Magnesium in PDB 7dz4: Crystal Structures of D-Allulose 3-Epimerase with D-Tagatose From Sinorhizobium Fredii

The structure of Crystal Structures of D-Allulose 3-Epimerase with D-Tagatose From Sinorhizobium Fredii, PDB code: 7dz4 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)	36.11 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.656, 87.921, 128.295, 90, 99.31, 90
R / Rfree (%)	20.3 / 24.5

The binding sites of Magnesium atom in the Crystal Structures of D-Allulose 3-Epimerase with D-Tagatose From Sinorhizobium Fredii (pdb code 7dz4). 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-Tagatose From Sinorhizobium Fredii, PDB code: 7dz4:
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-Tagatose 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-Tagatose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:12.0 occ:1.00 OE2 A:GLU146 2.0 22.2 1.0 OD2 A:ASP179 2.0 25.6 1.0 O A:HOH505 2.1 34.9 1.0 ND1 A:HIS205 2.2 25.6 1.0 OE1 A:GLU240 2.4 28.8 1.0 O A:HOH566 2.5 40.4 1.0 CE1 A:HIS205 2.9 28.4 1.0 HE1 A:HIS205 2.9 34.1 1.0 CD A:GLU146 3.1 26.4 1.0 CG A:ASP179 3.1 23.4 1.0 HB2 A:ASP179 3.1 24.0 1.0 HH22 A:ARG211 3.2 29.8 1.0 CG A:HIS205 3.3 24.1 1.0 CD A:GLU240 3.4 31.4 1.0 OE1 A:GLU146 3.5 24.5 1.0 HH12 A:ARG211 3.5 26.8 1.0 HB2 A:HIS205 3.6 25.1 1.0 CB A:ASP179 3.6 20.0 1.0 OE2 A:GLU240 3.6 35.5 1.0 HE2 A:HIS182 3.8 25.4 1.0 CB A:HIS205 3.8 20.9 1.0 HB3 A:HIS205 3.8 25.1 1.0 HE2 A:HIS177 3.9 33.6 1.0 HD2 A:HIS182 3.9 20.1 1.0 NH2 A:ARG211 4.0 24.8 1.0 HB3 A:ASP179 4.0 24.0 1.0 NE2 A:HIS205 4.1 27.2 1.0 OD1 A:ASP179 4.2 26.6 1.0 NH1 A:ARG211 4.3 22.3 1.0 CD2 A:HIS205 4.3 26.3 1.0 NE2 A:HIS182 4.4 21.2 1.0 CG A:GLU146 4.4 23.0 1.0 CD2 A:HIS182 4.5 16.8 1.0 NE2 A:HIS177 4.5 28.0 1.0 HG3 A:GLU146 4.5 27.6 1.0 O A:HOH464 4.6 37.4 1.0 HH21 A:ARG211 4.6 29.8 1.0 CZ A:ARG211 4.6 24.9 1.0 HG2 A:GLU146 4.6 27.6 1.0 CG A:GLU240 4.8 26.3 1.0 HE2 A:HIS205 4.9 32.7 1.0 HB3 A:GLU240 4.9 38.1 1.0 HB2 A:GLU240 4.9 38.1 1.0 HA A:ASP179 4.9 21.8 1.0 CA A:ASP179 5.0 18.1 1.0 HG12 A:VAL148 5.0 30.2 1.0 HH11 A:ARG211 5.0 26.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Tagatose 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-Tagatose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:14.4 occ:1.00 OE2 B:GLU146 1.9 24.9 1.0 OD2 B:ASP179 2.0 26.0 1.0 ND1 B:HIS205 2.1 23.7 1.0 OE1 B:GLU240 2.4 34.8 1.0 O B:HOH545 2.6 39.3 1.0 CE1 B:HIS205 2.9 32.9 1.0 HE1 B:HIS205 2.9 39.4 1.0 CD B:GLU146 3.0 33.0 1.0 CG B:ASP179 3.1 24.3 1.0 HB2 B:ASP179 3.1 25.4 1.0 CG B:HIS205 3.3 23.9 1.0 HH22 B:ARG211 3.3 28.0 1.0 OE1 B:GLU146 3.4 29.0 1.0 CD B:GLU240 3.4 28.8 1.0 HB2 B:HIS205 3.5 25.0 1.0 HH12 B:ARG211 3.5 30.6 1.0 CB B:ASP179 3.6 21.2 1.0 OE2 B:GLU240 3.6 33.6 1.0 HB3 B:HIS205 3.8 25.0 1.0 HE2 B:HIS177 3.8 36.2 1.0 CB B:HIS205 3.8 20.8 1.0 HE2 B:HIS182 3.8 27.4 1.0 HD2 B:HIS182 4.0 23.6 1.0 HB3 B:ASP179 4.0 25.4 1.0 NE2 B:HIS205 4.1 30.1 1.0 NH2 B:ARG211 4.1 23.3 1.0 OD1 B:ASP179 4.2 25.2 1.0 NH1 B:ARG211 4.3 25.4 1.0 CD2 B:HIS205 4.3 28.5 1.0 CG B:GLU146 4.4 27.9 1.0 NE2 B:HIS177 4.4 30.1 1.0 NE2 B:HIS182 4.4 22.8 1.0 CD2 B:HIS182 4.5 19.7 1.0 HG3 B:GLU146 4.5 33.5 1.0 HG2 B:GLU146 4.6 33.5 1.0 CZ B:ARG211 4.7 29.8 1.0 HH21 B:ARG211 4.7 28.0 1.0 CG B:GLU240 4.7 32.8 1.0 HE1 B:HIS177 4.8 38.6 1.0 HE2 B:HIS205 4.8 36.1 1.0 HB2 B:GLU240 4.9 32.9 1.0 HA B:ASP179 4.9 25.1 1.0 HB3 B:GLU240 4.9 32.9 1.0 CA B:ASP179 4.9 20.9 1.0 CE1 B:HIS177 4.9 32.1 1.0 HH11 B:ARG211 5.0 30.6 1.0 HG12 B:VAL148 5.0 31.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Tagatose 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-Tagatose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:12.5 occ:1.00 HO3 C:TAG301 1.4 34.4 1.0 O2 C:TAG301 1.9 26.6 1.0 OE2 C:GLU146 2.0 25.7 1.0 OD2 C:ASP179 2.0 24.2 1.0 OE1 C:GLU240 2.1 26.4 1.0 O3 C:TAG301 2.2 28.6 1.0 ND1 C:HIS205 2.2 24.5 1.0 C2 C:TAG301 2.7 32.4 1.0 C3 C:TAG301 2.8 38.7 1.0 CE1 C:HIS205 3.0 26.2 1.0 HE1 C:HIS205 3.0 31.4 1.0 CD C:GLU146 3.1 26.8 1.0 CG C:ASP179 3.2 22.4 1.0 CD C:GLU240 3.2 29.5 1.0 HB2 C:ASP179 3.2 20.0 1.0 H3 C:TAG301 3.3 46.5 1.0 HH12 C:ARG211 3.3 24.2 1.0 CG C:HIS205 3.3 23.4 1.0 OE1 C:GLU146 3.5 25.3 1.0 HH22 C:ARG211 3.5 25.5 1.0 OE2 C:GLU240 3.5 35.7 1.0 HB2 C:HIS205 3.6 22.2 1.0 CB C:ASP179 3.7 16.6 1.0 HE2 C:HIS177 3.8 30.4 1.0 HE2 C:HIS182 3.8 24.4 1.0 HB3 C:HIS205 3.8 22.2 1.0 CB C:HIS205 3.8 18.5 1.0 HD2 C:HIS182 3.9 25.5 1.0 C1 C:TAG301 4.1 31.3 1.0 NH1 C:ARG211 4.1 20.2 1.0 HB3 C:ASP179 4.1 20.0 1.0 NE2 C:HIS205 4.2 22.9 1.0 C4 C:TAG301 4.2 43.0 1.0 OD1 C:ASP179 4.2 21.8 1.0 NH2 C:ARG211 4.3 21.3 1.0 H4 C:TAG301 4.3 51.6 1.0 H11 C:TAG301 4.3 37.6 1.0 NE2 C:HIS182 4.3 20.3 1.0 CD2 C:HIS205 4.4 21.4 1.0 NE2 C:HIS177 4.4 25.3 1.0 CD2 C:HIS182 4.4 21.2 1.0 CG C:GLU146 4.4 23.8 1.0 CG C:GLU240 4.5 22.6 1.0 HG3 C:GLU146 4.6 28.6 1.0 H5 C:TAG301 4.6 61.0 1.0 HG2 C:GLU146 4.6 28.6 1.0 CZ C:ARG211 4.7 22.6 1.0 HB2 C:GLU240 4.7 21.6 1.0 HH11 C:ARG211 4.7 24.2 1.0 HB3 C:GLU240 4.7 21.6 1.0 H12 C:TAG301 4.7 37.6 1.0 HG2 C:GLU240 4.8 27.2 1.0 HE1 C:HIS177 4.8 27.4 1.0 O1 C:TAG301 4.8 34.8 1.0 HO1 C:TAG301 4.8 41.7 1.0 C5 C:TAG301 4.9 50.9 1.0 HE2 C:HIS205 4.9 27.5 1.0 HG12 C:VAL148 4.9 28.0 1.0 CB C:GLU240 4.9 18.0 1.0 CE1 C:HIS177 4.9 22.8 1.0 HH21 C:ARG211 4.9 25.5 1.0 HA C:ASP179 5.0 19.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Tagatose 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-Tagatose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:13.3 occ:1.00 HO3 D:TAG301 1.5 37.9 1.0 O2 D:TAG301 1.9 32.4 1.0 OE2 D:GLU145 2.0 28.4 1.0 OD2 D:ASP178 2.1 24.6 1.0 OE1 D:GLU239 2.1 28.9 1.0 O3 D:TAG301 2.2 31.6 1.0 ND1 D:HIS204 2.2 28.6 1.0 C2 D:TAG301 2.7 36.4 1.0 C3 D:TAG301 2.9 40.2 1.0 CE1 D:HIS204 3.0 31.1 1.0 HE1 D:HIS204 3.0 37.4 1.0 CD D:GLU145 3.1 33.6 1.0 CD D:GLU239 3.2 30.6 1.0 HH12 D:ARG210 3.2 30.9 1.0 CG D:ASP178 3.2 25.1 1.0 HB2 D:ASP178 3.2 24.3 1.0 CG D:HIS204 3.4 26.2 1.0 H3 D:TAG301 3.4 48.3 1.0 OE1 D:GLU145 3.4 32.3 1.0 OE2 D:GLU239 3.5 36.0 1.0 HH22 D:ARG210 3.5 33.3 1.0 HB2 D:HIS204 3.6 24.1 1.0 HE2 D:HIS176 3.7 34.6 1.0 CB D:ASP178 3.7 20.2 1.0 HE2 D:HIS181 3.8 28.6 1.0 HD2 D:HIS181 3.8 31.3 1.0 HB3 D:HIS204 3.8 24.1 1.0 CB D:HIS204 3.9 20.0 1.0 NH1 D:ARG210 4.0 25.8 1.0 C1 D:TAG301 4.1 35.7 1.0 NE2 D:HIS204 4.2 25.9 1.0 HB3 D:ASP178 4.2 24.3 1.0 C4 D:TAG301 4.2 44.8 1.0 OD1 D:ASP178 4.3 25.5 1.0 NH2 D:ARG210 4.3 27.8 1.0 H4 D:TAG301 4.3 53.8 1.0 H11 D:TAG301 4.3 42.9 1.0 NE2 D:HIS176 4.3 28.8 1.0 NE2 D:HIS181 4.3 23.8 1.0 CD2 D:HIS181 4.3 26.1 1.0 CD2 D:HIS204 4.4 28.1 1.0 CG D:GLU145 4.4 28.2 1.0 CG D:GLU239 4.5 28.0 1.0 HG3 D:GLU145 4.5 33.9 1.0 HH11 D:ARG210 4.6 30.9 1.0 CZ D:ARG210 4.6 24.0 1.0 HG2 D:GLU145 4.7 33.9 1.0 HB3 D:GLU239 4.7 26.0 1.0 HB2 D:GLU239 4.7 26.0 1.0 O1 D:TAG301 4.7 39.8 1.0 HG2 D:GLU239 4.7 33.6 1.0 H5 D:TAG301 4.8 68.6 1.0 H12 D:TAG301 4.8 42.9 1.0 HA D:ASP178 4.9 18.4 1.0 C5 D:TAG301 4.9 57.1 1.0 CB D:GLU239 4.9 21.7 1.0 HE2 D:HIS204 4.9 31.1 1.0 O5 D:TAG301 4.9 57.3 1.0 CA D:ASP178 5.0 15.4 1.0 HH21 D:ARG210 5.0 33.3 1.0 HG12 D:VAL147 5.0 32.1 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.