Magnesium in PDB 3iaf: Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate

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

The structure of Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate, PDB code: 3iaf 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)	47.89 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.962, 150.962, 195.560, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 26

The binding sites of Magnesium atom in the Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate (pdb code 3iaf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate, PDB code: 3iaf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg572 b:87.9 occ:1.00 OD1 A:ASP448 1.9 87.6 1.0 O1B A:TPP571 2.2 99.3 1.0 O3A A:TPP571 2.3 99.8 1.0 PB A:TPP571 2.6 99.5 1.0 O2A A:TPP571 2.6 0.2 1.0 OD1 A:ASN475 2.7 0.8 1.0 O A:SER477 2.9 0.8 1.0 PA A:TPP571 3.0 0.0 1.0 CG A:ASP448 3.0 88.6 1.0 O3B A:TPP571 3.1 99.6 1.0 CG A:ASN475 3.4 0.4 1.0 N A:ASP448 3.5 88.7 1.0 OD2 A:ASP448 3.6 88.9 1.0 ND2 A:ASN475 3.7 0.6 1.0 O1A A:TPP571 3.9 0.3 1.0 O A:MET473 3.9 0.1 1.0 O2B A:TPP571 4.0 98.9 1.0 CA A:GLY447 4.1 88.3 1.0 C A:SER477 4.1 0.9 1.0 CB A:ASP448 4.2 88.6 1.0 O7 A:TPP571 4.2 100.0 1.0 C A:GLY447 4.2 88.6 1.0 N A:GLY479 4.2 0.8 1.0 N A:GLY449 4.3 88.1 1.0 CA A:ASP448 4.3 88.7 1.0 N A:ASN475 4.4 1.0 1.0 CA A:GLY479 4.7 0.8 1.0 CB A:ASN475 4.8 0.1 1.0 OG1 A:THR396 4.8 97.9 1.0 C A:ASP448 4.8 88.5 1.0 N A:SER477 4.9 0.2 1.0 CA A:TRP478 4.9 0.1 1.0 N A:TRP478 5.0 0.4 1.0 C A:TRP478 5.0 0.9 1.0

Magnesium binding site 2 out of 4 in the Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg572 b:69.1 occ:1.00 OD1 B:ASN475 1.9 80.3 1.0 OD1 B:ASP448 2.1 71.3 1.0 O1B B:TPP571 2.1 66.4 1.0 O2A B:TPP571 2.2 65.4 1.0 O B:SER477 2.8 72.9 1.0 CG B:ASN475 3.0 80.2 1.0 PB B:TPP571 3.1 66.4 1.0 N B:ASP448 3.2 71.8 1.0 O3A B:TPP571 3.2 66.0 1.0 PA B:TPP571 3.2 65.5 1.0 CG B:ASP448 3.3 71.2 1.0 ND2 B:ASN475 3.5 80.3 1.0 O3B B:TPP571 3.6 66.6 1.0 O B:MET473 3.7 81.9 1.0 CA B:GLY447 3.9 73.2 1.0 C B:SER477 4.0 72.9 1.0 C B:GLY447 4.0 72.4 1.0 N B:ASN475 4.0 80.0 1.0 CB B:ASP448 4.0 71.1 1.0 CA B:ASP448 4.0 71.2 1.0 N B:GLY449 4.1 70.2 1.0 O7 B:TPP571 4.2 64.4 1.0 OD2 B:ASP448 4.3 70.7 1.0 CB B:ASN475 4.3 79.7 1.0 O1A B:TPP571 4.4 65.1 1.0 N B:GLY479 4.4 67.5 1.0 O2B B:TPP571 4.4 66.4 1.0 N B:SER477 4.6 76.0 1.0 CA B:ASN475 4.6 79.7 1.0 C B:ASP448 4.6 70.8 1.0 N B:TRP478 4.9 70.8 1.0 C B:MET473 4.9 82.0 1.0 CA B:SER477 4.9 74.3 1.0 CA B:TRP478 4.9 68.8 1.0 C B:ASN475 5.0 79.3 1.0 C B:ASN474 5.0 80.5 1.0 CA B:ASN474 5.0 80.9 1.0

Magnesium binding site 3 out of 4 in the Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg572 b:61.8 occ:1.00 OD1 C:ASP448 2.0 65.6 1.0 O1B C:TPP571 2.0 67.3 1.0 O2A C:TPP571 2.3 67.2 1.0 OD1 C:ASN475 2.4 78.1 1.0 O C:SER477 2.7 74.9 1.0 PB C:TPP571 3.0 67.0 1.0 O3A C:TPP571 3.2 66.5 1.0 CG C:ASP448 3.2 65.6 1.0 PA C:TPP571 3.3 67.1 1.0 N C:ASP448 3.4 65.0 1.0 O3B C:TPP571 3.5 66.9 1.0 CG C:ASN475 3.5 77.1 1.0 O C:MET473 3.6 70.6 1.0 CA C:GLY447 3.9 64.0 1.0 C C:SER477 3.9 75.0 1.0 OD2 C:ASP448 4.0 65.8 1.0 ND2 C:ASN475 4.0 77.8 1.0 C C:GLY447 4.1 64.6 1.0 N C:GLY479 4.1 74.4 1.0 N C:GLY449 4.2 64.3 1.0 CB C:ASP448 4.2 65.3 1.0 N C:ASN475 4.2 75.2 1.0 O7 C:TPP571 4.2 66.6 1.0 CA C:ASP448 4.3 65.2 1.0 O2B C:TPP571 4.3 66.0 1.0 O1A C:TPP571 4.4 67.2 1.0 N C:SER477 4.6 76.1 1.0 CA C:GLY479 4.7 75.1 1.0 CB C:ASN475 4.7 76.3 1.0 C C:MET473 4.8 70.3 1.0 OG1 C:THR396 4.8 67.5 1.0 C C:ASP448 4.8 64.8 1.0 N C:TRP478 4.8 74.3 1.0 CA C:SER477 4.8 75.5 1.0 CA C:ASN475 4.9 76.2 1.0 CA C:TRP478 4.9 73.7 1.0

Magnesium binding site 4 out of 4 in the Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Benzaldehyde Lyase A28S Mutant with Monomethyl Benzoylphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg572 b:77.7 occ:1.00 OD1 D:ASP448 1.9 56.0 1.0 O1B D:TPP571 2.0 53.3 1.0 O2A D:TPP571 2.0 49.0 1.0 OD1 D:ASN475 2.4 64.2 1.0 O D:SER477 2.7 58.7 1.0 PB D:TPP571 3.0 53.1 1.0 PA D:TPP571 3.0 49.4 1.0 CG D:ASN475 3.1 64.4 1.0 CG D:ASP448 3.1 55.7 1.0 O3A D:TPP571 3.2 50.9 1.0 ND2 D:ASN475 3.2 64.2 1.0 N D:ASP448 3.5 55.6 1.0 O3B D:TPP571 3.5 52.2 1.0 OD2 D:ASP448 3.8 56.1 1.0 O D:MET473 3.9 66.9 1.0 O7 D:TPP571 3.9 48.2 1.0 N D:GLY449 3.9 54.8 1.0 C D:SER477 3.9 58.8 1.0 N D:GLY479 4.1 56.1 1.0 CA D:GLY447 4.1 55.8 1.0 O1A D:TPP571 4.2 49.5 1.0 CB D:ASP448 4.2 55.4 1.0 C D:GLY447 4.2 55.8 1.0 CA D:ASP448 4.3 55.4 1.0 O2B D:TPP571 4.3 53.4 1.0 N D:ASN475 4.3 64.5 1.0 CB D:ASN475 4.5 64.0 1.0 C D:ASP448 4.6 55.2 1.0 CA D:TRP478 4.7 55.9 1.0 N D:SER477 4.7 61.3 1.0 CA D:GLY479 4.7 56.0 1.0 N D:TRP478 4.8 57.2 1.0 CA D:ASN475 4.8 64.1 1.0 CA D:GLY449 4.9 54.5 1.0 C D:TRP478 4.9 56.0 1.0 CA D:SER477 4.9 60.0 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