Magnesium in PDB 5knu: Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with 9-[N,N-(Bis-3-Phosphonopropyl)Aminomethyl]-9- Deazahypoxanthine

The structure of Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with 9-[N,N-(Bis-3-Phosphonopropyl)Aminomethyl]-9- Deazahypoxanthine, PDB code: 5knu was solved by W.S.Eng, D.T.Keough, O.Baszczynski, D.Hockova, Z.Janeba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.52 / 2.81
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.975, 84.975, 167.723, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with 9-[N,N-(Bis-3-Phosphonopropyl)Aminomethyl]-9- Deazahypoxanthine (pdb code 5knu). 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 E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with 9-[N,N-(Bis-3-Phosphonopropyl)Aminomethyl]-9- Deazahypoxanthine, PDB code: 5knu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with 9-[N,N-(Bis-3-Phosphonopropyl)Aminomethyl]-9- Deazahypoxanthine


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 9-[N,N-(Bis-3-Phosphonopropyl)Aminomethyl]-9- Deazahypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:0.5 occ:1.00 O A:HOH327 2.1 65.0 1.0 O A:HOH326 2.1 61.3 1.0 O A:HOH322 2.1 48.5 1.0 O A:HOH332 2.1 67.6 1.0 OE2 A:GLU103 2.1 66.5 1.0 OD1 A:ASP104 2.2 53.2 1.0 OE1 A:GLU103 2.2 79.2 1.0 CD A:GLU103 2.3 66.0 1.0 CG A:ASP104 3.2 44.2 1.0 OD2 A:ASP104 3.5 46.9 1.0 O A:HOH324 3.6 64.0 1.0 CG A:GLU103 3.7 46.2 1.0 N A:ASP104 4.1 40.9 1.0 O A:LEU45 4.2 35.6 1.0 O A:HOH330 4.2 56.2 1.0 O A:ILE105 4.5 45.8 1.0 CB A:LEU45 4.5 36.4 1.0 CB A:ASP104 4.5 31.7 1.0 N A:ILE105 4.6 38.3 1.0 CB A:GLU103 4.7 36.8 1.0 CA A:GLU103 4.8 32.2 1.0 CA A:ASP104 4.9 33.4 1.0 C A:GLU103 5.0 33.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of E. Coli Hypoxanthine Phosphoribosyltransferase in Complexed with 9-[N,N-(Bis-3-Phosphonopropyl)Aminomethyl]-9- Deazahypoxanthine


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 9-[N,N-(Bis-3-Phosphonopropyl)Aminomethyl]-9- Deazahypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:0.5 occ:1.00 OE2 B:GLU103 2.0 68.4 1.0 O B:HOH331 2.1 70.5 1.0 O B:HOH325 2.1 75.0 1.0 O B:HOH327 2.1 63.2 1.0 OE1 B:GLU103 2.1 81.0 1.0 OD1 B:ASP104 2.2 58.8 1.0 CD B:GLU103 2.3 64.4 1.0 CG B:ASP104 3.2 53.1 1.0 OD2 B:ASP104 3.6 48.3 1.0 CG B:GLU103 3.9 49.9 1.0 N B:ASP104 4.1 32.7 1.0 O B:ILE105 4.3 45.3 1.0 OG B:SER49 4.4 50.8 1.0 CB B:ASP104 4.5 30.3 1.0 N B:ILE105 4.5 35.3 1.0 O B:LEU45 4.6 45.7 1.0 CAN B:6WA201 4.7 85.7 1.0 CB B:GLU103 4.7 35.3 1.0 CB B:LEU45 4.7 37.1 1.0 CA B:ASP104 4.8 31.3 1.0 CA B:GLU103 4.9 32.2 1.0 CG2 B:ILE105 4.9 39.8 1.0 C B:GLU103 5.0 30.8 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