Magnesium in PDB 7dz6: Crystal Structures of D-Allulose 3-Epimerase with D-Allulose From Sinorhizobium Fredii

The structure of Crystal Structures of D-Allulose 3-Epimerase with D-Allulose From Sinorhizobium Fredii, PDB code: 7dz6 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)	37.15 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.558, 87.141, 128.881, 90, 99.39, 90
R / Rfree (%)	17.8 / 22.2

The binding sites of Magnesium atom in the Crystal Structures of D-Allulose 3-Epimerase with D-Allulose From Sinorhizobium Fredii (pdb code 7dz6). 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-Allulose From Sinorhizobium Fredii, PDB code: 7dz6:
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-Allulose 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-Allulose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:32.5 occ:1.00 ND1 A:HIS205 2.1 37.2 1.0 OE2 A:GLU146 2.1 37.5 1.0 OD2 A:ASP179 2.2 34.7 1.0 OE1 A:GLU240 2.8 51.9 1.0 HE1 A:HIS205 2.8 45.5 1.0 CE1 A:HIS205 2.8 37.9 1.0 HB2 A:ASP179 3.0 42.4 1.0 CD A:GLU146 3.2 44.9 1.0 CG A:ASP179 3.2 36.8 1.0 HH22 A:ARG211 3.3 44.1 1.0 CG A:HIS205 3.3 36.3 1.0 HH12 A:ARG211 3.3 36.4 1.0 CB A:ASP179 3.5 35.3 1.0 HB2 A:HIS205 3.6 37.5 1.0 CD A:GLU240 3.6 52.2 1.0 OE1 A:GLU146 3.7 45.7 1.0 HE2 A:HIS177 3.7 47.1 1.0 OE2 A:GLU240 3.8 50.0 1.0 CB A:HIS205 3.9 31.2 1.0 HB3 A:ASP179 3.9 42.4 1.0 HD2 A:HIS182 3.9 33.0 1.0 HB3 A:HIS205 4.0 37.5 1.0 HE2 A:HIS182 4.0 37.8 1.0 NE2 A:HIS205 4.0 38.9 1.0 NH2 A:ARG211 4.1 36.7 1.0 NH1 A:ARG211 4.1 30.3 1.0 CD2 A:HIS205 4.3 39.5 1.0 NE2 A:HIS177 4.3 39.2 1.0 O A:HOH427 4.3 42.2 1.0 OD1 A:ASP179 4.4 35.7 1.0 CD2 A:HIS182 4.4 27.5 1.0 CG A:GLU146 4.5 35.5 1.0 NE2 A:HIS182 4.5 31.4 1.0 HG3 A:GLU146 4.5 42.6 1.0 CZ A:ARG211 4.6 32.9 1.0 HG2 A:GLU146 4.7 42.6 1.0 HH21 A:ARG211 4.7 44.1 1.0 HE2 A:HIS205 4.7 46.7 1.0 HH11 A:ARG211 4.8 36.4 1.0 HA A:ASP179 4.9 38.4 1.0 CA A:ASP179 4.9 32.0 1.0 HG12 A:VAL148 4.9 40.0 1.0 HE1 A:HIS177 5.0 47.0 1.0 HB3 A:GLU240 5.0 51.2 1.0 CG A:GLU240 5.0 50.5 1.0 CE1 A:HIS177 5.0 39.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Allulose 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-Allulose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:33.4 occ:1.00 ND1 B:HIS205 2.1 42.8 1.0 OE2 B:GLU146 2.2 45.3 1.0 O B:HOH427 2.2 50.5 1.0 OD2 B:ASP179 2.2 36.8 1.0 OE1 B:GLU240 2.5 54.7 1.0 CE1 B:HIS205 2.8 41.3 1.0 HE1 B:HIS205 2.9 49.6 1.0 HB2 B:ASP179 3.0 39.2 1.0 CG B:ASP179 3.2 35.7 1.0 CG B:HIS205 3.2 40.0 1.0 HH12 B:ARG211 3.2 45.5 1.0 CD B:GLU146 3.3 50.1 1.0 HH22 B:ARG211 3.3 49.9 1.0 CD B:GLU240 3.4 53.1 1.0 HB2 B:HIS205 3.5 41.4 1.0 CB B:ASP179 3.6 32.6 1.0 OE2 B:GLU240 3.6 53.9 1.0 OE1 B:GLU146 3.7 50.0 1.0 HB3 B:HIS205 3.8 41.4 1.0 CB B:HIS205 3.8 34.5 1.0 HE2 B:HIS177 3.9 50.1 1.0 HE2 B:HIS182 3.9 41.6 1.0 HB3 B:ASP179 4.0 39.2 1.0 HD2 B:HIS182 4.0 37.4 1.0 NH1 B:ARG211 4.0 37.9 1.0 NE2 B:HIS205 4.0 41.5 1.0 NH2 B:ARG211 4.1 41.5 1.0 CD2 B:HIS205 4.2 38.8 1.0 OD1 B:ASP179 4.3 38.2 1.0 O B:HOH426 4.4 39.1 1.0 NE2 B:HIS177 4.4 41.7 1.0 NE2 B:HIS182 4.4 34.6 1.0 CD2 B:HIS182 4.5 31.1 1.0 CZ B:ARG211 4.5 43.6 1.0 CG B:GLU146 4.5 39.3 1.0 HG3 B:GLU146 4.6 47.2 1.0 HH11 B:ARG211 4.6 45.5 1.0 HH21 B:ARG211 4.7 49.9 1.0 HE2 B:HIS205 4.8 49.9 1.0 HE1 B:HIS177 4.8 49.0 1.0 HG2 B:GLU146 4.8 47.2 1.0 CG B:GLU240 4.8 48.2 1.0 HA B:ASP179 4.9 35.9 1.0 HB3 B:GLU240 4.9 54.0 1.0 CE1 B:HIS177 4.9 40.8 1.0 CA B:ASP179 4.9 29.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Allulose 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-Allulose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:26.1 occ:1.00 HO3 C:PSJ301 1.4 61.3 1.0 OD2 C:ASP179 2.0 31.5 1.0 O2 C:PSJ301 2.0 44.2 1.0 ND1 C:HIS205 2.0 32.8 1.0 OE2 C:GLU146 2.2 39.3 1.0 OE1 C:GLU240 2.2 36.4 1.0 O3 C:PSJ301 2.3 51.0 1.0 CE1 C:HIS205 2.8 32.5 1.0 HE1 C:HIS205 2.8 39.0 1.0 C2 C:PSJ301 2.8 48.1 1.0 C3 C:PSJ301 3.0 50.4 1.0 CG C:ASP179 3.1 34.0 1.0 HB2 C:ASP179 3.1 29.9 1.0 CG C:HIS205 3.2 30.5 1.0 CD C:GLU240 3.2 39.9 1.0 CD C:GLU146 3.3 36.2 1.0 HH12 C:ARG211 3.4 34.5 1.0 HH22 C:ARG211 3.4 32.0 1.0 H3 C:PSJ301 3.4 60.5 1.0 OE2 C:GLU240 3.5 40.2 1.0 HB2 C:HIS205 3.5 37.8 1.0 CB C:ASP179 3.6 24.9 1.0 OE1 C:GLU146 3.7 41.1 1.0 CB C:HIS205 3.8 31.5 1.0 HB3 C:HIS205 3.8 37.8 1.0 HE2 C:HIS182 3.8 32.2 1.0 HE2 C:HIS177 3.8 43.7 1.0 HD2 C:HIS182 3.9 31.5 1.0 NE2 C:HIS205 4.0 33.6 1.0 HB3 C:ASP179 4.0 29.9 1.0 NH1 C:ARG211 4.2 28.7 1.0 NH2 C:ARG211 4.2 26.6 1.0 OD1 C:ASP179 4.2 30.5 1.0 CD2 C:HIS205 4.2 31.7 1.0 C1 C:PSJ301 4.3 37.0 1.0 NE2 C:HIS182 4.3 26.8 1.0 NE2 C:HIS177 4.4 36.4 1.0 CD2 C:HIS182 4.4 26.2 1.0 C4 C:PSJ301 4.4 53.7 1.0 CG C:GLU146 4.6 31.2 1.0 CG C:GLU240 4.6 35.2 1.0 H11 C:PSJ301 4.6 44.4 1.0 H5 C:PSJ301 4.7 65.1 1.0 HB3 C:GLU240 4.7 40.3 1.0 HE1 C:HIS177 4.7 46.4 1.0 CZ C:ARG211 4.7 32.6 1.0 HE2 C:HIS205 4.7 40.4 1.0 HG3 C:GLU146 4.7 37.5 1.0 HB2 C:GLU240 4.8 40.3 1.0 HH11 C:ARG211 4.8 34.5 1.0 CE1 C:HIS177 4.8 38.6 1.0 HG2 C:GLU146 4.8 37.5 1.0 HH21 C:ARG211 4.8 32.0 1.0 O1 C:PSJ301 4.9 41.1 1.0 HO4 C:PSJ301 4.9 62.5 1.0 HG12 C:VAL148 4.9 30.7 1.0 HG2 C:GLU240 4.9 42.3 1.0 HA C:ASP179 4.9 35.3 1.0 H12 C:PSJ301 5.0 44.4 1.0 CA C:ASP179 5.0 29.4 1.0 CB C:GLU240 5.0 33.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Allulose 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-Allulose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:27.4 occ:1.00 O2 D:PSJ301 1.8 42.1 1.0 ND1 D:HIS205 2.0 31.2 1.0 OE1 D:GLU240 2.1 41.6 1.0 OE2 D:GLU146 2.2 38.3 1.0 OD2 D:ASP179 2.2 33.5 1.0 O3 D:PSJ301 2.3 53.0 1.0 C2 D:PSJ301 2.7 50.5 1.0 CE1 D:HIS205 2.8 32.8 1.0 HE1 D:HIS205 2.9 39.5 1.0 HO3 D:PSJ301 2.9 63.6 1.0 C3 D:PSJ301 3.0 47.0 1.0 HB2 D:ASP179 3.0 37.6 1.0 CG D:HIS205 3.2 35.3 1.0 CD D:GLU240 3.2 38.6 1.0 CD D:GLU146 3.3 41.4 1.0 CG D:ASP179 3.3 33.4 1.0 HH12 D:ARG211 3.4 35.5 1.0 H3 D:PSJ301 3.4 56.4 1.0 HB2 D:HIS205 3.5 33.9 1.0 HH22 D:ARG211 3.6 44.2 1.0 CB D:ASP179 3.6 31.3 1.0 OE2 D:GLU240 3.6 41.6 1.0 HE2 D:HIS177 3.7 49.6 1.0 CB D:HIS205 3.7 28.2 1.0 OE1 D:GLU146 3.7 41.4 1.0 HB3 D:HIS205 3.7 33.9 1.0 HD2 D:HIS182 4.0 40.0 1.0 HB3 D:ASP179 4.0 37.6 1.0 NE2 D:HIS205 4.0 37.5 1.0 HE2 D:HIS182 4.0 38.3 1.0 C1 D:PSJ301 4.1 45.0 1.0 NH1 D:ARG211 4.2 29.5 1.0 CD2 D:HIS205 4.2 37.2 1.0 NE2 D:HIS177 4.3 41.3 1.0 NH2 D:ARG211 4.3 36.8 1.0 H11 D:PSJ301 4.4 54.1 1.0 C4 D:PSJ301 4.4 54.5 1.0 OD1 D:ASP179 4.4 34.4 1.0 CG D:GLU240 4.5 33.1 1.0 H5 D:PSJ301 4.5 64.9 1.0 CD2 D:HIS182 4.5 33.3 1.0 NE2 D:HIS182 4.5 31.9 1.0 HO5 D:PSJ301 4.5 68.2 1.0 CG D:GLU146 4.5 33.8 1.0 HB2 D:GLU240 4.6 44.5 1.0 HE1 D:HIS177 4.6 44.3 1.0 HG3 D:GLU146 4.6 40.5 1.0 HB3 D:GLU240 4.6 44.5 1.0 O1 D:PSJ301 4.7 37.4 1.0 CE1 D:HIS177 4.7 36.9 1.0 CZ D:ARG211 4.7 37.0 1.0 HE2 D:HIS205 4.7 45.1 1.0 HH11 D:ARG211 4.7 35.5 1.0 H12 D:PSJ301 4.8 54.1 1.0 CB D:GLU240 4.8 37.1 1.0 HG2 D:GLU146 4.8 40.5 1.0 HG2 D:GLU240 4.8 39.8 1.0 CA D:ASP179 4.9 27.6 1.0 HA D:ASP179 4.9 33.2 1.0 H4 D:PSJ301 4.9 65.4 1.0 C5 D:PSJ301 5.0 54.1 1.0

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