Magnesium in PDB 3axk: Structure of Rice Rubisco in Complex with Nadp(H)

All present enzymatic activity of Structure of Rice Rubisco in Complex with Nadp(H):
4.1.1.39;

The structure of Structure of Rice Rubisco in Complex with Nadp(H), PDB code: 3axk was solved by H.Matsumura, E.Mizohata, H.Ishida, A.Kogami, T.Ueno, A.Makino, T.Inoue, A.Yokota, T.Mae, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.63 / 1.90
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	110.246, 110.246, 199.768, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 18.9

The binding sites of Magnesium atom in the Structure of Rice Rubisco in Complex with Nadp(H) (pdb code 3axk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Rice Rubisco in Complex with Nadp(H), PDB code: 3axk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Rice Rubisco in Complex with Nadp(H)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rice Rubisco in Complex with Nadp(H) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg478 b:29.2 occ:1.00 O A:HOH616 2.0 27.8 1.0 OE1 A:GLU204 2.0 16.8 1.0 O A:HOH693 2.0 28.6 1.0 OQ1 A:KCX201 2.1 23.9 1.0 OD2 A:ASP203 2.4 24.9 1.0 O A:HOH901 2.6 40.0 1.0 CX A:KCX201 2.9 23.3 1.0 OQ2 A:KCX201 3.0 23.0 1.0 CD A:GLU204 3.0 20.0 1.0 CG A:ASP203 3.3 25.5 1.0 OE2 A:GLU204 3.4 23.8 1.0 OD1 A:ASP203 3.8 25.2 1.0 N A:GLU204 3.9 16.9 1.0 CA A:ASP203 4.1 18.1 1.0 NE2 A:HIS294 4.1 13.0 1.0 CB A:ASP203 4.2 21.0 1.0 NZ A:KCX201 4.2 20.4 1.0 NZ A:LYS177 4.2 31.0 1.0 CG2 A:THR173 4.2 23.2 1.0 O2A A:NDP479 4.3 50.2 1.0 CG A:GLU204 4.4 18.8 1.0 C A:ASP203 4.6 18.5 1.0 O3B A:NDP479 4.6 44.5 1.0 CB A:GLU204 4.7 17.1 1.0 CD2 A:HIS294 4.8 13.7 1.0 CE A:LYS177 4.8 32.8 1.0 O5B A:NDP479 4.9 49.3 1.0 C5B A:NDP479 4.9 47.4 1.0 CA A:GLU204 4.9 17.2 1.0 CE1 A:HIS294 5.0 12.5 1.0

Magnesium binding site 2 out of 2 in the Structure of Rice Rubisco in Complex with Nadp(H)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rice Rubisco in Complex with Nadp(H) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg478 b:23.5 occ:1.00 O B:HOH855 2.0 36.1 1.0 OE1 B:GLU204 2.1 16.9 1.0 OQ1 B:KCX201 2.1 22.8 1.0 OD2 B:ASP203 2.2 16.6 1.0 O B:HOH787 2.2 26.4 1.0 O B:HOH734 2.3 26.4 1.0 CD B:GLU204 3.0 17.6 1.0 CG B:ASP203 3.1 19.3 1.0 CX B:KCX201 3.2 24.1 1.0 OE2 B:GLU204 3.3 21.2 1.0 OQ2 B:KCX201 3.5 25.1 1.0 OD1 B:ASP203 3.7 20.3 1.0 O A:HOH1093 3.8 51.5 1.0 N B:GLU204 3.9 16.3 1.0 CB B:ASP203 4.1 17.3 1.0 CA B:ASP203 4.2 16.5 1.0 NE2 B:HIS294 4.2 12.9 1.0 NZ B:LYS177 4.2 28.2 1.0 O B:HOH1112 4.3 44.6 1.0 O B:HOH1089 4.3 35.9 1.0 CG2 B:THR173 4.3 20.4 1.0 O2A A:NDP480 4.4 55.3 1.0 NZ B:KCX201 4.4 23.1 1.0 NZ B:LYS175 4.4 37.7 1.0 CG B:GLU204 4.4 15.3 1.0 C B:ASP203 4.6 17.3 1.0 O B:HOH1088 4.6 61.0 1.0 CE B:LYS177 4.7 31.1 1.0 CB B:GLU204 4.8 15.4 1.0 CD2 B:HIS294 4.8 14.1 1.0 O3B A:NDP480 4.8 48.5 1.0 O5B A:NDP480 4.9 54.5 1.0 CA B:GLU204 5.0 16.5 1.0 OG1 B:THR173 5.0 23.7 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