Magnesium in PDB 2ag0: Crystal Structure of Benzaldehyde Lyase (Bal)- Native

All present enzymatic activity of Crystal Structure of Benzaldehyde Lyase (Bal)- Native:
4.1.2.38;

The structure of Crystal Structure of Benzaldehyde Lyase (Bal)- Native, PDB code: 2ag0 was solved by T.G.Mosbacher, M.Mueller, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.58
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	154.720, 154.720, 200.700, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22

The binding sites of Magnesium atom in the Crystal Structure of Benzaldehyde Lyase (Bal)- Native (pdb code 2ag0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Benzaldehyde Lyase (Bal)- Native, PDB code: 2ag0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Benzaldehyde Lyase (Bal)- Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Benzaldehyde Lyase (Bal)- Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:47.5 occ:1.00 OD1 A:ASP448 1.9 53.7 1.0 O3B A:TPP602 2.0 40.7 1.0 O1A A:TPP602 2.2 42.0 1.0 O A:HOH5011 2.3 42.8 1.0 OD1 A:ASN475 2.3 57.0 1.0 O A:SER477 2.4 53.9 1.0 CG A:ASP448 3.1 54.3 1.0 PB A:TPP602 3.2 43.1 1.0 CG A:ASN475 3.3 57.3 1.0 PA A:TPP602 3.4 41.9 1.0 O3A A:TPP602 3.5 40.7 1.0 C A:SER477 3.6 54.5 1.0 OD2 A:ASP448 3.7 55.5 1.0 O1B A:TPP602 3.7 40.6 1.0 ND2 A:ASN475 3.7 55.8 1.0 N A:ASP448 3.8 50.2 1.0 N A:GLY449 4.1 48.6 1.0 N A:GLY479 4.2 51.9 1.0 O7 A:TPP602 4.2 42.5 1.0 O A:MET473 4.2 53.6 1.0 N A:ASN475 4.2 58.6 1.0 CB A:ASP448 4.2 53.5 1.0 N A:SER477 4.2 58.2 1.0 CA A:ASP448 4.4 51.1 1.0 CA A:SER477 4.5 57.1 1.0 O2B A:TPP602 4.5 39.5 1.0 CB A:ASN475 4.6 59.7 1.0 N A:TRP478 4.6 53.1 1.0 O2A A:TPP602 4.6 41.8 1.0 C A:GLY447 4.6 48.3 1.0 CA A:GLY447 4.6 47.4 1.0 CA A:TRP478 4.7 50.8 1.0 CA A:ASN475 4.7 60.5 1.0 C A:ASP448 4.7 49.7 1.0 OG A:SER477 4.7 59.5 1.0 CA A:GLY479 4.8 53.2 1.0 C A:ASN475 4.8 61.1 1.0 C A:TRP478 5.0 51.7 1.0 N A:GLN476 5.0 61.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Benzaldehyde Lyase (Bal)- Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Benzaldehyde Lyase (Bal)- Native within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg611 b:31.2 occ:1.00 O3B B:TPP612 2.0 38.3 1.0 OD1 B:ASN475 2.1 50.5 1.0 O B:SER477 2.2 47.5 1.0 OD1 B:ASP448 2.2 49.2 1.0 O1A B:TPP612 2.2 38.2 1.0 O B:HOH5022 2.3 31.9 1.0 CG B:ASN475 3.0 50.7 1.0 PB B:TPP612 3.3 37.3 1.0 CG B:ASP448 3.4 50.0 1.0 C B:SER477 3.4 47.4 1.0 ND2 B:ASN475 3.4 49.3 1.0 PA B:TPP612 3.4 37.8 1.0 O3A B:TPP612 3.6 36.1 1.0 N B:GLY479 3.8 44.4 1.0 OD2 B:ASP448 3.9 50.7 1.0 O1B B:TPP612 3.9 37.9 1.0 N B:SER477 4.1 51.2 1.0 O7 B:TPP612 4.1 38.0 1.0 N B:ASP448 4.2 47.3 1.0 N B:ASN475 4.2 53.2 1.0 CA B:SER477 4.3 49.7 1.0 CB B:ASN475 4.4 52.8 1.0 N B:TRP478 4.4 45.8 1.0 OG B:SER477 4.4 51.2 1.0 O B:MET473 4.4 50.2 1.0 CA B:GLY479 4.4 45.1 1.0 N B:GLY449 4.5 45.2 1.0 O2B B:TPP612 4.5 35.4 1.0 CA B:TRP478 4.5 43.6 1.0 CB B:ASP448 4.6 50.1 1.0 CA B:ASN475 4.6 54.1 1.0 C B:TRP478 4.7 44.0 1.0 C B:ASN475 4.7 54.2 1.0 O2A B:TPP612 4.7 35.5 1.0 CA B:ASP448 4.8 48.3 1.0 N B:GLN476 4.9 54.8 1.0 CA B:GLY447 5.0 45.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Benzaldehyde Lyase (Bal)- Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Benzaldehyde Lyase (Bal)- Native within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg621 b:22.7 occ:1.00 OD1 C:ASP448 1.9 31.4 1.0 O1A C:TPP622 2.2 27.2 1.0 OD1 C:ASN475 2.2 34.3 1.0 O C:SER477 2.3 32.4 1.0 O3B C:TPP622 2.3 23.6 1.0 O C:HOH5033 2.3 21.3 1.0 CG C:ASP448 3.0 31.4 1.0 CG C:ASN475 3.2 34.4 1.0 PA C:TPP622 3.5 25.9 1.0 C C:SER477 3.5 32.6 1.0 PB C:TPP622 3.6 25.5 1.0 OD2 C:ASP448 3.6 32.1 1.0 ND2 C:ASN475 3.6 33.7 1.0 O3A C:TPP622 3.7 25.5 1.0 N C:ASP448 3.9 28.5 1.0 N C:SER477 4.1 34.5 1.0 N C:GLY479 4.1 31.8 1.0 N C:ASN475 4.1 34.3 1.0 N C:GLY449 4.2 27.7 1.0 O C:MET473 4.2 31.2 1.0 CB C:ASP448 4.2 30.3 1.0 O1B C:TPP622 4.3 22.8 1.0 O7 C:TPP622 4.3 25.4 1.0 CA C:SER477 4.4 34.3 1.0 CB C:ASN475 4.4 35.8 1.0 CA C:ASP448 4.5 28.9 1.0 N C:TRP478 4.5 31.9 1.0 O2A C:TPP622 4.6 27.3 1.0 CA C:ASN475 4.6 36.0 1.0 OG C:SER477 4.6 36.8 1.0 CA C:TRP478 4.7 30.6 1.0 C C:ASN475 4.7 36.3 1.0 C C:GLY447 4.7 27.5 1.0 CA C:GLY447 4.7 27.2 1.0 O2B C:TPP622 4.8 23.4 1.0 C C:ASP448 4.8 28.1 1.0 CA C:GLY479 4.8 33.0 1.0 N C:GLN476 4.9 36.2 1.0 C C:TRP478 4.9 31.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Benzaldehyde Lyase (Bal)- Native


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Benzaldehyde Lyase (Bal)- Native within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg631 b:18.8 occ:1.00 O1A D:TPP632 2.0 16.8 1.0 OD1 D:ASP448 2.1 23.4 1.0 OD1 D:ASN475 2.2 24.6 1.0 O D:SER477 2.2 23.3 1.0 O D:HOH5044 2.3 15.0 1.0 O3B D:TPP632 2.4 20.8 1.0 CG D:ASP448 3.2 23.6 1.0 CG D:ASN475 3.2 24.6 1.0 PA D:TPP632 3.4 18.3 1.0 PB D:TPP632 3.4 20.0 1.0 C D:SER477 3.5 23.3 1.0 O3A D:TPP632 3.6 17.0 1.0 ND2 D:ASN475 3.7 23.7 1.0 OD2 D:ASP448 3.7 24.2 1.0 N D:ASP448 3.9 21.9 1.0 N D:GLY479 4.0 21.8 1.0 O1B D:TPP632 4.0 18.6 1.0 N D:SER477 4.2 25.1 1.0 N D:GLY449 4.2 20.9 1.0 O7 D:TPP632 4.3 18.8 1.0 N D:ASN475 4.3 25.1 1.0 O D:MET473 4.3 23.4 1.0 CA D:SER477 4.4 24.7 1.0 CB D:ASP448 4.4 23.3 1.0 N D:TRP478 4.4 22.5 1.0 O2A D:TPP632 4.5 16.1 1.0 CB D:ASN475 4.5 25.6 1.0 CA D:TRP478 4.5 21.4 1.0 CA D:ASP448 4.6 22.3 1.0 OG D:SER477 4.6 26.4 1.0 CA D:GLY479 4.7 22.5 1.0 O2B D:TPP632 4.7 19.0 1.0 CA D:ASN475 4.7 26.2 1.0 C D:TRP478 4.7 21.9 1.0 CA D:GLY447 4.8 20.6 1.0 C D:GLY447 4.8 21.3 1.0 C D:ASN475 4.8 26.4 1.0 C D:ASP448 4.9 21.7 1.0 N D:GLN476 5.0 26.7 1.0

T.G.Mosbacher, M.Mueller, G.E.Schulz. Structure and Mechanism of the Thdp-Dependent Benzaldehyde Lyase From Pseudomonas Fluorescens Febs J. V. 272 6067 2005.
ISSN: ISSN 1742-464X
PubMed: 16302970
DOI: 10.1111/J.1742-4658.2005.04998.X