Magnesium in PDB 4uph: Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter

The structure of Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter, PDB code: 4uph was solved by G.Fischer, B.V.Loo, M.Hyvonen, F.Hollfelder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.17 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	232.690, 232.690, 112.050, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.5

The structure of Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter (pdb code 4uph). 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 Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter, PDB code: 4uph:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter


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 Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:36.9 occ:1.00 OG1 A:DDZ64 1.9 58.7 1.0 OD1 A:ASP24 2.0 65.3 1.0 NE2 A:HIS329 2.1 51.3 1.0 OD2 A:ASP328 2.1 57.1 1.0 OD2 A:ASP24 2.5 67.5 1.0 CG A:ASP24 2.6 61.9 1.0 CE1 A:HIS329 2.9 50.7 1.0 CD2 A:HIS329 3.0 51.7 1.0 CG A:ASP328 3.0 55.4 1.0 CB A:DDZ64 3.0 52.3 1.0 OD1 A:ASP328 3.3 57.5 1.0 OG2 A:DDZ64 3.4 50.9 1.0 CA A:DDZ64 3.5 45.4 1.0 ND1 A:HIS329 3.9 50.9 1.0 CG A:HIS329 4.0 49.2 1.0 N A:DDZ64 4.0 44.2 1.0 CB A:ASP24 4.0 45.1 1.0 ND1 A:HIS222 4.3 51.8 1.0 CB A:ASP328 4.4 46.7 1.0 NH2 A:ARG68 4.6 36.9 1.0 N A:GLN25 4.6 42.9 1.0 OE1 A:GLN25 4.6 57.8 1.0 CA A:ASP24 4.7 44.0 1.0 NE A:ARG68 4.7 54.5 1.0 CE1 A:HIS222 4.8 51.3 1.0 C A:DDZ64 4.9 46.4 1.0 NZ A:LYS341 4.9 39.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter


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 Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:44.1 occ:1.00 OD2 B:ASP328 2.0 55.1 1.0 NE2 B:HIS329 2.1 52.6 1.0 OD1 B:ASP24 2.1 66.8 1.0 OG1 B:DDZ64 2.1 58.9 1.0 OD2 B:ASP24 2.4 74.1 1.0 CG B:ASP24 2.5 66.2 1.0 CE1 B:HIS329 2.8 51.8 1.0 CG B:ASP328 2.9 59.1 1.0 CD2 B:HIS329 3.1 52.7 1.0 CB B:DDZ64 3.1 56.1 1.0 OD1 B:ASP328 3.2 60.1 1.0 CA B:DDZ64 3.5 52.4 1.0 OG2 B:DDZ64 3.5 56.1 1.0 ND1 B:HIS329 3.8 52.4 1.0 CG B:HIS329 3.9 50.8 1.0 CB B:ASP24 4.0 57.0 1.0 N B:DDZ64 4.0 52.4 1.0 CB B:ASP328 4.3 51.6 1.0 ND1 B:HIS222 4.4 66.6 1.0 NH2 B:ARG68 4.4 67.1 1.0 O B:HOH2014 4.5 55.5 1.0 NE B:ARG68 4.6 64.0 1.0 N B:GLN25 4.6 54.0 1.0 OE1 B:GLN25 4.7 77.6 1.0 CA B:ASP24 4.7 55.1 1.0 C B:DDZ64 4.8 54.6 1.0 CE1 B:HIS222 4.8 65.7 1.0 NZ B:LYS341 4.9 61.6 1.0 C B:PRO63 5.0 55.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter


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 Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:35.9 occ:1.00 OD2 C:ASP328 2.0 60.1 1.0 OG1 C:DDZ64 2.1 65.5 1.0 OD2 C:ASP24 2.2 74.8 1.0 NE2 C:HIS329 2.3 61.3 1.0 OD1 C:ASP24 2.3 68.3 1.0 CG C:ASP24 2.5 66.0 1.0 CG C:ASP328 3.0 57.2 1.0 CB C:DDZ64 3.0 60.0 1.0 CE1 C:HIS329 3.1 60.8 1.0 CD2 C:HIS329 3.1 61.2 1.0 OG2 C:DDZ64 3.2 61.3 1.0 OD1 C:ASP328 3.2 58.4 1.0 CA C:DDZ64 3.6 52.1 1.0 CB C:ASP24 4.0 55.0 1.0 N C:DDZ64 4.1 52.5 1.0 CG C:HIS329 4.1 58.5 1.0 ND1 C:HIS329 4.1 60.9 1.0 ND1 C:HIS222 4.2 63.5 1.0 CB C:ASP328 4.3 53.5 1.0 NH2 C:ARG68 4.4 49.1 1.0 NE C:ARG68 4.5 52.8 1.0 N C:GLN25 4.6 52.9 1.0 OE1 C:GLN25 4.6 62.6 1.0 CE1 C:HIS222 4.7 63.3 1.0 CA C:ASP24 4.7 52.7 1.0 NZ C:LYS341 4.7 63.2 1.0 C C:DDZ64 4.9 54.3 1.0 O C:HOH2010 4.9 50.1 1.0 CZ C:ARG68 5.0 57.2 1.0 OH C:TYR112 5.0 75.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter


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 Phosphonate Monoester Hydrolase of Agrobacterium Radiobacter within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:56.5 occ:1.00 OD1 D:ASP24 2.1 78.8 1.0 OD2 D:ASP328 2.1 69.9 1.0 OG1 D:DDZ64 2.1 53.4 1.0 NE2 D:HIS329 2.2 65.7 1.0 OD2 D:ASP24 2.5 73.5 1.0 CG D:ASP24 2.5 74.9 1.0 CE1 D:HIS329 2.9 65.1 1.0 CB D:DDZ64 3.0 51.7 1.0 CG D:ASP328 3.0 67.0 1.0 OG2 D:DDZ64 3.2 53.3 1.0 CD2 D:HIS329 3.2 66.0 1.0 OD1 D:ASP328 3.3 68.2 1.0 CA D:DDZ64 3.5 51.3 1.0 ND1 D:HIS329 3.9 65.5 1.0 N D:DDZ64 4.0 50.5 1.0 CB D:ASP24 4.0 63.7 1.0 CG D:HIS329 4.1 63.4 1.0 ND1 D:HIS222 4.2 77.1 1.0 CB D:ASP328 4.4 57.4 1.0 NZ D:LYS341 4.4 60.6 1.0 O D:HOH2007 4.5 57.3 1.0 NH2 D:ARG68 4.5 53.9 1.0 OE1 D:GLN25 4.6 80.2 1.0 NE D:ARG68 4.6 68.5 1.0 CE1 D:HIS222 4.7 76.2 1.0 CA D:ASP24 4.7 61.8 1.0 N D:GLN25 4.7 63.3 1.0 C D:DDZ64 4.8 58.5 1.0

B.Van Loo, C.D.Bayer, G.Fischer, S.Jonas, E.Valkov, M.F.Mohamed, A.Vorobieva, C.Dutruel, M.Hyvonen, F.Hollfelder. Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily. J.Am.Chem.Soc. V. 141 370 2019.
ISSN: ESSN 1520-5126
PubMed: 30497259
DOI: 10.1021/JACS.8B10290