Calcium 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:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Benzoylformate Decarboxylase F464I and A460V Mutant From Pseudomonas Putida, PDB code: 5dgd:
Jump to Calcium binding site number: 1; 2; 3;

Calcium 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 Calcium with other atoms in the Ca 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:Ca604 b:8.8 occ:0.96 O13 A:TDP607 2.3 8.9 1.0 O A:THR457 2.3 9.7 1.0 OD1 A:ASN455 2.3 10.8 1.0 OD1 A:ASP428 2.3 11.2 1.0 O A:HOH740 2.3 10.7 1.0 O23 A:TDP607 2.3 9.0 1.0 CG A:ASN455 3.2 13.1 1.0 HD21 A:ASN455 3.2 20.8 1.0 H A:THR457 3.2 12.1 1.0 H A:GLY459 3.4 10.9 1.0 CG A:ASP428 3.4 10.1 1.0 P1 A:TDP607 3.4 8.1 1.0 H A:GLY429 3.5 9.4 1.0 C A:THR457 3.5 8.5 1.0 P2 A:TDP607 3.5 8.2 1.0 ND2 A:ASN455 3.6 17.4 1.0 H A:ASN455 3.6 12.0 1.0 H A:ASP428 3.6 9.9 1.0 O11 A:TDP607 3.6 8.1 1.0 OD2 A:ASP428 4.0 14.2 1.0 N A:THR457 4.0 10.0 1.0 HA A:TYR458 4.0 9.9 1.0 HG23 A:THR457 4.1 16.2 1.0 N A:ASP428 4.2 8.3 1.0 N A:GLY459 4.2 9.1 1.0 O5G A:TDP607 4.2 9.0 1.0 HG22 A:THR457 4.2 16.2 1.0 HA3 A:GLY427 4.3 10.4 1.0 N A:GLY429 4.3 7.8 1.0 O A:MET453 4.3 10.0 1.0 O22 A:TDP607 4.3 9.1 1.0 CA A:THR457 4.4 10.0 1.0 N A:ASN455 4.4 10.0 1.0 HD22 A:ASN455 4.4 20.8 1.0 H A:GLY456 4.4 12.4 1.0 N A:TYR458 4.5 8.2 1.0 O A:HOH751 4.5 10.0 1.0 CB A:ASN455 4.5 13.9 1.0 CG2 A:THR457 4.6 13.5 1.0 HA2 A:GLY427 4.6 10.4 1.0 HA3 A:GLY459 4.6 11.9 1.0 N A:GLY456 4.6 10.3 1.0 O12 A:TDP607 4.6 9.0 1.0 CB A:ASP428 4.6 8.9 1.0 CA A:TYR458 4.6 8.2 1.0 O21 A:TDP607 4.7 8.6 1.0 CA A:ASN455 4.7 11.5 1.0 C A:ASN455 4.8 10.8 1.0 CA A:ASP428 4.8 8.9 1.0 CA A:GLY427 4.8 8.7 1.0 HA3 A:GLY429 4.8 9.8 1.0 C A:GLY427 4.9 8.2 1.0 HA A:ASN454 4.9 11.8 1.0 HB3 A:ASN455 4.9 16.7 1.0 C A:TYR458 5.0 8.6 1.0 HB3 A:ASP428 5.0 10.7 1.0 CA A:GLY459 5.0 9.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca605 b:13.8 occ:0.68 O A:HOH800 2.5 12.9 1.0 OD1 A:ASP364 2.5 14.2 0.7 O A:HOH1235 2.6 22.4 1.0 O A:HOH713 2.6 22.4 1.0 O A:HOH1203 2.8 22.8 1.0 CG A:ASP364 3.4 17.6 1.0 OD2 A:ASP364 3.5 16.6 0.7 HD22 A:ASN363 4.1 17.4 1.0 HB3 A:ASP360 4.2 13.4 1.0 O A:ASP360 4.5 11.3 1.0 O A:HOH876 4.7 12.6 1.0 O A:HOH1178 4.7 51.6 1.0 CB A:ASP364 4.8 16.2 1.0 O A:HOH711 4.9 25.6 1.0 ND2 A:ASN363 4.9 14.5 1.0 HB3 A:ASN363 4.9 14.6 1.0 HA A:ASP364 4.9 18.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca606 b:11.9 occ:0.76 O A:ALA416 2.3 10.1 1.0 O A:HOH1115 2.4 16.6 1.0 O A:HOH1147 2.5 21.9 1.0 O A:HOH919 2.5 16.7 1.0 O A:HOH1012 2.5 16.3 1.0 O A:HOH1031 2.6 21.2 1.0 C A:ALA416 3.4 9.8 1.0 HA A:ALA416 3.5 10.8 1.0 HD2 A:PRO418 3.8 13.7 1.0 CA A:ALA416 4.0 9.0 1.0 HD3 A:PRO418 4.2 13.7 1.0 O A:HOH999 4.2 29.9 1.0 HB1 A:ALA416 4.2 11.0 1.0 HA A:GLU417 4.3 11.5 1.0 CD A:PRO418 4.5 11.4 1.0 N A:GLU417 4.5 9.3 1.0 O A:HOH878 4.7 16.8 1.0 CB A:ALA416 4.7 9.2 1.0 O A:LEU415 4.7 9.8 1.0 OG A:SER61 4.8 11.3 0.7 O A:HOH1128 4.8 27.5 1.0 O A:HOH1208 4.9 17.0 1.0 CA A:GLU417 5.0 9.6 1.0 HB3 A:SER61 5.0 11.1 0.3

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