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Magnesium in PDB 5etv: S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 Angstrom Resolution

Enzymatic activity of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 Angstrom Resolution

All present enzymatic activity of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 Angstrom Resolution:
2.7.6.3;

Protein crystallography data

The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 Angstrom Resolution, PDB code: 5etv 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) 42.57 / 1.72
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 84.250, 84.250, 52.411, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 20.7

Other elements in 5etv:

The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 Angstrom Resolution also contains other interesting chemical elements:

Bromine (Br) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 Angstrom Resolution (pdb code 5etv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 Angstrom Resolution, PDB code: 5etv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5etv

Go back to Magnesium Binding Sites List in 5etv
Magnesium binding site 1 out of 2 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 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 1.72 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:10.3
occ:1.00
 O A:HOH358 2.1 12.7 1.0
O1G A:APC201 2.1 11.3 1.0
OD2 A:ASP97 2.1 8.5 1.0
OD2 A:ASP95 2.1 8.6 1.0
O A:HOH320 2.1 12.4 1.0
O1B A:APC201 2.3 13.1 1.0
CG A:ASP97 3.0 7.5 1.0
CG A:ASP95 3.2 8.4 1.0
PG A:APC201 3.2 12.2 1.0
PB A:APC201 3.2 13.1 1.0
OD1 A:ASP97 3.3 6.9 1.0
O3B A:APC201 3.4 11.9 1.0
MG A:MG204 3.6 11.2 1.0
OD1 A:ASP95 3.6 6.8 1.0
O A:HOH335 3.8 13.7 1.0
O2G A:APC201 3.8 12.5 1.0
O2B A:APC201 3.8 14.2 1.0
O A:HOH382 4.0 15.9 1.0
O A:HOH346 4.1 13.8 1.0
NH1 A:ARG121 4.2 9.0 1.0
NH1 A:ARG92 4.2 9.7 1.0
CB A:ASP97 4.4 6.7 1.0
O A:HOH326 4.4 12.0 1.0
N17 A:5RZ202 4.4 13.8 1.0
O3G A:APC201 4.5 10.8 1.0
CB A:ASP95 4.5 7.8 1.0
C3A A:APC201 4.8 12.6 1.0
O20 A:5RZ202 4.9 12.1 1.0
O1A A:APC201 4.9 12.1 1.0
C13 A:5RZ202 4.9 22.6 1.0

Magnesium binding site 2 out of 2 in 5etv

Go back to Magnesium Binding Sites List in 5etv
Magnesium binding site 2 out of 2 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.72 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 1.72 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:11.2
occ:1.00
 OD1 A:ASP95 2.0 6.8 1.0
O A:HOH324 2.0 11.1 1.0
O1B A:APC201 2.0 13.1 1.0
O1A A:APC201 2.1 12.1 1.0
OD1 A:ASP97 2.1 6.9 1.0
O A:HOH326 2.2 12.0 1.0
CG A:ASP95 3.0 8.4 1.0
CG A:ASP97 3.2 7.5 1.0
PA A:APC201 3.3 14.2 1.0
PB A:APC201 3.3 13.1 1.0
OD2 A:ASP95 3.4 8.6 1.0
MG A:MG203 3.6 10.3 1.0
C3A A:APC201 3.6 12.6 1.0
OD2 A:ASP97 3.6 8.5 1.0
O5' A:APC201 3.8 16.0 1.0
O2G A:APC201 4.0 12.5 1.0
OE2 A:GLU78 4.0 10.6 1.0
O A:VAL96 4.2 7.5 1.0
O A:HOH321 4.3 28.2 1.0
O2B A:APC201 4.3 14.2 1.0
NH1 A:ARG83 4.4 11.1 1.0
CB A:ASP95 4.4 7.8 1.0
O3B A:APC201 4.4 11.9 1.0
C A:VAL96 4.5 7.3 1.0
O2A A:APC201 4.5 15.8 1.0
CB A:ASP97 4.5 6.7 1.0
C2 A:APC201 4.5 14.5 1.0
N3 A:APC201 4.5 14.5 1.0
N A:VAL96 4.6 7.8 1.0
O1G A:APC201 4.6 11.3 1.0
PG A:APC201 4.6 12.2 1.0
CA A:ASP97 4.7 7.2 1.0
CA A:ASP95 4.7 7.3 1.0
N A:ASP97 4.7 7.2 1.0
O A:HOH320 4.8 12.4 1.0
NH1 A:ARG92 4.9 9.7 1.0
C A:ASP95 4.9 7.6 1.0

Reference:

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
Page generated: Sun Sep 29 03:57:22 2024

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