Magnesium in PDB 7dz2: Crystal Structures of D-Allulose 3-Epimerase From Sinorhizobium Fredii

The structure of Crystal Structures of D-Allulose 3-Epimerase From Sinorhizobium Fredii, PDB code: 7dz2 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)	32.65 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.973, 88.297, 128.695, 90, 99.29, 90
R / Rfree (%)	16.9 / 18.8

The binding sites of Magnesium atom in the Crystal Structures of D-Allulose 3-Epimerase From Sinorhizobium Fredii (pdb code 7dz2). 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 From Sinorhizobium Fredii, PDB code: 7dz2:
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 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 From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:12.7 occ:1.00 O A:HOH499 1.9 30.2 1.0 OD2 A:ASP179 2.1 16.3 1.0 OE2 A:GLU146 2.2 20.0 1.0 ND1 A:HIS205 2.2 16.1 1.0 O A:HOH575 2.3 30.4 1.0 OE1 A:GLU240 2.4 23.9 1.0 CE1 A:HIS205 3.0 16.1 1.0 CG A:ASP179 3.2 17.0 1.0 CD A:GLU146 3.2 22.3 1.0 CG A:HIS205 3.3 16.3 1.0 CD A:GLU240 3.3 21.9 1.0 OE1 A:GLU146 3.5 24.4 1.0 OE2 A:GLU240 3.6 23.6 1.0 CB A:ASP179 3.7 14.7 1.0 CB A:HIS205 3.8 14.2 1.0 NH2 A:ARG211 4.0 21.5 1.0 NH1 A:ARG211 4.1 19.9 1.0 NE2 A:HIS205 4.2 16.5 1.0 OD1 A:ASP179 4.2 19.4 1.0 CD2 A:HIS205 4.4 17.1 1.0 CZ A:ARG211 4.5 18.5 1.0 CD2 A:HIS182 4.5 14.1 1.0 CG A:GLU146 4.5 16.1 1.0 NE2 A:HIS182 4.5 15.0 1.0 NE2 A:HIS177 4.6 18.2 1.0 O A:HOH450 4.7 28.0 1.0 CG A:GLU240 4.7 20.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase 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 From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:17.3 occ:1.00 O B:HOH474 1.9 32.2 1.0 OD2 B:ASP179 2.1 21.9 1.0 OE2 B:GLU146 2.2 27.5 1.0 ND1 B:HIS205 2.2 22.6 1.0 O B:HOH567 2.3 36.6 1.0 OE1 B:GLU240 2.3 27.7 1.0 CE1 B:HIS205 3.0 22.9 1.0 CG B:ASP179 3.2 19.5 1.0 CD B:GLU146 3.2 29.6 1.0 CG B:HIS205 3.3 19.2 1.0 CD B:GLU240 3.3 25.8 1.0 OE1 B:GLU146 3.6 29.6 1.0 OE2 B:GLU240 3.6 29.5 1.0 CB B:ASP179 3.7 17.0 1.0 CB B:HIS205 3.8 17.1 1.0 NH2 B:ARG211 3.9 25.9 1.0 NH1 B:ARG211 4.1 23.1 1.0 NE2 B:HIS205 4.1 19.5 1.0 OD1 B:ASP179 4.3 21.3 1.0 CD2 B:HIS205 4.3 20.3 1.0 NE2 B:HIS182 4.5 19.7 1.0 CZ B:ARG211 4.5 22.8 1.0 CD2 B:HIS182 4.5 17.8 1.0 CG B:GLU146 4.6 23.8 1.0 NE2 B:HIS177 4.6 22.0 1.0 O B:HOH469 4.7 31.8 1.0 CG B:GLU240 4.7 24.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase 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 From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:12.5 occ:1.00 O C:HOH551 1.9 26.1 1.0 OE2 C:GLU146 2.1 18.1 1.0 OD2 C:ASP179 2.1 16.5 1.0 ND1 C:HIS205 2.2 19.3 1.0 OE1 C:GLU240 2.2 23.8 1.0 O C:HOH425 2.4 26.9 1.0 CE1 C:HIS205 3.0 16.6 1.0 CD C:GLU146 3.1 20.6 1.0 CG C:ASP179 3.2 15.9 1.0 CD C:GLU240 3.3 22.1 1.0 CG C:HIS205 3.4 15.8 1.0 OE1 C:GLU146 3.5 22.5 1.0 OE2 C:GLU240 3.6 22.9 1.0 CB C:ASP179 3.8 12.9 1.0 CB C:HIS205 3.9 14.7 1.0 NH1 C:ARG211 4.1 16.4 1.0 NE2 C:HIS205 4.2 18.1 1.0 NH2 C:ARG211 4.2 18.3 1.0 OD1 C:ASP179 4.3 16.8 1.0 NE2 C:HIS182 4.3 14.4 1.0 CD2 C:HIS182 4.3 15.9 1.0 NE2 C:HIS177 4.3 17.7 1.0 CD2 C:HIS205 4.4 17.9 1.0 CG C:GLU146 4.5 16.1 1.0 CG C:GLU240 4.6 18.8 1.0 CZ C:ARG211 4.6 17.0 1.0 CE1 C:HIS177 4.9 17.8 1.0 CB C:GLU240 5.0 17.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structures of D-Allulose 3-Epimerase 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 From Sinorhizobium Fredii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:17.1 occ:1.00 O D:HOH484 2.0 30.0 1.0 OD2 D:ASP179 2.1 20.0 1.0 OE2 D:GLU146 2.1 22.3 1.0 ND1 D:HIS205 2.2 25.0 1.0 OE1 D:GLU240 2.2 28.0 1.0 O D:HOH482 2.3 29.3 1.0 CE1 D:HIS205 3.0 20.5 1.0 CD D:GLU146 3.1 26.1 1.0 CG D:ASP179 3.2 20.4 1.0 CD D:GLU240 3.2 27.9 1.0 CG D:HIS205 3.4 20.5 1.0 OE1 D:GLU146 3.5 27.3 1.0 OE2 D:GLU240 3.6 27.4 1.0 CB D:ASP179 3.8 18.3 1.0 CB D:HIS205 3.9 17.8 1.0 NH1 D:ARG211 4.0 20.6 1.0 NE2 D:HIS205 4.2 22.8 1.0 NH2 D:ARG211 4.2 22.5 1.0 NE2 D:HIS182 4.3 18.5 1.0 OD1 D:ASP179 4.3 22.4 1.0 CD2 D:HIS182 4.3 21.9 1.0 CD2 D:HIS205 4.4 21.2 1.0 NE2 D:HIS177 4.4 21.6 1.0 CG D:GLU146 4.5 22.4 1.0 CG D:GLU240 4.6 24.0 1.0 CZ D:ARG211 4.6 23.3 1.0 CE1 D:HIS177 4.9 23.2 1.0 CB D:GLU240 5.0 22.1 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.