Magnesium in PDB 7dz3: Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii

The structure of Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii, PDB code: 7dz3 was solved by Z.L.Zhu, T.Miyakawa, M.Tanokura, F.P.Lu, H.-M.Qin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.92 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.437, 120.648, 134.633, 90, 90, 90
R / Rfree (%)	18.2 / 21.8

The binding sites of Magnesium atom in the Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii (pdb code 7dz3). 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 Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii, PDB code: 7dz3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:31.6 occ:1.00 ND1 A:HIS205 2.0 26.1 1.0 OE2 A:GLU146 2.0 31.0 1.0 OD2 A:ASP179 2.2 24.5 1.0 O A:HOH457 2.3 40.6 1.0 CE1 A:HIS205 2.8 28.1 1.0 HE1 A:HIS205 2.8 33.8 1.0 HB2 A:ASP179 2.9 22.7 1.0 OE1 A:GLU240 3.0 40.5 1.0 CD A:GLU146 3.1 34.8 1.0 CG A:ASP179 3.2 27.6 1.0 CG A:HIS205 3.2 22.6 1.0 HH22 A:ARG211 3.3 36.1 1.0 HB2 A:HIS205 3.4 27.6 1.0 CB A:ASP179 3.5 18.9 1.0 HE2 A:HIS177 3.5 34.4 1.0 HH12 A:ARG211 3.5 36.0 1.0 OE1 A:GLU146 3.6 35.2 1.0 CB A:HIS205 3.7 23.0 1.0 HD2 A:HIS182 3.8 20.2 1.0 HB3 A:HIS205 3.8 27.6 1.0 HB3 A:ASP179 3.9 22.7 1.0 CD A:GLU240 4.0 37.5 1.0 NE2 A:HIS205 4.0 25.4 1.0 NH2 A:ARG211 4.1 30.1 1.0 NE2 A:HIS177 4.1 28.6 1.0 OE2 A:GLU240 4.1 46.5 1.0 CD2 A:HIS205 4.2 24.1 1.0 O A:HOH459 4.2 36.9 1.0 OD1 A:ASP179 4.3 28.6 1.0 NH1 A:ARG211 4.3 30.0 1.0 CD2 A:HIS182 4.4 16.8 1.0 CG A:GLU146 4.4 28.2 1.0 HG3 A:GLU146 4.4 33.9 1.0 NE2 A:HIS182 4.5 17.5 1.0 HE1 A:HIS177 4.7 35.9 1.0 CZ A:ARG211 4.7 24.2 1.0 HG2 A:GLU146 4.7 33.9 1.0 HH21 A:ARG211 4.7 36.1 1.0 HE2 A:HIS205 4.7 30.4 1.0 CE1 A:HIS177 4.7 29.9 1.0 HA A:ASP179 4.7 29.1 1.0 CA A:ASP179 4.8 24.3 1.0 HH11 A:ARG211 5.0 36.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:38.3 occ:1.00 OE2 B:GLU146 2.1 31.1 1.0 ND1 B:HIS205 2.1 26.3 1.0 OD2 B:ASP179 2.2 23.4 1.0 CE1 B:HIS205 2.8 29.1 1.0 HE1 B:HIS205 2.8 34.9 1.0 HB2 B:ASP179 2.9 26.0 1.0 OE1 B:GLU240 3.0 44.5 1.0 CD B:GLU146 3.1 33.8 1.0 CG B:ASP179 3.2 23.5 1.0 CG B:HIS205 3.3 24.8 1.0 HH22 B:ARG211 3.4 32.5 1.0 HH12 B:ARG211 3.5 32.3 1.0 CB B:ASP179 3.5 21.7 1.0 HB2 B:HIS205 3.5 28.6 1.0 OE1 B:GLU146 3.6 36.3 1.0 HE2 B:HIS177 3.6 34.8 1.0 HD2 B:HIS182 3.8 27.1 1.0 CB B:HIS205 3.8 23.8 1.0 HB3 B:ASP179 3.8 26.0 1.0 HE2 B:HIS182 3.9 24.0 1.0 HB3 B:HIS205 3.9 28.6 1.0 CD B:GLU240 4.0 33.9 1.0 NE2 B:HIS205 4.1 27.1 1.0 OE2 B:GLU240 4.2 39.0 1.0 NH2 B:ARG211 4.2 27.1 1.0 NE2 B:HIS177 4.2 29.0 1.0 NH1 B:ARG211 4.2 26.9 1.0 CD2 B:HIS205 4.3 26.1 1.0 OD1 B:ASP179 4.3 24.0 1.0 CD2 B:HIS182 4.3 22.6 1.0 NE2 B:HIS182 4.4 19.9 1.0 CG B:GLU146 4.4 26.0 1.0 HG3 B:GLU146 4.4 31.2 1.0 O B:HOH424 4.6 33.6 1.0 HG2 B:GLU146 4.7 31.2 1.0 HE1 B:HIS177 4.7 37.9 1.0 CZ B:ARG211 4.7 28.1 1.0 CE1 B:HIS177 4.8 31.5 1.0 HE2 B:HIS205 4.8 32.5 1.0 HA B:ASP179 4.8 23.0 1.0 CA B:ASP179 4.8 19.1 1.0 HG12 B:VAL148 4.8 26.0 1.0 HH21 B:ARG211 4.9 32.5 1.0 HH11 B:ARG211 4.9 32.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:23.4 occ:1.00 HO3 C:FUD301 1.6 56.6 1.0 O2 C:FUD301 1.9 35.3 1.0 ND1 C:HIS205 2.1 18.6 1.0 OD2 C:ASP179 2.1 21.3 1.0 OE2 C:GLU146 2.1 24.7 1.0 OE1 C:GLU240 2.5 32.7 1.0 O3 C:FUD301 2.5 47.1 1.0 CE1 C:HIS205 2.8 24.5 1.0 C2 C:FUD301 2.8 43.5 1.0 HE1 C:HIS205 2.8 29.4 1.0 HB2 C:ASP179 3.0 22.5 1.0 CG C:ASP179 3.2 21.8 1.0 CD C:GLU146 3.2 27.3 1.0 CG C:HIS205 3.2 20.8 1.0 HH12 C:ARG211 3.3 24.6 1.0 C3 C:FUD301 3.3 46.3 1.0 CD C:GLU240 3.5 27.9 1.0 HB2 C:HIS205 3.5 20.4 1.0 OE1 C:GLU146 3.5 29.9 1.0 HH22 C:ARG211 3.6 27.1 1.0 CB C:ASP179 3.6 18.7 1.0 HE2 C:HIS177 3.6 25.1 1.0 HD2 C:HIS182 3.8 21.1 1.0 CB C:HIS205 3.8 17.0 1.0 HE2 C:HIS182 3.9 21.5 1.0 HB3 C:HIS205 3.9 20.4 1.0 OE2 C:GLU240 3.9 29.9 1.0 H3 C:FUD301 3.9 55.6 1.0 NE2 C:HIS205 4.0 22.4 1.0 HB3 C:ASP179 4.0 22.5 1.0 NH1 C:ARG211 4.1 20.5 1.0 C1 C:FUD301 4.1 33.1 1.0 CD2 C:HIS205 4.2 20.9 1.0 NE2 C:HIS177 4.2 20.9 1.0 OD1 C:ASP179 4.3 23.4 1.0 H11 C:FUD301 4.3 39.7 1.0 CD2 C:HIS182 4.3 17.5 1.0 NH2 C:ARG211 4.3 22.5 1.0 NE2 C:HIS182 4.4 17.9 1.0 CG C:GLU146 4.5 20.1 1.0 HG3 C:GLU146 4.6 24.1 1.0 HO4 C:FUD301 4.6 56.8 1.0 O1 C:FUD301 4.6 25.0 1.0 C4 C:FUD301 4.6 47.6 1.0 HH11 C:ARG211 4.7 24.6 1.0 CZ C:ARG211 4.7 26.1 1.0 HE1 C:HIS177 4.7 29.1 1.0 HE2 C:HIS205 4.7 26.9 1.0 HG2 C:GLU146 4.7 24.1 1.0 HO1 C:FUD301 4.8 30.0 1.0 CG C:GLU240 4.8 25.1 1.0 HB3 C:GLU240 4.8 20.4 1.0 HB2 C:GLU240 4.8 20.4 1.0 CE1 C:HIS177 4.8 24.3 1.0 O4 C:FUD301 4.8 47.4 1.0 HA C:ASP179 4.8 20.6 1.0 HG12 C:VAL148 4.8 23.3 1.0 CA C:ASP179 4.9 17.1 1.0 H5 C:FUD301 4.9 61.6 1.0 H12 C:FUD301 4.9 39.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of D-Allulose 3-Epimerase with D-Fructose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:30.8 occ:1.00 O2 D:FUD301 1.9 35.7 1.0 ND1 D:HIS205 2.1 29.3 1.0 OD2 D:ASP179 2.1 26.3 1.0 OE2 D:GLU146 2.2 28.2 1.0 OE1 D:GLU240 2.4 37.5 1.0 HO3 D:FUD301 2.4 60.8 1.0 O3 D:FUD301 2.5 50.6 1.0 C2 D:FUD301 2.8 45.6 1.0 CE1 D:HIS205 2.8 30.9 1.0 HE1 D:HIS205 2.8 37.0 1.0 HB2 D:ASP179 3.1 27.3 1.0 C3 D:FUD301 3.2 50.3 1.0 CG D:ASP179 3.2 26.5 1.0 CD D:GLU146 3.2 37.1 1.0 CG D:HIS205 3.2 26.2 1.0 HH12 D:ARG211 3.3 35.7 1.0 CD D:GLU240 3.4 31.4 1.0 HB2 D:HIS205 3.5 31.1 1.0 OE1 D:GLU146 3.6 31.8 1.0 HE2 D:HIS177 3.6 38.3 1.0 HH22 D:ARG211 3.6 36.0 1.0 CB D:ASP179 3.7 22.8 1.0 H3 D:FUD301 3.7 60.3 1.0 OE2 D:GLU240 3.8 33.7 1.0 HD2 D:HIS182 3.8 27.7 1.0 CB D:HIS205 3.8 25.9 1.0 HB3 D:HIS205 3.9 31.1 1.0 HE2 D:HIS182 3.9 27.1 1.0 NE2 D:HIS205 4.0 29.8 1.0 HB3 D:ASP179 4.1 27.3 1.0 NH1 D:ARG211 4.1 29.7 1.0 C1 D:FUD301 4.1 34.9 1.0 NE2 D:HIS177 4.2 31.9 1.0 CD2 D:HIS205 4.2 28.8 1.0 OD1 D:ASP179 4.3 27.6 1.0 H11 D:FUD301 4.3 41.9 1.0 CD2 D:HIS182 4.4 23.1 1.0 NH2 D:ARG211 4.4 30.0 1.0 NE2 D:HIS182 4.4 22.6 1.0 C4 D:FUD301 4.5 56.9 1.0 CG D:GLU146 4.5 26.1 1.0 HE1 D:HIS177 4.6 39.1 1.0 HG3 D:GLU146 4.6 31.4 1.0 HH11 D:ARG211 4.6 35.7 1.0 O1 D:FUD301 4.7 31.9 1.0 CE1 D:HIS177 4.7 32.6 1.0 HE2 D:HIS205 4.7 35.8 1.0 CZ D:ARG211 4.7 27.9 1.0 HB3 D:GLU240 4.7 32.5 1.0 CG D:GLU240 4.7 30.8 1.0 O4 D:FUD301 4.8 55.6 1.0 H5 D:FUD301 4.8 70.6 1.0 HB2 D:GLU240 4.8 32.5 1.0 HG2 D:GLU146 4.9 31.4 1.0 H12 D:FUD301 4.9 41.9 1.0 HA D:ASP179 4.9 22.1 1.0 HG12 D:VAL148 5.0 26.3 1.0 CA D:ASP179 5.0 18.4 1.0

Z.L.Zhu, T.Miyakawa, M.Tanokura, F.P.Lu, H.-M.Qin. Structural Basis and Molecular Modification of D-Allulose 3-Epimerase From Sinorhizobium Fredii To Be Published.