Magnesium in PDB 5knx: Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid

The structure of Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid, PDB code: 5knx was solved by W.S.Eng, D.T.Keough, D.Hockova, Z.Janeba, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.83 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.380, 85.380, 167.475, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid (pdb code 5knx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid, PDB code: 5knx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid


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 E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:86.9 occ:1.00 O A:HOH372 2.1 67.2 1.0 O A:HOH373 2.1 65.3 1.0 O A:HOH302 2.1 48.5 1.0 OE2 A:GLU103 2.1 45.0 1.0 O A:HOH374 2.1 65.9 1.0 OD1 A:ASP104 2.2 53.7 1.0 CD A:GLU103 2.9 53.0 1.0 CG A:ASP104 3.2 49.4 1.0 OE1 A:GLU103 3.3 62.8 1.0 OD2 A:ASP104 3.6 41.6 1.0 O A:HOH365 3.9 54.4 1.0 CG A:GLU103 4.1 45.3 1.0 O A:ILE105 4.2 43.6 1.0 N A:ASP104 4.2 39.4 1.0 O A:HOH327 4.3 49.7 1.0 N A:ILE105 4.4 39.6 1.0 CB A:ASP104 4.5 36.0 1.0 CAL A:6WC201 4.5 0.5 1.0 CA A:ASP104 4.8 41.3 1.0 OAG A:6WC201 4.9 94.5 1.0 CAJ A:6WC201 4.9 96.0 1.0 O A:HOH378 4.9 64.0 1.0 O A:LEU45 5.0 40.2 1.0 CA A:GLY48 5.0 35.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid


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 E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:0.7 occ:1.00 O B:HOH341 2.1 69.6 1.0 O B:HOH378 2.1 57.8 1.0 O B:HOH306 2.1 52.8 1.0 O B:HOH362 2.1 68.1 1.0 O B:HOH333 2.1 49.4 1.0 OD1 B:ASP104 3.1 50.7 1.0 OD2 B:ASP104 3.3 47.5 1.0 CG B:ASP104 3.5 41.0 1.0 OE2 B:GLU103 3.8 50.6 1.0 CA B:GLY48 4.0 39.2 1.0 O B:HOH349 4.1 61.4 1.0 N B:GLY48 4.2 38.8 1.0 CAK B:6WC201 4.2 90.3 1.0 OAS B:6WC201 4.5 95.5 1.0 CD B:GLU103 4.6 45.1 1.0 OAR B:6WC201 4.6 82.2 1.0 OE1 B:GLU103 4.7 59.8 1.0 O B:LEU45 4.8 44.4 1.0 C B:GLY48 4.8 36.5 1.0 CB B:ASP104 5.0 32.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid


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 E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with {[(2-[(Hypoxanthin-9H-Yl)Methyl]Propane-1,3-Diyl) Bis(Oxy)]Bis- (Methylene)}Diphosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:0.7 occ:1.00 O B:HOH380 2.1 63.5 1.0 O B:HOH372 2.1 70.5 1.0 OAG B:6WC201 2.5 0.0 1.0 OAF B:6WC201 2.5 1.0 1.0 PAZ B:6WC201 2.8 0.7 1.0 CAM B:6WC201 3.2 0.1 1.0 OD1 B:ASP163 3.4 46.6 1.0 OD2 B:ASP163 3.6 50.6 1.0 CG B:ASP163 3.9 48.0 1.0 O B:HOH303 4.3 83.4 1.0 O B:HOH401 4.3 63.6 1.0 OAC B:6WC201 4.3 0.9 1.0 OAS B:6WC201 4.5 95.5 1.0 N B:ALA165 4.7 52.0 1.0 O B:ASP163 4.8 37.8 1.0 NE2 B:GLN166 4.8 54.1 1.0 N3 B:6WC201 4.9 61.4 1.0 O B:HOH361 4.9 55.5 1.0

W.S.Eng, D.Hockova, P.Spacek, O.Baszczynski, Z.Janeba, L.Naesens, D.T.Keough, L.W.Guddat. Crystal Structures of Acyclic Nucleoside Phosphonates in Complex with Escherichia Coli Hypoxanthine Phosphoribosyltransferase Chemistryselect V. 1 6267 2016.
ISSN: ESSN 2365-6549
DOI: 10.1002/SLCT.201601679