Calcium in PDB 1bfd: Benzoylformate Decarboxylase From Pseudomonas Putida

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

The structure of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 1bfd was solved by M.S.Hasson, A.Muscate, M.J.Mcleish, L.S.Polovnikova, J.A.Gerlt, G.L.Kenyon, G.A.Petsko, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	5.00 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.300, 96.600, 138.300, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.6

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

Magnesium

(Mg)

1 atom

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

Calcium binding site 1 out of 2 in the 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 Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca529 b:15.6 occ:1.00 O A:THR457 2.2 15.5 1.0 O2A A:TPP530 2.3 14.3 1.0 O1B A:TPP530 2.3 13.0 1.0 OD1 A:ASN455 2.4 16.8 1.0 O A:HOH533 2.4 14.2 1.0 OD1 A:ASP428 2.4 15.0 1.0 CG A:ASN455 3.3 18.2 1.0 PA A:TPP530 3.4 15.6 1.0 O3A A:TPP530 3.4 14.5 1.0 PB A:TPP530 3.5 14.2 1.0 C A:THR457 3.5 15.0 1.0 CG A:ASP428 3.5 16.5 1.0 ND2 A:ASN455 3.6 18.8 1.0 OD2 A:ASP428 4.0 20.0 1.0 N A:THR457 4.0 16.5 1.0 N A:ASP428 4.1 12.7 1.0 O7 A:TPP530 4.1 16.1 1.0 N A:GLY459 4.1 16.1 1.0 N A:GLY429 4.2 11.7 1.0 O2B A:TPP530 4.3 14.0 1.0 CA A:THR457 4.3 16.2 1.0 O A:MET453 4.4 15.6 1.0 N A:TYR458 4.4 15.3 1.0 O A:HOH540 4.5 13.5 1.0 CA A:TYR458 4.5 14.8 1.0 O1A A:TPP530 4.5 13.2 1.0 N A:ASN455 4.5 16.4 1.0 O3B A:TPP530 4.6 16.3 1.0 CB A:ASN455 4.6 16.6 1.0 CB A:ASP428 4.7 13.6 1.0 CA A:GLY427 4.7 12.7 1.0 CG2 A:THR457 4.7 16.4 1.0 N A:GLY456 4.8 16.7 1.0 C A:GLY427 4.8 13.5 1.0 CA A:ASP428 4.8 13.0 1.0 CA A:ASN455 4.9 16.6 1.0 C A:TYR458 4.9 17.1 1.0 C A:ASN455 4.9 17.9 1.0

Calcium binding site 2 out of 2 in the 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 Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca532 b:21.2 occ:1.00 O A:HOH703 2.3 32.9 1.0 O A:HOH844 2.3 37.9 1.0 O A:HOH845 2.4 31.1 1.0 O A:HOH691 2.5 13.9 1.0 OD1 A:ASP364 2.5 19.9 1.0 CG A:ASP364 3.5 20.6 1.0 OD2 A:ASP364 3.7 21.5 1.0 O A:HOH852 4.2 38.5 1.0 ND2 A:ASN363 4.6 13.2 1.0 O A:ASP360 4.6 15.0 1.0 O A:HOH694 4.6 48.7 1.0 O A:HOH681 4.7 16.8 1.0 CB A:ASP364 4.9 19.0 1.0

M.S.Hasson, A.Muscate, M.J.Mcleish, L.S.Polovnikova, J.A.Gerlt, G.L.Kenyon, G.A.Petsko, D.Ringe. The Crystal Structure of Benzoylformate Decarboxylase at 1.6 A Resolution: Diversity of Catalytic Residues in Thiamin Diphosphate-Dependent Enzymes. Biochemistry V. 37 9918 1998.
ISSN: ISSN 0006-2960
PubMed: 9665697
DOI: 10.1021/BI973047E