Sodium in PDB 5etq: S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution

The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution, PDB code: 5etq was solved by M.L.Dennis, T.S.Peat, J.D.Swarbrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.76 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.630, 68.200, 52.820, 90.00, 106.05, 90.00
R / Rfree (%)	18.2 / 21.6

The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution (pdb code 5etq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution, PDB code: 5etq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:15.6 occ:1.00 O A:ILE32 2.2 6.5 1.0 O A:HOH315 2.4 11.4 1.0 O A:TYR29 2.4 8.1 1.0 O A:HOH370 2.4 19.7 1.0 O A:ASN27 2.4 5.1 1.0 C A:ILE32 3.4 7.8 1.0 C A:TYR29 3.5 8.7 1.0 C A:ASN27 3.5 5.7 1.0 N A:ILE32 4.0 7.0 1.0 C A:GLU28 4.1 7.8 1.0 N A:TYR29 4.1 8.2 1.0 CA A:ILE32 4.2 7.8 1.0 N A:ASP30 4.3 11.2 1.0 N A:SER33 4.3 7.5 1.0 CA A:ASP30 4.3 11.8 1.0 N A:GLU28 4.3 6.9 1.0 CA A:GLU28 4.3 8.5 1.0 O A:GLU28 4.4 7.2 1.0 CA A:TYR29 4.4 10.3 1.0 OG A:SER33 4.4 16.5 1.0 CA A:SER33 4.4 9.1 1.0 CA A:ASN27 4.5 5.5 1.0 N A:GLY31 4.6 9.1 1.0 CB A:ILE32 4.7 8.3 1.0 C A:ASP30 4.7 10.8 1.0 OD1 A:ASN27 4.7 4.4 1.0 O A:LEU26 4.8 4.8 1.0 OD1 A:ASP30 4.9 21.1 1.0 CG A:ASN27 5.0 4.8 1.0 CB A:SER33 5.0 10.5 1.0

Sodium binding site 2 out of 3 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:29.8 occ:1.00 O B:HOH311 2.1 23.9 1.0 O B:HOH332 2.1 28.9 1.0 O A:HOH333 2.2 25.1 1.0 OD1 B:ASP107 2.3 27.6 1.0 OD1 A:ASP107 2.3 16.3 1.0 CG A:ASP107 3.4 17.7 1.0 CG B:ASP107 3.4 27.5 1.0 OD2 A:ASP107 3.8 21.2 1.0 OD2 B:ASP107 3.9 39.2 1.0 OG B:SER112 4.0 13.9 1.0 O B:LEU108 4.2 11.1 1.0 O A:LEU108 4.3 8.4 1.0 OG A:SER112 4.4 19.3 1.0 C A:ASP107 4.6 9.1 1.0 C A:LEU108 4.6 8.7 1.0 C B:ASP107 4.6 13.0 1.0 CB B:ASP107 4.7 19.4 1.0 C B:LEU108 4.7 9.7 1.0 O A:ASP107 4.7 8.9 1.0 CB A:ASP107 4.7 14.0 1.0 O B:ASP107 4.8 16.1 1.0 CA B:ASP107 4.8 14.4 1.0 N A:LEU108 4.9 7.8 1.0 N B:LEU108 4.9 8.9 1.0 CA A:ASP107 4.9 11.0 1.0

Sodium binding site 3 out of 3 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.96 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:18.8 occ:1.00 O B:ILE32 2.2 6.9 1.0 O B:ASN27 2.4 3.9 1.0 O B:HOH358 2.4 14.9 1.0 O B:TYR29 2.6 9.9 1.0 C B:ILE32 3.4 7.4 1.0 C B:ASN27 3.5 4.8 1.0 C B:TYR29 3.6 9.9 1.0 C B:GLU28 4.1 7.7 1.0 N B:TYR29 4.1 7.8 1.0 N B:ILE32 4.1 7.1 1.0 N B:SER33 4.3 8.1 1.0 CA B:ILE32 4.3 7.0 1.0 N B:GLU28 4.3 5.8 1.0 CA B:GLU28 4.3 7.1 1.0 CA B:SER33 4.3 10.2 1.0 OG B:SER33 4.4 19.4 1.0 CA B:ASN27 4.4 4.2 1.0 N B:ASP30 4.4 10.4 1.0 O B:GLU28 4.4 5.8 1.0 CA B:ASP30 4.5 11.5 1.0 CA B:TYR29 4.5 10.2 1.0 OD1 B:ASN27 4.6 3.1 1.0 N B:GLY31 4.8 8.1 1.0 CB B:ILE32 4.8 7.8 1.0 CG B:ASN27 4.9 3.5 1.0 CB B:SER33 4.9 11.1 1.0 C B:ASP30 4.9 9.5 1.0 O B:LEU26 4.9 4.3 1.0

M.L.Dennis, N.P.Pitcher, M.D.Lee, A.J.Debono, Z.C.Wang, J.R.Harjani, R.Rahmani, B.Cleary, T.S.Peat, J.B.Baell, J.D.Swarbrick. Structural Basis For the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase From Staphylococcus Aureus and Escherichia Coli. J.Med.Chem. V. 59 5248 2016.
ISSN: ISSN 0022-2623
PubMed: 27094768
DOI: 10.1021/ACS.JMEDCHEM.6B00002