Calcium in PDB 3iae: Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate

All present enzymatic activity of Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate:
4.1.2.38;

The structure of Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate, PDB code: 3iae was solved by G.S.Brandt, G.A.Petsko, D.Ringe, M.J.Mcleish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.55 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.856, 150.856, 97.240, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.4

The binding sites of Calcium atom in the Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate (pdb code 3iae). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate, PDB code: 3iae:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca572 b:78.4 occ:1.00 OD1 A:ASP448 2.5 42.7 1.0 O A:MET473 2.7 47.4 1.0 O2B A:D7K571 2.8 39.5 1.0 O1A A:D7K571 2.9 44.9 1.0 OD1 A:ASN475 3.0 49.4 1.0 O1B A:D7K571 3.1 41.5 1.0 PB A:D7K571 3.2 41.8 1.0 O3A A:D7K571 3.2 41.4 1.0 ND2 A:ASN475 3.3 48.6 1.0 CG A:ASN475 3.3 49.1 1.0 N A:ASP448 3.4 42.3 1.0 CA A:GLY447 3.5 42.5 1.0 PA A:D7K571 3.6 40.6 1.0 CG A:ASP448 3.7 42.5 1.0 O A:SER477 3.9 49.8 1.0 C A:GLY447 3.9 42.4 1.0 OG1 A:THR396 4.0 49.2 1.0 C A:MET473 4.0 47.4 1.0 N A:ASN475 4.0 48.9 1.0 O2A A:D7K571 4.4 43.8 1.0 CA A:ASP448 4.4 42.1 1.0 CB A:ASP448 4.5 42.2 1.0 CB A:ASN475 4.5 49.1 1.0 N A:GLY449 4.6 41.6 1.0 O3B A:D7K571 4.6 42.2 1.0 OD2 A:ASP448 4.6 43.0 1.0 CA A:ASN474 4.7 48.3 1.0 CA A:ASN475 4.8 49.1 1.0 O01 A:D7K571 4.8 40.9 1.0 N A:ASN474 4.8 47.8 1.0 CB A:MET473 4.9 47.0 1.0 N A:GLY447 4.9 42.5 1.0 C A:ASN474 4.9 48.5 1.0 CA A:MET473 5.0 46.9 1.0

Calcium binding site 2 out of 2 in the Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Benzaldehyde Lyase A28S Mutant with Benzoylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca572 b:75.2 occ:1.00 OD1 B:ASP448 2.3 37.4 1.0 O2B B:D7K571 2.5 36.8 1.0 O1A B:D7K571 2.5 34.3 1.0 OD1 B:ASN475 2.7 40.5 1.0 O B:MET473 3.0 40.5 1.0 PB B:D7K571 3.1 34.4 1.0 O3A B:D7K571 3.1 29.1 1.0 CG B:ASN475 3.2 40.1 1.0 O1B B:D7K571 3.3 39.0 1.0 N B:ASP448 3.4 36.8 1.0 ND2 B:ASN475 3.4 39.9 1.0 PA B:D7K571 3.4 29.2 1.0 CG B:ASP448 3.6 36.7 1.0 CA B:GLY447 3.6 37.2 1.0 O B:SER477 3.7 38.1 1.0 C B:GLY447 4.0 37.0 1.0 N B:ASN475 4.1 40.2 1.0 C B:MET473 4.2 40.6 1.0 OG1 B:THR396 4.2 38.3 1.0 CB B:ASP448 4.4 36.6 1.0 CA B:ASP448 4.4 36.6 1.0 O2A B:D7K571 4.4 25.6 1.0 OD2 B:ASP448 4.4 36.5 1.0 CB B:ASN475 4.5 40.2 1.0 O3B B:D7K571 4.5 33.7 1.0 N B:GLY449 4.6 36.3 1.0 O01 B:D7K571 4.7 34.6 1.0 CA B:ASN475 4.8 40.2 1.0 CA B:ASN474 4.9 40.3 1.0 N B:GLY479 4.9 36.0 1.0 O B:HOH647 4.9 43.2 1.0 N B:GLY447 4.9 37.4 1.0 C B:SER477 4.9 38.1 1.0 C B:ASN474 5.0 40.3 1.0 N B:ASN474 5.0 40.4 1.0

G.S.Brandt, M.M.Kneen, G.A.Petsko, D.Ringe, M.J.Mcleish. Active-Site Engineering of Benzaldehyde Lyase Shows That A Point Mutation Can Confer Both New Reactivity and Susceptibility to Mechanism-Based Inhibition. J.Am.Chem.Soc. V. 132 438 2010.
ISSN: ISSN 0002-7863
PubMed: 20030408
DOI: 10.1021/JA907064W