Magnesium in PDB 3ajx: Crystal Structure of 3-Hexulose-6-Phosphate Synthase

All present enzymatic activity of Crystal Structure of 3-Hexulose-6-Phosphate Synthase:
4.1.2.43;

The structure of Crystal Structure of 3-Hexulose-6-Phosphate Synthase, PDB code: 3ajx was solved by A.Kita, I.Orita, H.Yurimoto, N.Kato, Y.Sakai, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.04 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.043, 57.354, 113.623, 90.00, 90.69, 90.00
R / Rfree (%)	19.4 / 21.5

The structure of Crystal Structure of 3-Hexulose-6-Phosphate Synthase also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase (pdb code 3ajx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase, PDB code: 3ajx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase


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 3-Hexulose-6-Phosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9100 b:34.7 occ:1.00 O A:HOH5853 1.6 24.1 1.0 O A:HOH5854 2.0 35.9 1.0 OD2 A:ASP1059 2.1 13.0 1.0 O A:HOH5856 2.1 29.6 1.0 O A:HOH5852 2.7 30.8 1.0 OE2 A:GLU1030 2.7 17.4 1.0 CG A:ASP1059 3.2 11.5 1.0 O A:HOH5851 3.3 16.2 1.0 CD A:GLU1030 3.4 15.3 1.0 OE1 A:GLU1030 3.5 11.7 1.0 NZ A:LYS1061 3.7 17.2 1.0 OE2 A:GLU1132 3.7 22.1 1.0 CE1 A:HIS1134 3.7 17.1 1.0 OD1 A:ASP1059 3.9 9.5 1.0 O A:HOH5855 4.0 25.7 1.0 CB A:ASP1059 4.3 9.7 1.0 ND1 A:HIS1134 4.3 15.9 1.0 NE2 A:HIS1134 4.4 15.6 1.0 OE1 A:GLU1132 4.5 20.7 1.0 CD A:GLU1132 4.5 19.7 1.0 OD2 A:ASP1109 4.6 13.6 1.0 CG A:GLU1030 4.7 10.5 1.0 O A:HOH5859 4.8 34.0 1.0 CE2 A:PHE1057 4.8 9.0 1.0 CE A:LYS1061 4.9 11.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase


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 3-Hexulose-6-Phosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg9200 b:28.9 occ:1.00 O B:HOH5860 2.0 26.3 1.0 OD2 B:ASP2059 2.0 17.7 1.0 OE2 B:GLU2030 2.0 15.8 1.0 O B:HOH5861 2.2 31.2 1.0 O B:HOH5863 2.4 26.0 1.0 O B:HOH5862 2.4 29.4 1.0 CD B:GLU2030 3.2 13.6 1.0 CG B:ASP2059 3.2 13.1 1.0 OE1 B:GLU2030 3.7 12.5 1.0 O B:HOH5865 3.7 28.9 1.0 NZ B:LYS2061 3.7 15.5 1.0 CB B:ASP2059 4.0 10.3 1.0 OD2 B:ASP2008 4.0 25.9 1.0 OD1 B:ASP2059 4.2 12.1 1.0 O B:HOH5864 4.2 31.4 1.0 CG B:GLU2030 4.4 12.6 1.0 CE1 B:HIS2134 4.4 15.9 1.0 OD1 B:ASP2008 4.5 29.8 1.0 CA B:GLY2032 4.5 10.2 1.0 CB B:ALA2006 4.6 11.1 1.0 O A:HOH5866 4.7 33.0 1.0 CG B:ASP2008 4.7 24.5 1.0 N B:THR2033 4.8 9.7 1.0 OG1 B:THR2033 4.8 11.5 1.0 OE2 B:GLU2132 4.9 25.0 1.0 NE2 B:HIS2134 5.0 14.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 3-Hexulose-6-Phosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg9300 b:42.3 occ:1.00 OD2 C:ASP3059 2.1 16.0 1.0 O C:HOH5871 2.1 24.0 1.0 O C:HOH5874 2.3 28.5 1.0 O C:HOH5872 2.6 28.7 1.0 OE2 C:GLU3030 2.6 18.0 1.0 O C:HOH5870 2.8 29.0 1.0 CG C:ASP3059 3.2 12.6 1.0 CD C:GLU3030 3.3 14.2 1.0 OE1 C:GLU3030 3.4 11.2 1.0 OE2 C:GLU3132 3.7 24.8 1.0 O C:HOH5869 3.7 19.4 1.0 NZ C:LYS3061 3.7 16.4 1.0 CE1 C:HIS3134 3.8 12.9 1.0 OD1 C:ASP3059 3.9 12.2 1.0 O C:HOH5873 3.9 26.0 1.0 CB C:ASP3059 4.2 9.6 1.0 ND1 C:HIS3134 4.4 13.3 1.0 NE2 C:HIS3134 4.5 13.2 1.0 OE1 C:GLU3132 4.5 25.0 1.0 CD C:GLU3132 4.5 21.2 1.0 OD2 C:ASP3109 4.6 14.1 1.0 CG C:GLU3030 4.6 11.1 1.0 CE1 C:PHE3057 4.7 8.1 1.0 CE C:LYS3061 5.0 11.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 3-Hexulose-6-Phosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg9400 b:35.4 occ:1.00 O D:HOH5878 1.9 29.7 1.0 OE2 D:GLU4030 2.0 15.5 1.0 OD2 D:ASP4059 2.0 18.2 1.0 O D:HOH5879 2.3 30.8 1.0 O D:HOH5880 2.4 33.6 1.0 O D:HOH5877 2.5 25.6 1.0 CD D:GLU4030 3.0 13.9 1.0 O D:HOH5882 3.2 36.6 1.0 CG D:ASP4059 3.2 13.3 1.0 OE1 D:GLU4030 3.4 12.0 1.0 NZ D:LYS4061 3.8 15.3 1.0 CB D:ASP4059 4.0 10.3 1.0 OD1 D:ASP4059 4.1 12.1 1.0 O D:HOH5881 4.2 37.4 1.0 CG D:GLU4030 4.3 12.6 1.0 CE1 D:HIS4134 4.4 17.9 1.0 O C:HOH5883 4.5 32.1 1.0 OE2 D:GLU4132 4.6 23.2 1.0 CB D:ALA4006 4.6 8.4 1.0 OD2 D:ASP4008 4.7 25.6 1.0 OD1 D:ASP4008 4.8 31.0 1.0 CA D:GLY4032 4.8 9.0 1.0 NE2 D:HIS4134 4.9 15.7 1.0

I.Orita, A.Kita, H.Yurimoto, N.Kato, Y.Sakai, K.Miki. Crystal Structure of 3-Hexulose-6-Phosphate Synthase, A Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily Proteins V. 78 3488 2010.
ISSN: ISSN 0887-3585
PubMed: 20938979
DOI: 10.1002/PROT.22860