Magnesium in PDB 2ioh: Crystal Structure of Phosphonoacetaldehyde Hydrolase with A K53R Mutation

The structure of Crystal Structure of Phosphonoacetaldehyde Hydrolase with A K53R Mutation, PDB code: 2ioh was solved by K.A.Allen, S.D.Lahiri, G.Zhang, D.Dunaway-Mariano, E.Peisach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	251.728, 251.728, 156.340, 90.00, 90.00, 120.00
R / Rfree (%)	25.3 / 26.5

The binding sites of Magnesium atom in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with A K53R Mutation (pdb code 2ioh). 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 Phosphonoacetaldehyde Hydrolase with A K53R Mutation, PDB code: 2ioh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with A K53R Mutation


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 A K53R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg321 b:23.1 occ:1.00 OD1 A:ASP186 2.1 32.7 1.0 O1 A:PO4320 2.3 66.0 1.0 O A:ALA14 2.4 27.0 1.0 OD1 A:ASP12 2.6 34.7 1.0 CG A:ASP186 2.8 31.9 1.0 OD2 A:ASP186 2.9 31.5 1.0 C A:ALA14 3.5 28.1 1.0 P A:PO4320 3.7 65.7 1.0 CG A:ASP12 3.8 35.7 1.0 CG2 A:THR187 4.0 27.8 1.0 OD2 A:ASP12 4.2 38.0 1.0 O2 A:PO4320 4.3 65.7 1.0 CB A:ASP186 4.3 31.2 1.0 OD1 A:ASP190 4.4 38.1 1.0 N A:GLY15 4.4 27.8 1.0 CA A:GLY15 4.5 27.3 1.0 CA A:ALA14 4.5 29.5 1.0 O3 A:PO4320 4.5 67.4 1.0 CB A:ALA14 4.6 28.5 1.0 O4 A:PO4320 4.6 65.4 1.0 OG A:SER209 4.7 42.9 1.0 N A:ALA14 4.7 32.2 1.0 OG1 A:THR16 4.8 24.4 1.0 N A:ASP186 4.9 32.6 1.0 C A:GLY15 5.0 26.8 1.0 CA A:ASP186 5.0 32.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with A K53R Mutation


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 A K53R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg321 b:23.1 occ:1.00 OD1 B:ASP186 2.1 32.7 1.0 O1 B:PO4320 2.3 66.0 1.0 O B:ALA14 2.4 27.0 1.0 OD1 B:ASP12 2.6 34.7 1.0 CG B:ASP186 2.8 31.9 1.0 OD2 B:ASP186 2.9 31.5 1.0 C B:ALA14 3.6 28.1 1.0 P B:PO4320 3.7 65.7 1.0 CG B:ASP12 3.8 35.7 1.0 CG2 B:THR187 4.0 27.8 1.0 OD2 B:ASP12 4.2 38.0 1.0 O2 B:PO4320 4.3 65.7 1.0 CB B:ASP186 4.3 31.2 1.0 OD1 B:ASP190 4.4 38.1 1.0 N B:GLY15 4.4 27.8 1.0 CA B:GLY15 4.5 27.3 1.0 CA B:ALA14 4.5 29.5 1.0 O3 B:PO4320 4.5 67.4 1.0 CB B:ALA14 4.6 28.5 1.0 O4 B:PO4320 4.6 65.4 1.0 OG B:SER209 4.7 42.9 1.0 N B:ALA14 4.7 32.2 1.0 OG1 B:THR16 4.8 24.4 1.0 N B:ASP186 4.9 32.6 1.0 C B:GLY15 5.0 26.8 1.0 CA B:ASP186 5.0 32.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with A K53R Mutation


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 Phosphonoacetaldehyde Hydrolase with A K53R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg321 b:23.1 occ:1.00 OD1 C:ASP186 2.1 32.7 1.0 O1 C:PO4320 2.3 66.0 1.0 O C:ALA14 2.4 27.0 1.0 OD1 C:ASP12 2.6 34.7 1.0 CG C:ASP186 2.8 31.9 1.0 OD2 C:ASP186 2.9 31.5 1.0 C C:ALA14 3.5 28.1 1.0 P C:PO4320 3.7 65.7 1.0 CG C:ASP12 3.8 35.7 1.0 CG2 C:THR187 4.0 27.8 1.0 OD2 C:ASP12 4.2 38.0 1.0 O2 C:PO4320 4.3 65.7 1.0 CB C:ASP186 4.3 31.2 1.0 OD1 C:ASP190 4.4 38.1 1.0 N C:GLY15 4.4 27.8 1.0 CA C:GLY15 4.5 27.3 1.0 CA C:ALA14 4.5 29.5 1.0 O3 C:PO4320 4.5 67.4 1.0 CB C:ALA14 4.6 28.5 1.0 O4 C:PO4320 4.6 65.4 1.0 OG C:SER209 4.7 42.9 1.0 N C:ALA14 4.7 32.2 1.0 OG1 C:THR16 4.8 24.4 1.0 N C:ASP186 4.9 32.6 1.0 C C:GLY15 5.0 26.8 1.0 CA C:ASP186 5.0 32.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Phosphonoacetaldehyde Hydrolase with A K53R Mutation


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 Phosphonoacetaldehyde Hydrolase with A K53R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg321 b:23.1 occ:1.00 OD1 D:ASP186 2.1 32.7 1.0 O1 D:PO4320 2.3 66.0 1.0 O D:ALA14 2.4 27.0 1.0 OD1 D:ASP12 2.6 34.7 1.0 CG D:ASP186 2.8 31.9 1.0 OD2 D:ASP186 2.9 31.5 1.0 C D:ALA14 3.5 28.1 1.0 P D:PO4320 3.7 65.7 1.0 CG D:ASP12 3.8 35.7 1.0 CG2 D:THR187 4.0 27.8 1.0 OD2 D:ASP12 4.2 38.0 1.0 O2 D:PO4320 4.3 65.7 1.0 CB D:ASP186 4.3 31.2 1.0 OD1 D:ASP190 4.4 38.1 1.0 N D:GLY15 4.4 27.8 1.0 CA D:GLY15 4.5 27.3 1.0 CA D:ALA14 4.5 29.5 1.0 O3 D:PO4320 4.5 67.4 1.0 CB D:ALA14 4.6 28.5 1.0 O4 D:PO4320 4.6 65.4 1.0 OG D:SER209 4.7 42.9 1.0 N D:ALA14 4.7 32.2 1.0 OG1 D:THR16 4.8 24.4 1.0 N D:ASP186 4.9 32.6 1.0 C D:GLY15 5.0 26.8 1.0 CA D:ASP186 5.0 32.3 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