Magnesium in PDB 5wsk: Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat

All present enzymatic activity of Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat:
4.1.1.39;

The structure of Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat, PDB code: 5wsk was solved by Y.Ma, C.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.42 / 1.78
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	110.720, 110.720, 200.956, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.7

The binding sites of Magnesium atom in the Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat (pdb code 5wsk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat, PDB code: 5wsk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:42.2 occ:1.00 O A:HOH826 1.9 44.5 1.0 OE1 A:GLU204 2.1 40.0 1.0 O A:HOH624 2.1 46.6 1.0 OQ2 A:KCX201 2.2 20.0 1.0 O A:HOH644 2.3 37.2 1.0 OD1 A:ASP203 2.5 42.0 1.0 CD A:GLU204 3.0 44.5 1.0 CX A:KCX201 3.2 20.0 1.0 OE2 A:GLU204 3.3 43.3 1.0 H A:GLU204 3.4 34.5 1.0 OQ1 A:KCX201 3.4 20.0 1.0 CG A:ASP203 3.5 46.1 1.0 HG21 A:THR173 3.7 30.8 1.0 HZ1 A:LYS177 3.8 51.5 1.0 HA A:ASP203 3.9 33.4 1.0 OD2 A:ASP203 4.0 37.2 1.0 HZ3 A:LYS177 4.0 51.5 1.0 NE2 A:HIS294 4.2 27.2 1.0 N A:GLU204 4.2 28.8 1.0 NZ A:LYS177 4.3 42.9 1.0 HB3 A:GLU204 4.4 32.4 1.0 NZ A:KCX201 4.4 20.0 1.0 CG A:GLU204 4.4 33.2 1.0 HE2 A:LYS177 4.5 63.0 1.0 CB A:ASP203 4.5 38.4 1.0 HG1 A:THR173 4.6 41.2 1.0 CG2 A:THR173 4.6 25.7 1.0 CA A:ASP203 4.6 27.8 1.0 HB2 A:ASP203 4.7 46.0 1.0 HG2 A:GLU204 4.7 39.8 1.0 O B:HOH670 4.8 42.8 1.0 CB A:GLU204 4.8 27.0 1.0 CE1 A:HIS294 4.9 29.6 1.0 HE1 A:HIS294 4.9 35.5 1.0 HG23 A:THR173 5.0 30.8 1.0 C A:ASP203 5.0 28.5 1.0

Magnesium binding site 2 out of 4 in the Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:41.8 occ:1.00 OQ1 B:KCX201 1.9 20.0 1.0 O B:HOH748 2.0 44.1 1.0 OE1 B:GLU204 2.1 39.5 1.0 O B:HOH787 2.5 46.0 1.0 OD1 B:ASP203 2.5 43.5 1.0 CD B:GLU204 2.9 39.1 1.0 CX B:KCX201 3.1 20.0 1.0 OE2 B:GLU204 3.2 47.2 1.0 H B:GLU204 3.3 33.4 1.0 OQ2 B:KCX201 3.5 20.0 1.0 CG B:ASP203 3.5 43.1 1.0 HG21 B:THR173 3.6 32.2 1.0 HZ1 B:LYS177 3.8 68.9 1.0 HA B:ASP203 3.8 24.3 1.0 HZ3 B:LYS177 4.0 68.9 1.0 HZ2 B:LYS175 4.1 84.1 1.0 OD2 B:ASP203 4.1 37.9 1.0 N B:GLU204 4.2 27.8 1.0 NZ B:KCX201 4.2 20.0 1.0 CG B:GLU204 4.3 33.2 1.0 HB3 B:GLU204 4.3 33.9 1.0 NZ B:LYS177 4.3 57.4 1.0 NE2 B:HIS294 4.3 22.7 1.0 HG2 B:GLU204 4.5 39.9 1.0 CB B:ASP203 4.5 34.0 1.0 CG2 B:THR173 4.5 26.9 1.0 HE2 B:LYS177 4.5 61.3 1.0 CA B:ASP203 4.5 20.3 1.0 HB2 B:ASP203 4.6 40.8 1.0 HG1 B:THR173 4.7 37.7 1.0 CB B:GLU204 4.7 28.2 1.0 HZ3 B:LYS175 4.8 84.1 1.0 NZ B:LYS175 4.8 70.1 1.0 HG23 B:THR173 4.9 32.2 1.0 HG22 B:THR173 4.9 32.2 1.0 HE1 B:HIS294 4.9 37.3 1.0 C B:ASP203 4.9 29.4 1.0 CE1 B:HIS294 4.9 31.1 1.0 HG3 B:GLU204 4.9 39.9 1.0

Magnesium binding site 3 out of 4 in the Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:27.4 occ:1.00 OQ2 C:KCX201 1.9 20.0 1.0 OE1 C:GLU204 2.0 22.8 1.0 O C:HOH839 2.1 30.9 1.0 OD1 C:ASP203 2.1 24.5 1.0 O C:HOH638 2.2 32.6 1.0 O C:HOH647 2.4 26.9 1.0 CD C:GLU204 3.0 24.3 1.0 CX C:KCX201 3.0 20.0 1.0 CG C:ASP203 3.1 32.7 1.0 H C:GLU204 3.2 25.1 1.0 OE2 C:GLU204 3.3 31.9 1.0 OQ1 C:KCX201 3.3 20.0 1.0 HG21 C:THR173 3.4 20.1 1.0 HZ1 C:LYS177 3.5 40.5 1.0 HA C:ASP203 3.6 23.7 1.0 OD2 C:ASP203 3.7 26.2 1.0 HZ3 C:LYS177 3.8 40.5 1.0 N C:GLU204 4.1 20.9 1.0 NZ C:KCX201 4.1 20.0 1.0 NZ C:LYS177 4.1 33.8 1.0 CB C:ASP203 4.1 28.2 1.0 CA C:ASP203 4.3 19.8 1.0 NE2 C:HIS294 4.3 19.2 1.0 HB2 C:ASP203 4.3 33.8 1.0 CG C:GLU204 4.4 19.5 1.0 HE2 C:LYS177 4.4 42.7 1.0 CG2 C:THR173 4.4 16.8 1.0 HB3 C:GLU204 4.4 28.2 1.0 HG1 C:THR173 4.4 33.2 1.0 HG23 C:THR173 4.7 20.1 1.0 C C:ASP203 4.7 24.7 1.0 HG2 C:GLU204 4.7 23.4 1.0 CB C:GLU204 4.8 23.5 1.0 HZ2 C:LYS177 4.8 40.5 1.0 HG22 C:THR173 4.8 20.1 1.0 CE C:LYS177 4.8 35.6 1.0 CD2 C:HIS294 4.9 18.2 1.0 HG3 C:GLU204 4.9 23.4 1.0 HD2 C:HIS294 5.0 21.9 1.0 HB3 C:ASP203 5.0 33.8 1.0

Magnesium binding site 4 out of 4 in the Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:34.8 occ:1.00 O D:HOH851 1.9 37.8 1.0 OE1 D:GLU204 2.0 27.4 1.0 OQ1 D:KCX201 2.1 20.0 1.0 O D:HOH617 2.1 46.1 1.0 OD1 D:ASP203 2.2 38.2 1.0 O D:HOH753 2.3 36.2 1.0 CD D:GLU204 2.9 37.4 1.0 CX D:KCX201 3.2 20.0 1.0 OE2 D:GLU204 3.2 35.6 1.0 CG D:ASP203 3.2 44.2 1.0 H D:GLU204 3.3 27.1 1.0 OQ2 D:KCX201 3.5 20.0 1.0 HG21 D:THR173 3.5 28.6 1.0 HZ1 D:LYS177 3.6 42.7 1.0 HA D:ASP203 3.7 22.8 1.0 OD2 D:ASP203 3.8 38.6 1.0 HZ3 D:LYS177 3.8 42.7 1.0 N D:GLU204 4.1 22.6 1.0 NZ D:LYS177 4.1 35.6 1.0 NZ D:KCX201 4.2 20.0 1.0 CG D:GLU204 4.3 25.3 1.0 CB D:ASP203 4.3 27.8 1.0 HZ1 D:LYS175 4.3 69.7 1.0 NE2 D:HIS294 4.3 19.3 1.0 HB3 D:GLU204 4.3 31.5 1.0 CA D:ASP203 4.4 19.0 1.0 HE2 D:LYS177 4.4 50.5 1.0 HB2 D:ASP203 4.5 33.3 1.0 CG2 D:THR173 4.5 23.8 1.0 HZ3 D:LYS175 4.5 69.7 1.0 HG1 D:THR173 4.5 33.4 1.0 HG2 D:GLU204 4.6 30.3 1.0 O D:HOH603 4.6 34.6 1.0 CB D:GLU204 4.7 26.2 1.0 HG23 D:THR173 4.8 28.6 1.0 HD22 C:ASN123 4.8 68.2 1.0 C D:ASP203 4.8 24.0 1.0 NZ D:LYS175 4.8 58.1 1.0 O D:HOH839 4.8 37.4 1.0 HZ2 D:LYS177 4.8 42.7 1.0 CE D:LYS177 4.9 42.0 1.0 HG3 D:GLU204 4.9 30.3 1.0 HG22 D:THR173 4.9 28.6 1.0 HZ2 D:LYS175 4.9 69.7 1.0

Y.Ma, C.Liu. Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Wheat To Be Published.