Calcium in PDB 1pi3: E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida

All present enzymatic activity of E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida:
4.1.1.7;

The structure of E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 1pi3 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)	20.00 / 1.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.960, 95.528, 137.061, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 13.6

The structure of E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida (pdb code 1pi3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 1pi3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the E28Q Mutant Benzoylformate Decarboxylase 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 E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca532 b:10.8 occ:0.79 O12 A:TZD530 2.2 12.6 1.0 O A:THR457 2.2 12.6 1.0 OD1 A:ASP428 2.3 14.6 1.0 O21 A:TZD530 2.3 12.2 1.0 OD1 A:ASN455 2.3 12.3 0.8 O A:HOH936 2.3 14.3 1.0 CG A:ASN455 3.2 16.5 1.0 P1 A:TZD530 3.4 11.7 1.0 CG A:ASP428 3.4 11.4 1.0 C A:THR457 3.5 12.0 1.0 P2 A:TZD530 3.5 11.9 1.0 O11 A:TZD530 3.6 11.9 1.0 ND2 A:ASN455 3.6 19.1 1.0 N A:THR457 4.0 14.1 1.0 OD2 A:ASP428 4.0 16.8 1.0 N A:ASP428 4.1 11.0 1.0 O5G A:TZD530 4.1 12.3 1.0 N A:GLY459 4.2 12.7 1.0 N A:GLY429 4.2 10.2 1.0 O A:MET453 4.3 12.9 1.0 O22 A:TZD530 4.3 12.6 1.0 CA A:THR457 4.3 13.1 1.0 N A:TYR458 4.4 12.1 1.0 N A:ASN455 4.4 13.3 1.0 O A:HOH540 4.5 13.7 1.0 O13 A:TZD530 4.6 11.8 1.0 CB A:ASN455 4.6 17.4 1.0 CA A:TYR458 4.6 11.6 1.0 CB A:ASP428 4.6 11.2 1.0 O23 A:TZD530 4.6 12.5 1.0 N A:GLY456 4.7 13.7 1.0 CG2 A:THR457 4.7 16.8 1.0 CA A:ASP428 4.8 10.8 1.0 CA A:GLY427 4.8 10.3 1.0 CA A:ASN455 4.8 14.7 1.0 C A:ASN455 4.8 14.2 1.0 C A:GLY427 4.8 10.8 1.0 C A:TYR458 4.9 12.2 1.0 C A:ASP428 5.0 9.8 1.0

Calcium binding site 2 out of 3 in the E28Q Mutant Benzoylformate Decarboxylase 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 E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca533 b:18.9 occ:0.86 OD1 A:ASP364 2.5 19.8 1.0 O A:HOH690 2.5 15.5 1.0 O A:HOH849 3.5 33.5 1.0 CG A:ASP364 3.5 18.3 1.0 OD2 A:ASP364 3.9 22.2 1.0 O A:ASP360 4.5 14.3 1.0 O A:HOH680 4.7 16.2 1.0 O A:HOH693 4.7 32.9 0.9 ND2 A:ASN363 4.7 17.9 1.0 CB A:ASP364 4.8 18.1 1.0

Calcium binding site 3 out of 3 in the E28Q Mutant Benzoylformate Decarboxylase 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 E28Q Mutant Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca534 b:14.4 occ:0.84 O A:ALA416 2.3 13.2 1.0 O A:HOH883 2.4 24.8 0.9 O A:HOH711 2.5 17.4 0.9 O A:HOH700 2.5 18.6 0.9 C A:ALA416 3.4 12.6 1.0 CA A:ALA416 4.0 11.8 1.0 O A:HOH892 4.2 25.2 1.0 CD A:PRO418 4.5 14.8 1.0 N A:GLU417 4.6 11.7 1.0 O A:HOH701 4.6 25.8 0.8 O A:HOH725 4.6 18.4 0.9 CB A:ALA416 4.7 12.9 1.0 OG A:SER61 4.7 14.1 1.0 O A:HOH1023 4.7 33.0 1.0 O A:HOH888 4.8 23.2 0.9 O A:LEU415 4.8 12.8 1.0 CA A:GLU417 4.9 12.2 1.0

A.K.Bera, M.S.Hasson. High Resolution Structure of Benzoylformate Decarboxylate E28Q Mutant To Be Published.