:THR173 4.3 15.7 1.0 C1 E:CAP2001 4.3 13.5 1.0 CG E:GLU204 4.3 12.2 1.0 C E:ASP203 4.5 12.2 1.0 CB E:GLU204 4.6 11.6 1.0 CD2 E:HIS294 4.6 13.0 1.0 C5 E:CAP2001 4.7 15.6 1.0 CB E:THR173 4.7 14.7 1.0 CA E:GLU204 4.8 11.4 1.0 O1 E:CAP2001 4.8 14.3 1.0 CE1 E:HIS294 4.9 13.0 1.0 O A:HOH3032 5.0 16.2 1.0

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