Magnesium in PDB 2ag1: Crystal Structure of Benzaldehyde Lyase (Bal)- Semet

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

The structure of Crystal Structure of Benzaldehyde Lyase (Bal)- Semet, PDB code: 2ag1 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)	24.82 / 2.58
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.165, 150.165, 195.607, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 24.5

The binding sites of Magnesium atom in the Crystal Structure of Benzaldehyde Lyase (Bal)- Semet (pdb code 2ag1). 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)- Semet, PDB code: 2ag1:
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)- Semet


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)- Semet within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:55.7 occ:1.00 OD1 A:ASP448 1.6 71.2 1.0 O A:HOH5011 1.9 99.8 1.0 OD1 A:ASN475 2.3 77.2 1.0 O3B A:TPP602 2.4 54.2 1.0 O A:SER477 2.5 71.7 1.0 O1A A:TPP602 2.7 54.7 1.0 CG A:ASP448 2.8 72.9 1.0 CG A:ASN475 3.2 77.8 1.0 OD2 A:ASP448 3.4 74.2 1.0 O1B A:TPP602 3.4 48.0 1.0 PB A:TPP602 3.4 54.3 1.0 N A:ASP448 3.5 68.8 1.0 ND2 A:ASN475 3.6 75.5 1.0 PA A:TPP602 3.6 53.5 1.0 C A:SER477 3.7 71.6 1.0 O A:MSE473 3.8 74.6 1.0 N A:ASN475 3.9 79.7 1.0 O3A A:TPP602 3.9 52.5 1.0 CB A:ASP448 3.9 72.8 1.0 N A:GLY449 4.0 65.9 1.0 N A:SER477 4.2 76.3 1.0 CA A:ASP448 4.2 69.7 1.0 O2A A:TPP602 4.3 52.6 1.0 N A:GLY479 4.3 68.7 1.0 CB A:ASN475 4.4 80.6 1.0 C A:GLY447 4.4 66.6 1.0 CA A:GLY447 4.4 66.0 1.0 CA A:ASN475 4.5 81.7 1.0 CA A:SER477 4.5 74.6 1.0 C A:ASP448 4.6 67.6 1.0 N A:TRP478 4.7 69.4 1.0 C A:ASN475 4.7 81.5 1.0 N A:GLN476 4.7 81.0 1.0 O2B A:TPP602 4.8 50.0 1.0 CA A:TRP478 4.9 66.7 1.0 OG A:SER477 4.9 77.3 1.0 C A:MSE473 4.9 76.7 1.0 C A:ASN474 4.9 81.7 1.0 CA A:ASN474 4.9 79.6 1.0 CA A:GLY449 5.0 63.7 1.0 O7 A:TPP602 5.0 54.9 1.0 CA A:GLY479 5.0 70.4 1.0

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


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)- Semet within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg611 b:44.6 occ:1.00 O3B B:TPP612 1.8 51.1 1.0 O1A B:TPP612 2.1 49.5 1.0 OD1 B:ASN475 2.1 63.3 1.0 O B:SER477 2.2 58.6 1.0 OD1 B:ASP448 2.3 60.0 1.0 O B:HOH5022 2.3 61.1 1.0 PB B:TPP612 2.9 51.5 1.0 CG B:ASN475 3.0 63.6 1.0 PA B:TPP612 3.2 46.9 1.0 ND2 B:ASN475 3.3 61.0 1.0 O3A B:TPP612 3.3 47.6 1.0 CG B:ASP448 3.4 62.4 1.0 O1B B:TPP612 3.4 50.4 1.0 C B:SER477 3.4 58.0 1.0 N B:GLY479 3.7 54.0 1.0 O7 B:TPP612 3.9 46.0 1.0 OD2 B:ASP448 3.9 63.1 1.0 N B:ASP448 4.1 59.7 1.0 N B:SER477 4.2 62.6 1.0 O2B B:TPP612 4.2 48.4 1.0 O B:MSE473 4.3 64.3 1.0 N B:ASN475 4.3 66.8 1.0 CA B:GLY479 4.3 54.6 1.0 N B:TRP478 4.3 55.8 1.0 CA B:SER477 4.3 60.3 1.0 CB B:ASN475 4.4 65.9 1.0 N B:GLY449 4.4 56.8 1.0 CA B:TRP478 4.4 53.0 1.0 O2A B:TPP612 4.4 44.4 1.0 OG B:SER477 4.5 61.1 1.0 C B:TRP478 4.5 53.2 1.0 CB B:ASP448 4.6 63.3 1.0 CA B:ASN475 4.7 67.5 1.0 CA B:GLY447 4.7 57.2 1.0 C B:ASN475 4.8 67.0 1.0 CA B:ASP448 4.8 61.1 1.0 C B:GLY447 4.8 58.2 1.0 C7 B:TPP612 5.0 46.8 1.0

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


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)- Semet within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg621 b:33.7 occ:1.00 OD1 C:ASP448 1.6 35.4 1.0 OD1 C:ASN475 2.0 41.7 1.0 O C:HOH5033 2.2 17.7 1.0 O3B C:TPP622 2.4 27.8 1.0 O C:SER477 2.4 38.1 1.0 O1A C:TPP622 2.4 32.5 1.0 CG C:ASP448 2.7 36.4 1.0 CG C:ASN475 2.9 42.1 1.0 OD2 C:ASP448 3.3 37.2 1.0 ND2 C:ASN475 3.5 41.0 1.0 C C:SER477 3.6 37.7 1.0 PB C:TPP622 3.7 29.9 1.0 N C:ASN475 3.7 41.2 1.0 PA C:TPP622 3.7 32.0 1.0 N C:ASP448 3.7 34.0 1.0 O C:MSE473 3.7 38.5 1.0 O3A C:TPP622 3.9 31.2 1.0 CB C:ASP448 3.9 35.7 1.0 N C:SER477 4.0 39.7 1.0 CB C:ASN475 4.1 43.4 1.0 N C:GLY449 4.2 32.4 1.0 O1B C:TPP622 4.2 28.4 1.0 CA C:ASN475 4.2 43.3 1.0 CA C:ASP448 4.3 34.0 1.0 N C:GLY479 4.3 37.3 1.0 CA C:SER477 4.4 39.2 1.0 C C:ASN475 4.4 43.2 1.0 N C:GLN476 4.5 42.2 1.0 CA C:GLY447 4.5 33.0 1.0 C C:GLY447 4.5 32.5 1.0 O2A C:TPP622 4.6 36.0 1.0 N C:TRP478 4.6 36.5 1.0 C C:ASP448 4.7 32.5 1.0 C C:ASN474 4.7 42.1 1.0 OG C:SER477 4.8 42.6 1.0 CA C:ASN474 4.8 40.3 1.0 O7 C:TPP622 4.8 29.0 1.0 C C:MSE473 4.8 39.4 1.0 CA C:TRP478 4.9 35.2 1.0 O2B C:TPP622 4.9 25.2 1.0 O C:ASN475 5.0 43.5 1.0 CA C:GLY479 5.0 39.0 1.0

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


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)- Semet within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg631 b:20.1 occ:1.00 OD1 D:ASP448 2.0 23.8 1.0 OD1 D:ASN475 2.1 27.3 1.0 O D:SER477 2.1 24.1 1.0 O1A D:TPP632 2.1 20.4 1.0 O3B D:TPP632 2.2 22.9 1.0 O D:HOH5044 2.2 22.1 1.0 CG D:ASN475 3.0 27.3 1.0 CG D:ASP448 3.1 25.3 1.0 C D:SER477 3.3 24.1 1.0 ND2 D:ASN475 3.4 25.6 1.0 PA D:TPP632 3.4 21.9 1.0 PB D:TPP632 3.4 22.7 1.0 OD2 D:ASP448 3.5 25.8 1.0 O3A D:TPP632 3.6 20.3 1.0 N D:GLY479 3.8 22.5 1.0 N D:ASP448 4.0 24.0 1.0 N D:SER477 4.0 26.1 1.0 O1B D:TPP632 4.1 19.2 1.0 O7 D:TPP632 4.1 23.5 1.0 CA D:SER477 4.2 25.1 1.0 N D:GLY449 4.2 22.7 1.0 O D:MSE473 4.2 27.0 1.0 N D:ASN475 4.2 28.1 1.0 N D:TRP478 4.3 23.1 1.0 CB D:ASN475 4.4 28.0 1.0 CB D:ASP448 4.4 25.7 1.0 CA D:TRP478 4.4 21.8 1.0 OG D:SER477 4.4 26.4 1.0 CA D:GLY479 4.5 22.8 1.0 C D:TRP478 4.6 22.1 1.0 O2B D:TPP632 4.6 22.9 1.0 O2A D:TPP632 4.6 20.1 1.0 CA D:ASP448 4.6 24.8 1.0 CA D:ASN475 4.6 28.8 1.0 C D:ASN475 4.7 28.5 1.0 CA D:GLY447 4.7 22.8 1.0 C D:GLY447 4.8 23.3 1.0 N D:GLN476 4.8 28.4 1.0 C D:ASP448 4.9 23.9 1.0 CB D:SER477 5.0 25.8 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