Magnesium in PDB 2iof: Crystal Structure of Phosphonoacetaldehyde Hydrolase with Sodium Borohydride-Reduced Substrate Intermediate

The structure of Crystal Structure of Phosphonoacetaldehyde Hydrolase with Sodium Borohydride-Reduced Substrate Intermediate, PDB code: 2iof was solved by K.A.Allen, S.D.Lahiri, G.Zhang, D.Dunaway-Mariano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	159.820, 64.020, 98.330, 90.00, 123.52, 90.00
R / Rfree (%)	23.1 / 29.8

The binding sites of Magnesium atom in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with Sodium Borohydride-Reduced Substrate Intermediate (pdb code 2iof). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with Sodium Borohydride-Reduced Substrate Intermediate, PDB code: 2iof:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with Sodium Borohydride-Reduced Substrate Intermediate


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 Phosphonoacetaldehyde Hydrolase with Sodium Borohydride-Reduced Substrate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg462 b:13.3 occ:1.00 O A:ALA14 2.3 18.3 1.0 O3 A:PO4361 2.4 39.1 1.0 OD1 A:ASP186 2.4 28.0 1.0 OD2 A:ASP12 2.5 23.2 1.0 OD2 A:ASP186 2.7 27.1 1.0 CG A:ASP186 2.9 27.1 1.0 C A:ALA14 3.5 19.2 1.0 CG A:ASP12 3.7 20.9 1.0 P A:PO4361 3.8 38.6 1.0 CG2 A:THR187 3.9 22.6 1.0 O1 A:PO4361 4.2 39.0 1.0 OD2 A:ASP190 4.3 32.4 1.0 OD1 A:ASP12 4.3 22.0 1.0 CB A:ASP186 4.4 25.5 1.0 O A:HOH576 4.4 35.4 1.0 CA A:ALA14 4.4 18.0 1.0 O4 A:PO4361 4.5 38.0 1.0 SG A:CYS22 4.5 33.7 1.0 N A:GLY15 4.5 21.2 1.0 N A:ALA14 4.5 16.6 1.0 CB A:ALA14 4.6 18.2 1.0 CA A:GLY15 4.7 23.2 1.0 O2 A:PO4361 4.7 36.5 1.0 OG1 A:THR16 4.8 25.0 1.0 N A:ASP186 4.8 24.5 1.0 NH1 A:ARG160 4.9 33.1 1.0 CB A:ASP12 4.9 17.4 1.0 CA A:ASP186 4.9 24.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with Sodium Borohydride-Reduced Substrate Intermediate


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 Phosphonoacetaldehyde Hydrolase with Sodium Borohydride-Reduced Substrate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg462 b:2.9 occ:1.00 O K:HOH535 2.2 2.3 1.0 OD1 K:ASP186 2.3 25.1 1.0 O1 K:PO4361 2.4 42.9 1.0 O K:ALA14 2.5 11.9 1.0 OD2 K:ASP186 2.7 21.4 1.0 OD1 K:ASP12 2.7 15.3 1.0 CG K:ASP186 2.8 22.6 1.0 O K:HOH631 3.3 45.5 1.0 C K:ALA14 3.7 11.4 1.0 CG K:ASP12 3.8 12.2 1.0 P K:PO4361 3.8 43.4 1.0 OG1 K:THR187 4.0 19.6 1.0 OD2 K:ASP12 4.1 11.5 1.0 OD1 K:ASP190 4.2 23.3 1.0 O K:HOH527 4.2 6.2 1.0 CG2 K:THR187 4.2 20.2 1.0 CB K:ASP186 4.3 20.8 1.0 O3 K:PO4361 4.3 42.2 1.0 O2 K:PO4361 4.4 43.4 1.0 O K:HOH616 4.5 35.9 1.0 N K:GLY15 4.6 11.1 1.0 CA K:GLY15 4.6 10.3 1.0 CA K:ALA14 4.7 11.2 1.0 N K:ASP186 4.7 18.9 1.0 NH1 K:ARG160 4.7 21.9 1.0 O4 K:PO4361 4.8 43.2 1.0 CB K:THR187 4.8 19.8 1.0 CB K:ALA14 4.8 10.7 1.0 N K:ALA14 4.8 10.9 1.0 CA K:ASP186 4.9 19.8 1.0 O K:HOH588 4.9 29.4 1.0 C K:ASP186 4.9 19.4 1.0 OG1 K:THR16 4.9 1.4 1.0 N K:THR187 5.0 18.9 1.0

S.D.Lahiri, G.Zhang, D.Dunaway-Mariano, K.N.Allen. Diversification of Function in the Haloacid Dehalogenase Enzyme Superfamily: the Role of the Cap Domain in Hydrolytic Phosphoruscarbon Bond Cleavage. Bioorg.Chem. V. 34 394 2006.
ISSN: ISSN 0045-2068
PubMed: 17070898
DOI: 10.1016/J.BIOORG.2006.09.007