Magnesium in PDB 7ern: Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3

The structure of Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3, PDB code: 7ern 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)	46.84 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.191, 97.953, 160.172, 90, 90, 90
R / Rfree (%)	16 / 21

The binding sites of Magnesium atom in the Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3 (pdb code 7ern). 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 Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3, PDB code: 7ern:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:15.7 occ:1.00 OE2 A:GLU144 2.0 23.4 1.0 OD2 A:ASP177 2.0 28.1 1.0 OE2 A:GLU238 2.1 39.0 1.0 O2 A:FUD301 2.2 34.3 1.0 ND1 A:HIS203 2.2 27.4 1.0 O3 A:FUD301 2.2 43.4 1.0 C2 A:FUD301 2.9 42.5 1.0 C3 A:FUD301 3.0 49.8 1.0 CD A:GLU144 3.1 29.7 1.0 CE1 A:HIS203 3.1 28.3 1.0 CG A:ASP177 3.1 23.0 1.0 CD A:GLU238 3.1 43.2 1.0 CG A:HIS203 3.3 28.0 1.0 OE1 A:GLU144 3.5 30.4 1.0 OE1 A:GLU238 3.5 50.7 1.0 CB A:HIS203 3.6 22.3 1.0 CB A:ASP177 3.6 21.6 1.0 NH2 A:ARG209 4.1 32.9 1.0 NH1 A:ARG209 4.1 27.9 1.0 OD1 A:ASP177 4.2 29.3 1.0 NE2 A:HIS203 4.2 27.2 1.0 CD2 A:HIS203 4.3 24.0 1.0 C1 A:FUD301 4.4 35.6 1.0 C4 A:FUD301 4.4 51.9 1.0 CG A:GLU144 4.4 25.0 1.0 CG A:GLU238 4.4 31.6 1.0 CD2 A:HIS180 4.4 28.4 1.0 NE2 A:HIS180 4.4 29.2 1.0 CZ A:ARG209 4.6 33.4 1.0 O4 A:FUD301 4.6 56.0 1.0 O1 A:FUD301 4.6 34.4 1.0 NE2 A:HIS175 4.8 26.1 1.0 CB A:GLU238 4.9 32.1 1.0 CA A:ASP177 4.9 23.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:18.1 occ:1.00 OE2 B:GLU144 2.0 33.5 1.0 OE2 B:GLU238 2.1 37.2 1.0 OD2 B:ASP177 2.1 27.7 1.0 O3 B:FUD301 2.1 34.5 1.0 ND1 B:HIS203 2.2 25.0 1.0 O2 B:FUD301 2.2 42.6 1.0 C2 B:FUD301 3.0 51.1 1.0 C3 B:FUD301 3.0 52.8 1.0 CE1 B:HIS203 3.0 30.3 1.0 CD B:GLU144 3.1 35.8 1.0 CD B:GLU238 3.2 42.2 1.0 CG B:ASP177 3.2 31.0 1.0 CG B:HIS203 3.2 25.9 1.0 OE1 B:GLU144 3.5 33.0 1.0 OE1 B:GLU238 3.6 48.0 1.0 CB B:HIS203 3.6 24.6 1.0 CB B:ASP177 3.8 32.0 1.0 NH2 B:ARG209 4.1 29.9 1.0 NE2 B:HIS203 4.2 27.2 1.0 NH1 B:ARG209 4.2 27.2 1.0 OD1 B:ASP177 4.3 27.2 1.0 CD2 B:HIS203 4.3 23.4 1.0 C4 B:FUD301 4.3 63.9 1.0 C1 B:FUD301 4.4 46.2 1.0 CG B:GLU144 4.4 34.8 1.0 CG B:GLU238 4.4 35.5 1.0 O4 B:FUD301 4.5 69.2 1.0 NE2 B:HIS180 4.5 26.8 1.0 CD2 B:HIS180 4.5 27.5 1.0 CZ B:ARG209 4.6 31.1 1.0 NE2 B:HIS175 4.7 27.0 1.0 CB B:GLU238 4.9 30.5 1.0 O1 B:FUD301 4.9 41.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:19.4 occ:1.00 OE2 C:GLU144 2.0 30.8 1.0 OD2 C:ASP177 2.0 28.5 1.0 OE2 C:GLU238 2.1 36.8 1.0 O3 C:FUD301 2.1 38.9 1.0 ND1 C:HIS203 2.1 31.9 1.0 O2 C:FUD301 2.3 48.0 1.0 C2 C:FUD301 3.0 50.1 1.0 C3 C:FUD301 3.0 52.2 1.0 CD C:GLU144 3.0 35.9 1.0 CE1 C:HIS203 3.1 33.0 1.0 CG C:ASP177 3.1 34.0 1.0 CD C:GLU238 3.2 41.9 1.0 CG C:HIS203 3.2 30.8 1.0 OE1 C:GLU144 3.3 38.1 1.0 CB C:HIS203 3.5 28.3 1.0 OE1 C:GLU238 3.6 51.8 1.0 CB C:ASP177 3.7 31.7 1.0 NH2 C:ARG209 4.2 32.1 1.0 OD1 C:ASP177 4.2 32.7 1.0 NH1 C:ARG209 4.2 38.0 1.0 NE2 C:HIS203 4.2 35.7 1.0 CD2 C:HIS203 4.3 31.7 1.0 C4 C:FUD301 4.3 58.5 1.0 CG C:GLU144 4.4 32.4 1.0 C1 C:FUD301 4.4 42.1 1.0 CG C:GLU238 4.5 31.5 1.0 CD2 C:HIS180 4.5 31.1 1.0 O4 C:FUD301 4.5 62.6 1.0 NE2 C:HIS180 4.6 32.4 1.0 CZ C:ARG209 4.6 35.7 1.0 NE2 C:HIS175 4.7 31.7 1.0 O1 C:FUD301 4.9 39.9 1.0 CB C:GLU238 4.9 30.7 1.0 CA C:ASP177 4.9 27.9 1.0 C5 C:FUD301 5.0 62.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of D-Allulose 3-Epimerase with D-Fructose From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:19.2 occ:1.00 OE2 D:GLU144 2.0 30.9 1.0 OD2 D:ASP177 2.0 29.5 1.0 ND1 D:HIS203 2.2 31.9 1.0 OE2 D:GLU238 2.2 43.6 1.0 O2 D:FUD301 2.2 43.6 1.0 O3 D:FUD301 2.3 49.9 1.0 C2 D:FUD301 2.9 48.3 1.0 C3 D:FUD301 2.9 55.6 1.0 CD D:GLU144 3.0 31.4 1.0 CE1 D:HIS203 3.0 36.1 1.0 CG D:ASP177 3.1 29.2 1.0 CD D:GLU238 3.2 43.3 1.0 CG D:HIS203 3.2 34.8 1.0 OE1 D:GLU144 3.3 28.1 1.0 OE1 D:GLU238 3.6 48.8 1.0 CB D:HIS203 3.6 31.4 1.0 CB D:ASP177 3.7 22.7 1.0 NH2 D:ARG209 4.1 34.9 1.0 OD1 D:ASP177 4.2 32.5 1.0 NH1 D:ARG209 4.2 30.4 1.0 NE2 D:HIS203 4.2 34.9 1.0 CD2 D:HIS203 4.3 30.7 1.0 CG D:GLU144 4.3 25.6 1.0 C1 D:FUD301 4.3 43.5 1.0 C4 D:FUD301 4.4 69.7 1.0 CD2 D:HIS180 4.5 28.9 1.0 NE2 D:HIS180 4.5 27.1 1.0 CG D:GLU238 4.6 31.2 1.0 CZ D:ARG209 4.6 33.8 1.0 NE2 D:HIS175 4.8 37.6 1.0 O4 D:FUD301 4.8 72.2 1.0 O1 D:FUD301 4.8 43.2 1.0 CB D:GLU238 4.9 28.8 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 Agrobacterium Sp. SUL3 To Be Published.