Magnesium in PDB 4cwb: Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor

All present enzymatic activity of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor:
2.7.6.3;

The structure of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor, PDB code: 4cwb was solved by M.L.Dennis, J.D.Swarbrick, T.S.Peat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.33 / 1.56
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	83.817, 83.817, 52.040, 90.00, 90.00, 120.00
R / Rfree (%)	15.877 / 17.816

The binding sites of Magnesium atom in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor (pdb code 4cwb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor, PDB code: 4cwb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1159 b:6.9 occ:1.00 OD2 A:ASP97 2.0 9.0 1.0 O3G A:APC1161 2.0 10.0 1.0 O1B A:APC1161 2.0 12.6 1.0 O A:HOH2083 2.0 16.9 1.0 OD2 A:ASP95 2.1 9.4 1.0 O A:HOH2084 2.7 20.6 1.0 CG A:ASP97 2.9 7.8 1.0 PG A:APC1161 3.1 11.7 1.0 CG A:ASP95 3.1 8.6 1.0 OD1 A:ASP97 3.1 8.2 1.0 PB A:APC1161 3.1 11.9 1.0 MG A:MG1160 3.3 9.4 1.0 O3B A:APC1161 3.4 11.9 1.0 OD1 A:ASP95 3.5 9.4 1.0 O2G A:APC1161 3.6 12.6 1.0 O2B A:APC1161 3.8 13.8 1.0 O A:HOH2086 3.9 12.6 1.0 O A:HOH2008 4.1 17.6 1.0 O A:HOH2082 4.1 12.5 1.0 O A:HOH2085 4.1 9.4 1.0 NH1 A:ARG121 4.2 9.9 1.0 CB A:ASP97 4.3 8.0 1.0 O12 A:X6L1163 4.3 11.5 1.0 NH1 A:ARG92 4.3 10.3 1.0 O1G A:APC1161 4.4 12.8 1.0 CB A:ASP95 4.4 8.6 1.0 C3A A:APC1161 4.6 12.3 1.0 O1A A:APC1161 4.7 10.8 1.0 NE2 A:HIS115 4.8 10.0 1.0

Magnesium binding site 2 out of 2 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1160 b:9.4 occ:1.00 OD1 A:ASP95 2.0 9.4 1.0 O A:HOH2065 2.0 11.5 1.0 O1A A:APC1161 2.1 10.8 1.0 OD1 A:ASP97 2.1 8.2 1.0 O A:HOH2085 2.1 9.4 1.0 O1B A:APC1161 2.1 12.6 1.0 CG A:ASP95 3.0 8.6 1.0 CG A:ASP97 3.2 7.8 1.0 PA A:APC1161 3.2 12.7 1.0 OD2 A:ASP95 3.3 9.4 1.0 PB A:APC1161 3.3 11.9 1.0 MG A:MG1159 3.3 6.9 1.0 C3A A:APC1161 3.5 12.3 1.0 OD2 A:ASP97 3.6 9.0 1.0 O5' A:APC1161 3.8 15.9 1.0 O2G A:APC1161 4.0 12.6 1.0 OE2 A:GLU78 4.0 11.1 1.0 O A:VAL96 4.2 8.4 1.0 NH1 A:ARG83 4.3 12.2 1.0 CB A:ASP95 4.3 8.6 1.0 O2B A:APC1161 4.3 13.8 1.0 O A:HOH2063 4.4 21.0 1.0 O3B A:APC1161 4.4 11.9 1.0 CB A:ASP97 4.5 8.0 1.0 C A:VAL96 4.5 8.0 1.0 N3 A:APC1161 4.5 12.8 1.0 O2A A:APC1161 4.5 13.9 1.0 O3G A:APC1161 4.5 10.0 1.0 C2 A:APC1161 4.5 12.2 1.0 PG A:APC1161 4.6 11.7 1.0 N A:VAL96 4.6 8.3 1.0 CA A:ASP97 4.7 8.1 1.0 CA A:ASP95 4.8 8.6 1.0 N A:ASP97 4.8 8.2 1.0 O A:HOH2083 4.9 16.9 1.0 NH1 A:ARG92 4.9 10.3 1.0 C A:ASP95 5.0 8.2 1.0

M.L.Dennis, S.Chhabra, Z.Wang, A.Debono, O.Dolezal, J.Newman, N.P.Pitcher, R.Rahmani, B.Cleary, N.Barlow, M.Hattarki, B.Graham, T.S.Peat, J.B.Baell, J.D.Swarbrick. Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives As Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase From Staphylococcus Aureus. J.Med.Chem. V. 57 9612 2014.
ISSN: ISSN 0022-2623
PubMed: 25357262
DOI: 10.1021/JM501417F