Magnesium in PDB 7dz5: Crystal Structures of D-Allulose 3-Epimerase with D-Sorbose From Sinorhizobium Fredii

The structure of Crystal Structures of D-Allulose 3-Epimerase with D-Sorbose From Sinorhizobium Fredii, PDB code: 7dz5 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)	42.61 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.143, 87.934, 128.928, 90, 99.58, 90
R / Rfree (%)	15.3 / 17.8

The binding sites of Magnesium atom in the Crystal Structures of D-Allulose 3-Epimerase with D-Sorbose From Sinorhizobium Fredii (pdb code 7dz5). 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-Sorbose From Sinorhizobium Fredii, PDB code: 7dz5:
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-Sorbose 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-Sorbose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:9.3 occ:1.00 OD2 A:ASP179 2.0 12.7 1.0 OE2 A:GLU146 2.1 14.2 1.0 O2 A:SDD301 2.2 23.0 1.0 ND1 A:HIS205 2.2 14.2 1.0 OE1 A:GLU240 2.3 23.0 1.0 O3 A:SDD301 2.4 24.2 1.0 HO3 A:SDD301 3.0 29.1 1.0 C2 A:SDD301 3.0 22.2 1.0 CE1 A:HIS205 3.1 16.7 1.0 CD A:GLU146 3.1 19.3 1.0 HE1 A:HIS205 3.1 20.1 1.0 CG A:ASP179 3.2 13.8 1.0 C3 A:SDD301 3.2 27.1 1.0 HB2 A:ASP179 3.2 16.9 1.0 CD A:GLU240 3.3 20.8 1.0 CG A:HIS205 3.3 13.8 1.0 HH22 A:ARG211 3.4 21.9 1.0 HH12 A:ARG211 3.4 18.8 1.0 OE1 A:GLU146 3.5 20.1 1.0 HB2 A:HIS205 3.5 17.1 1.0 OE2 A:GLU240 3.6 25.6 1.0 CB A:ASP179 3.7 14.1 1.0 HB3 A:HIS205 3.7 17.1 1.0 H3 A:SDD301 3.8 32.5 1.0 CB A:HIS205 3.8 14.2 1.0 HD2 A:HIS182 3.9 13.7 1.0 HE2 A:HIS177 3.9 21.6 1.0 HE2 A:HIS182 4.0 16.2 1.0 HB3 A:ASP179 4.1 16.9 1.0 NH2 A:ARG211 4.2 18.3 1.0 NH1 A:ARG211 4.2 15.6 1.0 OD1 A:ASP179 4.2 17.9 1.0 NE2 A:HIS205 4.3 16.8 1.0 O4 A:SDD301 4.3 36.4 1.0 CD2 A:HIS205 4.4 18.8 1.0 C4 A:SDD301 4.4 32.5 1.0 C1 A:SDD301 4.4 25.6 1.0 CG A:GLU146 4.5 13.1 1.0 CD2 A:HIS182 4.5 11.4 1.0 NE2 A:HIS182 4.5 13.5 1.0 NE2 A:HIS177 4.5 18.0 1.0 HG3 A:GLU146 4.6 15.8 1.0 CG A:GLU240 4.6 20.5 1.0 CZ A:ARG211 4.7 14.8 1.0 HG2 A:GLU146 4.7 15.8 1.0 HH21 A:ARG211 4.8 21.9 1.0 HH11 A:ARG211 4.8 18.8 1.0 HB3 A:GLU240 4.8 22.4 1.0 O1 A:SDD301 4.9 24.0 1.0 HB2 A:GLU240 4.9 22.4 1.0 HO4 A:SDD301 4.9 43.7 1.0 HA A:ASP179 4.9 13.6 1.0 HG2 A:GLU240 4.9 24.6 1.0 H11 A:SDD301 4.9 30.7 1.0 HG12 A:VAL148 5.0 18.7 1.0 CA A:ASP179 5.0 11.3 1.0 HE2 A:HIS205 5.0 20.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Sorbose 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-Sorbose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:10.5 occ:1.00 OD2 B:ASP179 2.1 15.1 1.0 OE2 B:GLU146 2.1 17.4 1.0 O2 B:SDD301 2.1 23.9 1.0 ND1 B:HIS205 2.2 15.1 1.0 OE1 B:GLU240 2.3 21.7 1.0 O3 B:SDD301 2.4 24.7 1.0 HO3 B:SDD301 2.9 29.7 1.0 C2 B:SDD301 3.0 29.6 1.0 CE1 B:HIS205 3.0 18.6 1.0 HE1 B:HIS205 3.0 22.3 1.0 CD B:GLU146 3.1 19.3 1.0 CG B:ASP179 3.2 13.8 1.0 C3 B:SDD301 3.2 30.8 1.0 HB2 B:ASP179 3.2 14.8 1.0 CG B:HIS205 3.3 11.9 1.0 CD B:GLU240 3.3 22.7 1.0 HH22 B:ARG211 3.4 23.1 1.0 HH12 B:ARG211 3.4 20.2 1.0 OE1 B:GLU146 3.5 21.1 1.0 HB2 B:HIS205 3.5 13.7 1.0 OE2 B:GLU240 3.6 26.4 1.0 CB B:ASP179 3.7 12.4 1.0 HB3 B:HIS205 3.7 13.7 1.0 CB B:HIS205 3.8 11.4 1.0 H3 B:SDD301 3.8 37.0 1.0 HE2 B:HIS177 3.9 19.2 1.0 HD2 B:HIS182 4.0 16.1 1.0 HE2 B:HIS182 4.0 18.0 1.0 HB3 B:ASP179 4.1 14.8 1.0 NH2 B:ARG211 4.2 19.2 1.0 NE2 B:HIS205 4.2 16.0 1.0 OD1 B:ASP179 4.2 16.5 1.0 NH1 B:ARG211 4.2 16.8 1.0 O4 B:SDD301 4.3 38.1 1.0 CD2 B:HIS205 4.3 17.2 1.0 C4 B:SDD301 4.4 38.3 1.0 C1 B:SDD301 4.4 26.4 1.0 CG B:GLU146 4.5 15.7 1.0 CD2 B:HIS182 4.5 13.4 1.0 NE2 B:HIS177 4.5 16.0 1.0 NE2 B:HIS182 4.5 15.0 1.0 HG3 B:GLU146 4.6 18.9 1.0 HG2 B:GLU146 4.7 18.9 1.0 CG B:GLU240 4.7 22.2 1.0 CZ B:ARG211 4.7 17.6 1.0 HH21 B:ARG211 4.8 23.1 1.0 HO4 B:SDD301 4.8 45.7 1.0 HB3 B:GLU240 4.8 23.1 1.0 HB2 B:GLU240 4.8 23.1 1.0 O1 B:SDD301 4.9 27.0 1.0 HH11 B:ARG211 4.9 20.2 1.0 HE2 B:HIS205 4.9 19.2 1.0 H12 B:SDD301 4.9 31.7 1.0 HA B:ASP179 4.9 13.2 1.0 HG12 B:VAL148 5.0 21.3 1.0 HG2 B:GLU240 5.0 26.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Sorbose 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-Sorbose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:9.3 occ:1.00 HO3 C:SDD301 1.7 22.1 1.0 OD2 C:ASP179 2.0 14.2 1.0 O2 C:SDD301 2.0 21.8 1.0 OE1 C:GLU240 2.1 18.1 1.0 ND1 C:HIS205 2.1 16.1 1.0 OE2 C:GLU146 2.2 16.1 1.0 O3 C:SDD301 2.4 18.4 1.0 C2 C:SDD301 2.8 19.3 1.0 CE1 C:HIS205 2.9 18.2 1.0 HE1 C:HIS205 3.0 21.9 1.0 C3 C:SDD301 3.0 26.6 1.0 CD C:GLU240 3.1 22.3 1.0 CG C:ASP179 3.1 13.3 1.0 CD C:GLU146 3.2 17.5 1.0 HB2 C:ASP179 3.2 16.4 1.0 CG C:HIS205 3.2 15.3 1.0 HH12 C:ARG211 3.3 18.4 1.0 H3 C:SDD301 3.4 31.9 1.0 OE1 C:GLU146 3.5 19.7 1.0 OE2 C:GLU240 3.5 27.5 1.0 HB2 C:HIS205 3.5 15.2 1.0 HH22 C:ARG211 3.6 21.2 1.0 CB C:ASP179 3.7 13.7 1.0 HB3 C:HIS205 3.7 15.2 1.0 CB C:HIS205 3.7 12.6 1.0 HE2 C:HIS177 3.8 20.4 1.0 HD2 C:HIS182 3.9 15.6 1.0 HE2 C:HIS182 4.0 17.3 1.0 NH1 C:ARG211 4.1 15.3 1.0 NE2 C:HIS205 4.1 16.3 1.0 HB3 C:ASP179 4.1 16.4 1.0 OD1 C:ASP179 4.2 17.7 1.0 CD2 C:HIS205 4.3 17.8 1.0 C1 C:SDD301 4.3 20.9 1.0 NH2 C:ARG211 4.3 17.7 1.0 NE2 C:HIS177 4.4 17.0 1.0 C4 C:SDD301 4.4 34.7 1.0 CD2 C:HIS182 4.5 13.0 1.0 CG C:GLU240 4.5 16.6 1.0 CG C:GLU146 4.5 16.9 1.0 NE2 C:HIS182 4.5 14.4 1.0 HB2 C:GLU240 4.6 17.3 1.0 HB3 C:GLU240 4.6 17.3 1.0 O4 C:SDD301 4.6 44.5 1.0 HH11 C:ARG211 4.7 18.4 1.0 HG3 C:GLU146 4.7 20.3 1.0 CZ C:ARG211 4.7 16.1 1.0 HG2 C:GLU146 4.7 20.3 1.0 H12 C:SDD301 4.8 25.2 1.0 HG2 C:GLU240 4.8 19.9 1.0 HO4 C:SDD301 4.8 53.5 1.0 CB C:GLU240 4.8 14.4 1.0 O1 C:SDD301 4.8 20.6 1.0 HE2 C:HIS205 4.8 19.6 1.0 HE1 C:HIS177 4.9 23.4 1.0 H11 C:SDD301 4.9 25.2 1.0 HA C:ASP179 4.9 14.9 1.0 CE1 C:HIS177 5.0 19.5 1.0 HG12 C:VAL148 5.0 20.1 1.0 CA C:ASP179 5.0 12.4 1.0 H4 C:SDD301 5.0 41.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase with D-Sorbose 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-Sorbose From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:8.2 occ:1.00 OD2 D:ASP179 2.0 13.7 1.0 OE2 D:GLU146 2.0 14.2 1.0 O2 D:SDD302 2.1 21.2 1.0 OE1 D:GLU240 2.1 16.7 1.0 ND1 D:HIS205 2.2 14.2 1.0 O3 D:SDD302 2.3 17.5 1.0 HO3 D:SDD302 2.7 21.1 1.0 C2 D:SDD302 2.9 18.6 1.0 CE1 D:HIS205 3.0 15.8 1.0 HE1 D:HIS205 3.1 18.9 1.0 CD D:GLU146 3.1 15.8 1.0 CG D:ASP179 3.1 13.6 1.0 CD D:GLU240 3.1 19.5 1.0 HB2 D:ASP179 3.2 13.0 1.0 C3 D:SDD302 3.2 23.4 1.0 HH12 D:ARG211 3.3 17.1 1.0 CG D:HIS205 3.3 14.4 1.0 OE1 D:GLU146 3.5 17.1 1.0 OE2 D:GLU240 3.5 30.8 1.0 HH22 D:ARG211 3.5 15.9 1.0 HB2 D:HIS205 3.5 12.7 1.0 CB D:ASP179 3.6 10.8 1.0 HB3 D:HIS205 3.8 12.7 1.0 CB D:HIS205 3.8 10.6 1.0 H3 D:SDD302 3.8 28.1 1.0 HE2 D:HIS177 3.8 18.8 1.0 HD2 D:HIS182 3.8 16.8 1.0 HE2 D:HIS182 4.0 14.8 1.0 HB3 D:ASP179 4.1 13.0 1.0 NH1 D:ARG211 4.1 14.2 1.0 NE2 D:HIS205 4.2 15.8 1.0 OD1 D:ASP179 4.2 14.7 1.0 NH2 D:ARG211 4.3 13.2 1.0 CD2 D:HIS205 4.3 17.9 1.0 C1 D:SDD302 4.4 19.8 1.0 NE2 D:HIS177 4.4 15.6 1.0 CD2 D:HIS182 4.4 14.0 1.0 CG D:GLU146 4.5 11.8 1.0 NE2 D:HIS182 4.5 12.3 1.0 CG D:GLU240 4.5 12.9 1.0 C4 D:SDD302 4.5 34.5 1.0 O4 D:SDD302 4.5 40.2 1.0 HG3 D:GLU146 4.6 14.1 1.0 HB2 D:GLU240 4.6 14.8 1.0 HB3 D:GLU240 4.6 14.8 1.0 CZ D:ARG211 4.7 15.4 1.0 HH11 D:ARG211 4.7 17.1 1.0 HG2 D:GLU146 4.7 14.1 1.0 HO5 D:SDD302 4.7 51.4 1.0 O1 D:SDD302 4.7 16.9 1.0 HG2 D:GLU240 4.8 15.5 1.0 CB D:GLU240 4.8 12.3 1.0 HE1 D:HIS177 4.9 17.1 1.0 H12 D:SDD302 4.9 23.8 1.0 HG12 D:VAL148 4.9 16.6 1.0 HE2 D:HIS205 4.9 19.0 1.0 HA D:ASP179 4.9 13.3 1.0 O5 D:SDD302 4.9 42.8 1.0 HH21 D:ARG211 4.9 15.9 1.0 CE1 D:HIS177 4.9 14.2 1.0 CA D:ASP179 5.0 11.1 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.