Magnesium in PDB 4il2: Crystal Structure of D-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585)

The structure of Crystal Structure of D-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585), PDB code: 4il2 was solved by T.Lukk, D.Wichelecki, H.J.Imker, J.A.Gerlt, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 1.95
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	123.780, 123.780, 112.210, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.9

The binding sites of Magnesium atom in the Crystal Structure of D-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585) (pdb code 4il2). 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-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585), PDB code: 4il2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of D-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585)


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-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:19.3 occ:1.00 OE2 A:GLU275 2.6 21.6 1.0 OD2 A:ASP223 2.7 18.1 1.0 OD1 A:ASP223 2.7 19.3 1.0 OE2 A:GLU249 2.7 16.2 1.0 OD2 A:ASP250 2.9 19.9 1.0 OE1 A:GLU275 3.0 14.0 1.0 CG A:ASP223 3.1 17.1 1.0 CD A:GLU275 3.1 11.5 1.0 CD A:GLU249 3.7 19.2 1.0 OH B:TYR86 3.7 17.9 1.0 CG A:ASP250 3.8 20.1 1.0 CG A:GLU249 4.1 18.7 1.0 ND1 A:HIS225 4.3 38.5 1.0 CB A:ASP250 4.4 19.7 1.0 O A:HOH610 4.5 36.2 1.0 CB A:ASP223 4.5 17.2 1.0 CG A:GLU275 4.6 15.7 1.0 CE1 A:HIS225 4.6 40.6 1.0 OD1 A:ASP250 4.6 19.1 1.0 OE1 A:GLU249 4.7 14.5 1.0 NE2 A:HIS226 4.7 24.5 1.0 O A:HOH663 4.7 36.8 1.0 NH2 A:ARG296 4.8 10.4 1.0 CA A:HIS225 4.8 27.2 1.0 N A:HIS225 4.9 24.4 1.0 CE1 A:HIS226 5.0 24.0 1.0 CG A:HIS225 5.0 35.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585)


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-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:11.4 occ:1.00 OE2 B:GLU275 2.5 18.8 1.0 OD2 B:ASP223 2.5 11.2 1.0 OE2 B:GLU249 2.6 9.0 1.0 OD2 B:ASP250 2.8 11.8 1.0 OD1 B:ASP223 3.0 8.1 1.0 CG B:ASP223 3.0 13.2 1.0 CD B:GLU275 3.1 18.3 1.0 OE1 B:GLU275 3.1 15.3 1.0 CD B:GLU249 3.6 6.5 1.0 CG B:ASP250 3.8 8.3 1.0 CG B:GLU249 4.2 8.5 1.0 OH A:TYR86 4.2 7.4 1.0 ND1 B:HIS225 4.4 33.3 1.0 CB B:ASP250 4.4 4.3 1.0 CB B:ASP223 4.5 6.6 1.0 O B:HOH614 4.5 29.5 1.0 NH2 B:ARG158 4.5 42.6 1.0 CG B:GLU275 4.6 25.8 1.0 O B:HOH617 4.6 33.9 1.0 OE1 B:GLU249 4.6 7.6 1.0 CE1 B:HIS225 4.7 31.0 1.0 NH2 B:ARG296 4.7 9.8 1.0 OD1 B:ASP250 4.7 6.7 1.0 CB B:GLU275 4.9 17.1 1.0 NE B:ARG296 5.0 9.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585)


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-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:11.2 occ:1.00 OE2 C:GLU249 2.4 8.8 1.0 OD2 C:ASP223 2.5 12.1 1.0 OE2 C:GLU275 2.5 10.1 1.0 O C:HOH658 2.9 37.4 1.0 OD1 C:ASP223 2.9 11.8 1.0 CG C:ASP223 3.0 7.9 1.0 CD C:GLU275 3.2 15.3 1.0 OD2 C:ASP250 3.3 15.2 1.0 CD C:GLU249 3.3 11.3 1.0 OE1 C:GLU275 3.4 13.6 1.0 CG C:GLU249 4.0 7.3 1.0 OE1 C:GLU249 4.1 9.8 1.0 CG C:ASP250 4.2 11.3 1.0 CB C:ASP223 4.3 10.8 1.0 CD2 C:HIS225 4.3 15.6 1.0 O C:HOH638 4.3 28.2 1.0 NH2 C:ARG296 4.4 7.1 1.0 CG C:GLU275 4.5 8.6 1.0 CB C:ASP250 4.7 11.5 1.0 O C:HOH617 4.8 31.9 1.0 O C:MET224 4.9 25.4 1.0 NE C:ARG296 4.9 8.4 1.0 NE2 C:HIS225 5.0 19.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585)


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-Mannonate Dehydratase (Rspa) From E. Coli CFT073 (Efi Target Efi-501585) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:35.7 occ:1.00 OE2 D:GLU275 2.6 31.7 1.0 OD2 D:ASP223 2.6 18.4 1.0 OD1 D:ASP223 2.8 18.1 1.0 OD2 D:ASP250 2.9 24.3 1.0 OE2 D:GLU249 3.0 23.3 1.0 CG D:ASP223 3.1 21.3 1.0 OE1 D:GLU275 3.1 15.6 1.0 CD D:GLU275 3.2 19.2 1.0 CG D:ASP250 3.9 16.2 1.0 CD D:GLU249 4.0 22.0 1.0 ND1 D:HIS225 4.3 39.5 1.0 CG D:GLU249 4.4 14.6 1.0 CB D:ASP250 4.5 16.1 1.0 CG D:GLU275 4.6 24.0 1.0 CB D:ASP223 4.6 16.4 1.0 O D:HOH649 4.6 47.0 1.0 CA D:HIS225 4.7 29.2 1.0 CE1 D:HIS225 4.7 39.6 1.0 N D:HIS225 4.8 23.4 1.0 OD1 D:ASP250 4.8 15.6 1.0

S.Wichelecki, T.Lukk, H.J.Imker, S.K.Nair, J.A.Gerlt. Mannonate Degradation Pathway in E. Coli CFT073 To Be Published.