Calcium in PDB 3d7k: Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp

All present enzymatic activity of Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp:
4.1.2.38;

The structure of Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp, PDB code: 3d7k was solved by G.S.Brandt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.00 / 2.49
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.936, 151.936, 98.217, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 25

The binding sites of Calcium atom in the Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp (pdb code 3d7k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp, PDB code: 3d7k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca571 b:56.3 occ:1.00 O2B A:D7K572 2.1 43.6 1.0 OD1 A:ASP448 2.2 46.9 1.0 O A:HOH596 2.2 38.2 1.0 OD1 A:ASN475 2.2 47.7 1.0 O1A A:D7K572 2.3 43.3 1.0 O A:SER477 2.4 44.2 1.0 CG A:ASN475 3.2 46.8 1.0 PB A:D7K572 3.2 44.3 1.0 CG A:ASP448 3.2 44.1 1.0 O3A A:D7K572 3.3 40.7 1.0 PA A:D7K572 3.3 43.6 1.0 ND2 A:ASN475 3.6 44.9 1.0 C A:SER477 3.6 44.5 1.0 N A:ASP448 3.6 42.9 1.0 OD2 A:ASP448 3.7 47.2 1.0 O1B A:D7K572 3.8 40.9 1.0 N A:GLY479 4.0 44.1 1.0 N A:GLY449 4.1 42.1 1.0 O A:MET473 4.1 44.9 1.0 O01 A:D7K572 4.2 45.3 1.0 N A:SER477 4.2 45.8 1.0 N A:ASN475 4.3 44.5 1.0 CB A:ASP448 4.4 42.8 1.0 CA A:GLY447 4.4 42.9 1.0 CA A:ASP448 4.5 42.7 1.0 C A:GLY447 4.5 43.2 1.0 O3B A:D7K572 4.5 42.6 1.0 O2A A:D7K572 4.5 44.1 1.0 CB A:ASN475 4.5 44.8 1.0 N A:TRP478 4.5 44.0 1.0 CA A:SER477 4.5 45.6 1.0 OG A:SER477 4.6 46.7 1.0 CA A:TRP478 4.6 43.4 1.0 CA A:GLY479 4.7 45.6 1.0 CA A:ASN475 4.8 44.5 1.0 C A:ASP448 4.8 41.9 1.0 C A:ASN475 4.8 44.4 1.0 C A:TRP478 4.8 43.5 1.0 N A:GLN476 4.9 45.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Benzaldehyde Lyase in Complex with the Inhibitor Mbp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca571 b:57.2 occ:1.00 O1A B:D7K572 2.0 34.2 1.0 O2B B:D7K572 2.1 37.5 1.0 OD1 B:ASP448 2.2 31.7 1.0 OD1 B:ASN475 2.2 37.1 1.0 O B:HOH618 2.3 35.4 1.0 O B:SER477 2.4 39.5 1.0 PA B:D7K572 3.1 35.1 1.0 CG B:ASP448 3.2 34.5 1.0 O3A B:D7K572 3.3 34.2 1.0 PB B:D7K572 3.3 37.8 1.0 CG B:ASN475 3.3 40.4 1.0 C B:SER477 3.6 39.1 1.0 N B:ASP448 3.7 35.0 1.0 OD2 B:ASP448 3.7 37.4 1.0 ND2 B:ASN475 3.7 41.7 1.0 O1B B:D7K572 3.9 34.6 1.0 O01 B:D7K572 3.9 35.6 1.0 N B:GLY479 3.9 32.9 1.0 N B:GLY449 4.0 36.0 1.0 O B:MET473 4.2 41.5 1.0 N B:SER477 4.3 41.2 1.0 O2A B:D7K572 4.3 32.8 1.0 CB B:ASP448 4.4 34.8 1.0 CA B:GLY447 4.4 36.6 1.0 N B:ASN475 4.4 40.8 1.0 CA B:ASP448 4.5 34.6 1.0 C B:GLY447 4.5 36.0 1.0 CA B:TRP478 4.5 34.0 1.0 N B:TRP478 4.5 36.5 1.0 O3B B:D7K572 4.5 33.4 1.0 CA B:SER477 4.5 40.7 1.0 CA B:GLY479 4.6 32.9 1.0 CB B:ASN475 4.6 41.1 1.0 C B:TRP478 4.7 33.4 1.0 C B:ASP448 4.8 35.4 1.0 OG B:SER477 4.8 43.5 1.0 CA B:ASN475 4.9 40.8 1.0 N B:GLN476 4.9 42.7 1.0 C B:ASN475 4.9 41.5 1.0 CA B:GLY449 4.9 36.4 1.0

G.S.Brandt, N.Nemeria, S.Chakraborty, M.J.Mcleish, A.Yep, G.L.Kenyon, G.A.Petsko, F.Jordan, D.Ringe. Probing the Active Center of Benzaldehyde Lyase with Substitutions and the Pseudosubstrate Analogue Benzoylphosphonic Acid Methyl Ester Biochemistry V. 47 7734 2008.
ISSN: ISSN 0006-2960
PubMed: 18570438
DOI: 10.1021/BI8004413