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

The structure of Crystal Structure of D-Allulose 3-Epimerase From Agrobacterium Sp. SUL3, PDB code: 7erm 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)	47.19 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.381, 98.711, 161.003, 90, 90, 90
R / Rfree (%)	17.9 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of D-Allulose 3-Epimerase From Agrobacterium Sp. SUL3 (pdb code 7erm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of D-Allulose 3-Epimerase From Agrobacterium Sp. SUL3, PDB code: 7erm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of D-Allulose 3-Epimerase 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 From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:11.5 occ:1.00 OD2 A:ASP177 2.0 34.9 1.0 OE2 A:GLU144 2.0 29.2 1.0 ND1 A:HIS203 2.0 30.8 1.0 OE1 A:GLU238 2.2 38.1 1.0 O A:HOH435 2.4 61.1 1.0 CE1 A:HIS203 2.8 34.5 1.0 CD A:GLU144 3.0 34.0 1.0 CG A:ASP177 3.1 32.4 1.0 CG A:HIS203 3.1 33.6 1.0 CD A:GLU238 3.2 42.2 1.0 OE1 A:GLU144 3.4 37.2 1.0 CB A:HIS203 3.6 28.2 1.0 OE2 A:GLU238 3.6 51.1 1.0 CB A:ASP177 3.7 24.4 1.0 NE2 A:HIS203 4.0 30.0 1.0 OD1 A:ASP177 4.1 35.9 1.0 CD2 A:HIS203 4.2 28.2 1.0 NH2 A:ARG209 4.3 40.1 1.0 NH1 A:ARG209 4.3 27.3 1.0 CG A:GLU144 4.4 30.7 1.0 O A:HOH441 4.4 38.3 1.0 CG A:GLU238 4.6 36.4 1.0 CD2 A:HIS180 4.6 29.4 1.0 NE2 A:HIS180 4.7 32.6 1.0 NE2 A:HIS175 4.8 33.5 1.0 CZ A:ARG209 4.8 40.5 1.0 CA A:ASP177 4.9 27.5 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of D-Allulose 3-Epimerase 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 From Agrobacterium Sp. SUL3 within 5.0Å range:

Magnesium binding site 3 out of 5 in the Crystal Structure of D-Allulose 3-Epimerase 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 From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:12.0 occ:1.00 OE2 B:GLU144 2.0 35.2 1.0 OD2 B:ASP177 2.0 33.5 1.0 OE1 B:GLU238 2.0 40.1 1.0 ND1 B:HIS203 2.1 36.8 1.0 CE1 B:HIS203 2.9 39.3 1.0 CD B:GLU144 3.0 40.1 1.0 CD B:GLU238 3.0 46.5 1.0 CG B:ASP177 3.1 41.4 1.0 CG B:HIS203 3.1 35.3 1.0 OE2 B:GLU238 3.3 51.6 1.0 O B:HOH418 3.3 69.9 1.0 OE1 B:GLU144 3.4 42.2 1.0 CB B:HIS203 3.6 33.1 1.0 CB B:ASP177 3.8 40.0 1.0 NE2 B:HIS203 4.0 32.4 1.0 OD1 B:ASP177 4.2 35.2 1.0 CD2 B:HIS203 4.2 34.6 1.0 NH2 B:ARG209 4.2 40.0 1.0 NH1 B:ARG209 4.2 36.8 1.0 CG B:GLU144 4.3 32.7 1.0 CG B:GLU238 4.4 42.4 1.0 O B:HOH425 4.5 37.4 1.0 CZ B:ARG209 4.7 37.8 1.0 CD2 B:HIS180 4.7 40.6 1.0 CB B:GLU238 4.8 38.6 1.0 NE2 B:HIS180 4.9 41.3 1.0 NE2 B:HIS175 4.9 43.1 1.0 CA B:ASP177 5.0 24.6 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of D-Allulose 3-Epimerase 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 From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:12.4 occ:1.00 ND1 C:HIS203 2.0 36.4 1.0 OD2 C:ASP177 2.0 39.5 1.0 OE2 C:GLU144 2.1 38.4 1.0 OE1 C:GLU238 2.2 40.9 1.0 CE1 C:HIS203 2.8 39.2 1.0 CG C:HIS203 3.1 37.6 1.0 CD C:GLU238 3.1 43.7 1.0 CD C:GLU144 3.2 35.7 1.0 CG C:ASP177 3.2 44.6 1.0 OE2 C:GLU238 3.4 47.9 1.0 OE1 C:GLU144 3.6 38.3 1.0 CB C:HIS203 3.6 30.9 1.0 CB C:ASP177 3.9 40.2 1.0 NE2 C:HIS203 4.0 36.1 1.0 CD2 C:HIS203 4.1 36.6 1.0 OD1 C:ASP177 4.2 39.1 1.0 O C:HOH431 4.3 37.5 1.0 NH2 C:ARG209 4.4 30.4 1.0 NH1 C:ARG209 4.4 37.3 1.0 CG C:GLU144 4.5 36.4 1.0 CG C:GLU238 4.5 44.5 1.0 NE2 C:HIS175 4.7 36.2 1.0 CD2 C:HIS180 4.7 39.2 1.0 NE2 C:HIS180 4.7 37.6 1.0 CZ C:ARG209 4.9 39.3 1.0 CB C:GLU238 4.9 37.1 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of D-Allulose 3-Epimerase From Agrobacterium Sp. SUL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of D-Allulose 3-Epimerase From Agrobacterium Sp. SUL3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:8.6 occ:1.00 O D:HOH418 1.9 38.9 1.0 OE1 D:GLU238 2.0 45.2 1.0 ND1 D:HIS203 2.0 34.7 1.0 OD2 D:ASP177 2.1 30.9 1.0 OE2 D:GLU144 2.1 37.1 1.0 CE1 D:HIS203 2.9 38.0 1.0 CD D:GLU238 3.1 47.2 1.0 CD D:GLU144 3.2 36.0 1.0 CG D:HIS203 3.2 35.6 1.0 CG D:ASP177 3.2 30.6 1.0 OE2 D:GLU238 3.4 50.7 1.0 OE1 D:GLU144 3.5 39.0 1.0 CB D:HIS203 3.6 30.7 1.0 CB D:ASP177 3.8 33.2 1.0 O D:HOH437 4.0 44.8 1.0 NE2 D:HIS203 4.1 33.9 1.0 NH1 D:ARG209 4.1 35.2 1.0 NH2 D:ARG209 4.1 46.4 1.0 CD2 D:HIS203 4.2 31.7 1.0 OD1 D:ASP177 4.3 34.4 1.0 CG D:GLU238 4.4 45.0 1.0 CD2 D:HIS180 4.4 31.0 1.0 CG D:GLU144 4.5 35.9 1.0 NE2 D:HIS180 4.5 29.1 1.0 CZ D:ARG209 4.6 41.3 1.0 NE2 D:HIS175 4.9 27.2 1.0 CA D:ASP177 5.0 32.0 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.