Magnesium 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:

Sodium

(Na)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg201 b:12.3 occ:1.00 O2B A:APC203 2.0 13.5 1.0 O3G A:APC203 2.1 10.9 1.0 O A:HOH342 2.1 12.6 1.0 OD2 A:ASP97 2.1 7.5 1.0 OD2 A:ASP95 2.1 6.4 1.0 O A:HOH355 2.2 11.1 1.0 CG A:ASP97 3.0 7.2 1.0 CG A:ASP95 3.1 7.0 1.0 PB A:APC203 3.2 11.3 1.0 PG A:APC203 3.2 12.9 1.0 OD1 A:ASP97 3.2 7.0 1.0 O3B A:APC203 3.3 12.2 1.0 MG A:MG202 3.4 11.0 1.0 OD1 A:ASP95 3.5 6.5 1.0 O1B A:APC203 3.8 12.2 1.0 O A:HOH345 3.9 11.8 1.0 O2G A:APC203 3.9 13.1 1.0 O A:HOH354 4.0 22.2 1.0 O A:HOH360 4.1 16.9 1.0 N11 A:YH2204 4.3 13.7 1.0 NH1 A:ARG121 4.4 7.5 1.0 O1G A:APC203 4.4 10.9 1.0 CB A:ASP97 4.4 7.1 1.0 CB A:ASP95 4.4 6.8 1.0 O A:HOH327 4.5 6.3 1.0 C3A A:APC203 4.7 10.4 1.0 NE2 A:HIS115 4.7 9.1 1.0 NH1 A:ARG92 4.7 18.8 1.0 S12 A:YH2204 4.8 18.2 1.0 O2A A:APC203 4.9 9.5 1.0 C10 A:YH2204 5.0 17.0 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg202 b:11.0 occ:1.00 O A:HOH327 2.0 6.3 1.0 O2A A:APC203 2.0 9.5 1.0 O A:HOH310 2.0 9.1 1.0 OD1 A:ASP95 2.1 6.5 1.0 OD1 A:ASP97 2.1 7.0 1.0 O2B A:APC203 2.2 13.5 1.0 PB A:APC203 3.0 11.3 1.0 CG A:ASP95 3.1 7.0 1.0 PA A:APC203 3.2 12.1 1.0 CG A:ASP97 3.2 7.2 1.0 OD2 A:ASP95 3.4 6.4 1.0 MG A:MG201 3.4 12.3 1.0 C3A A:APC203 3.5 10.4 1.0 OD2 A:ASP97 3.6 7.5 1.0 O5' A:APC203 3.6 11.8 1.0 OE2 A:GLU78 4.1 9.2 1.0 O1B A:APC203 4.2 12.2 1.0 O A:VAL96 4.2 6.9 1.0 O A:HOH311 4.3 25.9 1.0 O3B A:APC203 4.3 12.2 1.0 NH1 A:ARG83 4.4 8.2 1.0 CB A:ASP95 4.5 6.8 1.0 O A:HOH301 4.5 21.6 1.0 CB A:ASP97 4.5 7.1 1.0 C A:VAL96 4.6 7.6 1.0 N3 A:APC203 4.6 15.1 1.0 C2 A:APC203 4.6 13.0 1.0 O1A A:APC203 4.6 12.0 1.0 O3G A:APC203 4.6 10.9 1.0 O A:HOH342 4.6 12.6 1.0 N A:VAL96 4.7 7.4 1.0 NH2 A:ARG83 4.7 7.8 1.0 O2G A:APC203 4.7 13.1 1.0 CA A:ASP97 4.7 7.2 1.0 N A:ASP97 4.8 8.3 1.0 PG A:APC203 4.9 12.9 1.0 CA A:ASP95 4.9 6.6 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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:Mg201 b:14.1 occ:1.00 O1A B:APC203 2.0 14.1 1.0 O2B B:APC203 2.1 11.2 1.0 O B:HOH309 2.1 11.6 1.0 O B:HOH341 2.1 9.9 1.0 OD1 B:ASP97 2.1 5.6 1.0 OD1 B:ASP95 2.1 4.8 1.0 CG B:ASP95 3.1 6.1 1.0 PB B:APC203 3.1 13.8 1.0 PA B:APC203 3.2 14.1 1.0 CG B:ASP97 3.2 5.8 1.0 C3A B:APC203 3.4 13.1 1.0 OD2 B:ASP95 3.4 6.3 1.0 MG B:MG202 3.6 13.3 1.0 OD2 B:ASP97 3.7 6.4 1.0 O5' B:APC203 3.7 16.9 1.0 O1B B:APC203 3.9 14.1 1.0 OE2 B:GLU78 4.1 10.6 1.0 O B:VAL96 4.2 5.8 1.0 O B:HOH301 4.2 22.7 1.0 NH1 B:ARG83 4.3 13.6 1.0 O3B B:APC203 4.5 13.4 1.0 CB B:ASP95 4.5 6.1 1.0 O2A B:APC203 4.5 14.2 1.0 CB B:ASP97 4.5 6.3 1.0 C B:VAL96 4.6 5.6 1.0 O B:HOH313 4.6 19.3 1.0 N3 B:APC203 4.6 15.7 1.0 C2 B:APC203 4.6 11.5 1.0 N B:VAL96 4.6 6.9 1.0 O1G B:APC203 4.7 10.2 1.0 O B:HOH329 4.7 12.3 1.0 CA B:ASP97 4.7 6.2 1.0 O2G B:APC203 4.8 13.5 1.0 N B:ASP97 4.8 6.3 1.0 NH2 B:ARG83 4.8 10.2 1.0 CA B:ASP95 4.9 6.7 1.0 PG B:APC203 4.9 14.0 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg202 b:13.3 occ:1.00 O1G B:APC203 2.0 10.2 1.0 O B:HOH348 2.1 12.0 1.0 O B:HOH329 2.1 12.3 1.0 O2B B:APC203 2.1 11.2 1.0 OD2 B:ASP97 2.2 6.4 1.0 OD2 B:ASP95 2.2 6.3 1.0 CG B:ASP97 3.1 5.8 1.0 PB B:APC203 3.1 13.8 1.0 PG B:APC203 3.2 14.0 1.0 CG B:ASP95 3.2 6.1 1.0 OD1 B:ASP97 3.3 5.6 1.0 O3B B:APC203 3.3 13.4 1.0 MG B:MG201 3.6 14.1 1.0 OD1 B:ASP95 3.6 4.8 1.0 O1B B:APC203 3.8 14.1 1.0 O B:HOH326 3.9 10.5 1.0 O2G B:APC203 4.0 13.5 1.0 O B:HOH347 4.1 12.3 1.0 O B:HOH350 4.1 23.5 1.0 NH1 B:ARG121 4.2 6.6 1.0 N11 B:YH2204 4.3 14.7 1.0 O3G B:APC203 4.3 11.4 1.0 CB B:ASP95 4.5 6.1 1.0 CB B:ASP97 4.5 6.3 1.0 NE2 B:HIS115 4.6 11.6 1.0 C3A B:APC203 4.7 13.1 1.0 O B:HOH341 4.7 9.9 1.0 NH1 B:ARG92 4.8 14.8 1.0 S12 B:YH2204 4.8 18.5 1.0 O1A B:APC203 4.9 14.1 1.0 C10 B:YH2204 5.0 17.9 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