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

The structure of Crystal Structure of D-Allulose 3-Epimerase with D-Allulose From Agrobacterium Sp. SUL3, PDB code: 7ero 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)	48.76 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.173, 97.517, 159.922, 90, 90, 90
R / Rfree (%)	18 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of D-Allulose 3-Epimerase with D-Allulose From Agrobacterium Sp. SUL3 (pdb code 7ero). 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-Allulose From Agrobacterium Sp. SUL3, PDB code: 7ero:
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-Allulose 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-Allulose From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:15.2 occ:1.00 OE2 A:GLU144 2.0 23.9 1.0 OD2 A:ASP177 2.0 22.4 1.0 O2 A:PSJ301 2.1 31.3 1.0 OE2 A:GLU238 2.1 24.1 1.0 ND1 A:HIS203 2.2 21.2 1.0 O3 A:PSJ301 2.3 32.2 1.0 C2 A:PSJ301 2.9 34.4 1.0 CD A:GLU144 3.0 28.6 1.0 CE1 A:HIS203 3.1 25.4 1.0 CG A:ASP177 3.1 23.6 1.0 C3 A:PSJ301 3.2 38.1 1.0 CD A:GLU238 3.2 30.9 1.0 CG A:HIS203 3.3 24.4 1.0 OE1 A:GLU144 3.3 30.0 1.0 OE1 A:GLU238 3.6 37.1 1.0 CB A:HIS203 3.7 21.1 1.0 CB A:ASP177 3.7 23.0 1.0 C4 A:PSJ301 4.0 40.0 1.0 NH2 A:ARG209 4.0 28.0 1.0 OD1 A:ASP177 4.2 28.2 1.0 NH1 A:ARG209 4.2 25.4 1.0 NE2 A:HIS203 4.2 22.5 1.0 CD2 A:HIS203 4.4 20.9 1.0 CD2 A:HIS180 4.4 25.6 1.0 NE2 A:HIS180 4.4 25.7 1.0 CG A:GLU144 4.4 21.8 1.0 C1 A:PSJ301 4.4 31.9 1.0 CG A:GLU238 4.5 26.1 1.0 CZ A:ARG209 4.6 31.6 1.0 O4 A:PSJ301 4.7 45.5 1.0 NE2 A:HIS175 4.8 24.7 1.0 O1 A:PSJ301 4.9 33.5 1.0 CB A:GLU238 4.9 25.1 1.0 CA A:ASP177 4.9 22.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Allulose 3-Epimerase with D-Allulose 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-Allulose From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:19.9 occ:1.00 O2 B:PSJ301 2.0 35.2 1.0 OE2 B:GLU144 2.0 30.4 1.0 OD2 B:ASP177 2.1 26.0 1.0 O3 B:PSJ301 2.1 36.2 1.0 ND1 B:HIS203 2.1 31.6 1.0 OE2 B:GLU238 2.2 29.5 1.0 C2 B:PSJ301 2.8 38.5 1.0 C3 B:PSJ301 3.0 39.1 1.0 CD B:GLU144 3.0 33.6 1.0 CE1 B:HIS203 3.0 34.2 1.0 CG B:ASP177 3.2 27.7 1.0 CG B:HIS203 3.2 31.5 1.0 CD B:GLU238 3.3 30.9 1.0 OE1 B:GLU144 3.3 33.3 1.0 CB B:HIS203 3.6 28.0 1.0 OE1 B:GLU238 3.7 40.0 1.0 CB B:ASP177 3.8 26.5 1.0 NH2 B:ARG209 4.2 30.4 1.0 NE2 B:HIS203 4.2 35.1 1.0 NH1 B:ARG209 4.2 32.3 1.0 OD1 B:ASP177 4.2 25.5 1.0 C4 B:PSJ301 4.2 43.2 1.0 CD2 B:HIS203 4.3 31.3 1.0 C1 B:PSJ301 4.3 38.0 1.0 CG B:GLU144 4.4 32.5 1.0 C5 B:PSJ301 4.4 45.6 1.0 CG B:GLU238 4.6 28.3 1.0 CD2 B:HIS180 4.6 27.3 1.0 CZ B:ARG209 4.7 29.7 1.0 NE2 B:HIS180 4.7 30.1 1.0 O1 B:PSJ301 4.8 34.9 1.0 NE2 B:HIS175 4.8 30.8 1.0 CB B:GLU238 4.9 29.8 1.0 O4 B:PSJ301 4.9 47.2 1.0 C6 B:PSJ301 5.0 48.6 1.0 CA B:ASP177 5.0 27.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Allulose 3-Epimerase with D-Allulose 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-Allulose From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:19.3 occ:1.00 OE2 C:GLU144 1.9 29.3 1.0 OD2 C:ASP177 2.0 24.1 1.0 O2 C:PSJ301 2.1 33.9 1.0 OE2 C:GLU238 2.1 34.9 1.0 ND1 C:HIS203 2.2 27.4 1.0 O3 C:PSJ301 2.3 36.3 1.0 C2 C:PSJ301 2.9 36.1 1.0 CD C:GLU144 3.0 30.8 1.0 C3 C:PSJ301 3.1 37.7 1.0 CE1 C:HIS203 3.1 29.0 1.0 CG C:ASP177 3.1 24.1 1.0 CD C:GLU238 3.2 30.7 1.0 CG C:HIS203 3.3 29.3 1.0 OE1 C:GLU144 3.4 29.1 1.0 CB C:HIS203 3.6 26.2 1.0 CB C:ASP177 3.6 20.8 1.0 OE1 C:GLU238 3.7 34.1 1.0 NH1 C:ARG209 4.1 25.6 1.0 NH2 C:ARG209 4.1 27.2 1.0 OD1 C:ASP177 4.2 24.4 1.0 NE2 C:HIS203 4.3 30.2 1.0 CG C:GLU144 4.3 29.5 1.0 CD2 C:HIS203 4.4 27.6 1.0 CD2 C:HIS180 4.4 26.1 1.0 NE2 C:HIS180 4.4 24.1 1.0 C1 C:PSJ301 4.4 34.7 1.0 C4 C:PSJ301 4.5 48.5 1.0 CG C:GLU238 4.5 29.7 1.0 CZ C:ARG209 4.6 28.9 1.0 C5 C:PSJ301 4.8 48.8 1.0 O1 C:PSJ301 4.8 32.2 1.0 NE2 C:HIS175 4.9 28.9 1.0 CB C:GLU238 4.9 26.5 1.0 CA C:ASP177 5.0 23.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Allulose 3-Epimerase with D-Allulose 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-Allulose From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:19.1 occ:1.00 OE2 D:GLU144 1.9 29.8 1.0 OD2 D:ASP177 2.1 21.9 1.0 OE2 D:GLU238 2.1 28.9 1.0 ND1 D:HIS203 2.2 26.0 1.0 O3 D:PSJ301 2.2 31.4 1.0 O2 D:PSJ301 2.2 34.4 1.0 C2 D:PSJ301 3.0 36.8 1.0 CD D:GLU144 3.0 32.8 1.0 CE1 D:HIS203 3.0 29.7 1.0 C3 D:PSJ301 3.1 37.6 1.0 CG D:ASP177 3.2 27.2 1.0 CD D:GLU238 3.2 31.8 1.0 CG D:HIS203 3.3 27.1 1.0 OE1 D:GLU144 3.4 34.5 1.0 CB D:ASP177 3.7 27.4 1.0 OE1 D:GLU238 3.7 38.5 1.0 CB D:HIS203 3.7 23.8 1.0 NH2 D:ARG209 4.1 30.4 1.0 NH1 D:ARG209 4.2 22.9 1.0 NE2 D:HIS203 4.2 28.4 1.0 OD1 D:ASP177 4.2 25.0 1.0 CG D:GLU144 4.3 29.8 1.0 CD2 D:HIS203 4.4 26.3 1.0 C4 D:PSJ301 4.4 44.2 1.0 NE2 D:HIS180 4.4 24.4 1.0 C1 D:PSJ301 4.4 35.4 1.0 CD2 D:HIS180 4.4 28.0 1.0 CG D:GLU238 4.6 30.4 1.0 CZ D:ARG209 4.7 27.7 1.0 NE2 D:HIS175 4.7 27.6 1.0 C5 D:PSJ301 4.7 45.4 1.0 O1 D:PSJ301 4.8 35.2 1.0 CB D:GLU238 4.9 25.6 1.0 CA D:ASP177 4.9 22.8 1.0 O4 D:PSJ301 5.0 42.4 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.