Magnesium in PDB 5dgd: Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida

All present enzymatic activity of Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida:
4.1.1.7;

The structure of Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida, PDB code: 5dgd was solved by A.K.Bera, M.S.Hasson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.65 / 1.13
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.500, 95.656, 137.345, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 15

The structure of Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida (pdb code 5dgd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida, PDB code: 5dgd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:18.7 occ:1.00 H A:ASP168 2.0 16.1 1.0 HG A:SER171 2.1 17.3 1.0 HG2 A:PRO136 2.7 23.7 1.0 HB1 A:ALA167 2.7 16.9 1.0 O A:ALA133 2.7 10.6 1.0 N A:ASP168 2.8 13.4 1.0 OG A:SER171 2.8 14.4 1.0 HB3 A:ASP168 2.9 18.2 1.0 HD2 A:PRO136 2.9 9.2 1.0 HA A:ALA167 3.0 15.6 1.0 O A:HOH737 3.2 18.9 1.0 HB2 A:ASP168 3.4 18.2 1.0 CB A:ALA167 3.4 14.1 1.0 CB A:ASP168 3.4 15.2 1.0 CG A:PRO136 3.4 19.8 1.0 HA A:ALA133 3.4 11.1 1.0 CA A:ALA167 3.5 13.0 1.0 CD A:PRO136 3.6 7.6 1.0 HB1 A:ALA133 3.6 12.9 1.0 C A:ALA167 3.6 13.0 1.0 CA A:ASP168 3.6 14.3 1.0 HB2 A:SER171 3.6 13.8 1.0 HB2 A:PRO136 3.7 10.5 1.0 C A:ALA133 3.7 8.7 1.0 CB A:SER171 3.8 11.5 1.0 HB2 A:ALA167 3.8 16.9 1.0 O A:ASP168 3.8 11.9 1.0 CA A:ALA133 4.0 9.2 1.0 HD3 A:PRO136 4.0 9.2 1.0 HG21 A:THR7 4.0 12.1 1.0 HG22 A:VAL4 4.1 12.0 1.0 CB A:PRO136 4.1 8.8 1.0 HB3 A:SER171 4.1 13.8 1.0 HB3 A:ALA167 4.2 16.9 1.0 HG3 A:PRO136 4.2 23.7 1.0 C A:ASP168 4.2 12.4 1.0 CB A:ALA133 4.2 10.8 1.0 HA A:ASP168 4.5 17.1 1.0 HB2 A:ALA133 4.7 12.9 1.0 H A:SER171 4.7 12.6 1.0 HB3 A:PRO136 4.7 10.5 1.0 N A:PRO136 4.8 7.2 1.0 O A:ALA167 4.8 16.9 1.0 H A:HIS137 4.8 8.7 1.0 O A:HOH1131 4.8 22.4 1.0 CG A:ASP168 4.8 16.7 1.0 N A:ALA167 4.9 13.2 1.0 N A:GLU134 4.9 8.5 1.0 CG2 A:THR7 4.9 10.1 1.0 CG2 A:VAL4 5.0 10.0 1.0 HB3 A:ALA133 5.0 12.9 1.0

Magnesium binding site 2 out of 3 in the Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:13.5 occ:1.00 H A:ASP187 2.4 14.3 1.0 HA A:ASN186 3.1 13.3 1.0 HB2 A:ASN186 3.1 14.4 1.0 N A:ASP187 3.2 11.9 1.0 O A:HOH1099 3.3 19.7 1.0 HB2 A:ASP187 3.3 17.1 1.0 CA A:ASN186 3.8 11.1 1.0 CG A:ASP187 3.8 18.6 1.0 CB A:ASN186 3.9 12.0 1.0 CB A:ASP187 3.9 14.2 1.0 OD2 A:ASP187 3.9 15.5 0.4 C A:ASN186 4.0 11.5 1.0 CA A:ASP187 4.2 12.7 1.0 HB3 A:ASN186 4.3 14.4 1.0 OD1 A:ASP187 4.3 16.9 0.6 HH12 A:ARG184 4.5 19.2 1.0 H A:GLN188 4.6 15.4 1.0 HA A:ASP187 4.7 15.3 1.0 HB3 A:ASP187 4.8 17.1 1.0 NH1 A:ARG184 5.0 16.0 1.0

Magnesium binding site 3 out of 3 in the Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:10.6 occ:0.66 O A:ARG120 2.5 8.6 1.0 O A:LEU118 2.5 8.3 1.0 O A:ASN117 2.7 7.6 1.0 O A:HOH984 3.1 10.1 0.5 C A:LEU118 3.3 7.1 1.0 HA A:LEU118 3.3 8.4 1.0 C A:ARG120 3.6 8.0 1.0 HE1 A:MET79 3.7 23.6 0.5 H A:ARG120 3.7 8.6 1.0 C A:ASN117 3.8 7.2 1.0 CA A:LEU118 3.8 7.0 1.0 HB2 A:ARG120 3.8 10.1 1.0 N A:ARG120 3.9 7.1 1.0 CA A:ARG120 4.2 7.3 1.0 N A:LEU118 4.2 6.5 1.0 HD12 A:LEU118 4.2 12.1 1.0 N A:PRO119 4.2 7.3 1.0 C A:PRO119 4.3 8.0 1.0 HE2 A:MET79 4.5 25.2 0.5 HD3 A:PRO121 4.5 10.0 1.0 CB A:ARG120 4.5 8.4 1.0 HA A:PRO119 4.6 9.4 1.0 CA A:PRO119 4.6 7.9 1.0 HB3 A:ASN117 4.6 9.7 1.0 CE A:MET79 4.6 19.7 0.5 N A:PRO121 4.7 7.6 1.0 HE3 A:MET79 4.7 23.6 0.5 HD2 A:PRO121 4.9 10.0 1.0 CD A:PRO121 4.9 8.4 1.0 O A:PRO119 5.0 8.9 1.0 CA A:ASN117 5.0 6.9 1.0 HE1 A:MET79 5.0 25.2 0.5

A.K.Bera, M.S.Hasson. Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida To Be Published.