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Magnesium in PDB 5ett: S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.55 Angstrom Resolution

Enzymatic activity of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.55 Angstrom Resolution

All present enzymatic activity of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.55 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 1.55 Angstrom Resolution, PDB code: 5ett 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) 40.93 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.546, 68.404, 53.125, 90.00, 105.94, 90.00
R / Rfree (%) 15.8 / 19.2

Other elements in 5ett:

The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.55 Angstrom Resolution also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Sodium (Na) 3 atoms

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 1.55 Angstrom Resolution (pdb code 5ett). 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 1.55 Angstrom Resolution, PDB code: 5ett:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ett

Go back to Magnesium Binding Sites List in 5ett
Magnesium binding site 1 out of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.55 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 1.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:7.6
occ:1.00
 OD1 B:ASP95 2.0 7.6 1.0
O1A B:APC201 2.0 8.3 1.0
O B:HOH331 2.1 7.1 1.0
OD1 B:ASP97 2.1 8.2 1.0
O1B B:APC201 2.1 8.7 1.0
O B:HOH368 2.1 8.9 1.0
CG B:ASP95 3.0 8.5 1.0
CG B:ASP97 3.2 7.9 1.0
PA B:APC201 3.2 8.3 1.0
PB B:APC201 3.2 8.6 1.0
OD2 B:ASP95 3.3 8.2 1.0
C3A B:APC201 3.5 8.0 1.0
MG B:MG205 3.5 7.9 1.0
OD2 B:ASP97 3.7 7.4 1.0
O5' B:APC201 3.8 9.7 1.0
OE2 B:GLU78 4.0 8.7 1.0
O2B B:APC201 4.0 8.6 1.0
O B:VAL96 4.2 7.1 1.0
O B:HOH313 4.2 12.7 1.0
NH1 B:ARG83 4.3 11.7 1.0
CB B:ASP95 4.4 7.4 1.0
O3B B:APC201 4.5 8.2 1.0
CB B:ASP97 4.5 8.0 1.0
C B:VAL96 4.5 6.9 1.0
O2A B:APC201 4.5 9.0 1.0
N B:VAL96 4.6 6.7 1.0
O B:HOH304 4.6 16.9 1.0
C2 B:APC201 4.6 9.5 1.0
N3 B:APC201 4.7 10.2 1.0
O B:HOH362 4.7 8.6 1.0
O1G B:APC201 4.7 7.9 1.0
CA B:ASP97 4.7 7.7 1.0
NH2 B:ARG83 4.8 12.4 1.0
CA B:ASP95 4.8 7.4 1.0
O2G B:APC201 4.8 11.9 1.0
N B:ASP97 4.8 7.4 1.0
PG B:APC201 4.9 9.4 1.0
C B:ASP95 5.0 7.4 1.0

Magnesium binding site 2 out of 4 in 5ett

Go back to Magnesium Binding Sites List in 5ett
Magnesium binding site 2 out of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.55 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 1.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:7.9
occ:1.00
 O1G B:APC201 2.0 7.9 1.0
OD2 B:ASP95 2.0 8.2 1.0
OD2 B:ASP97 2.1 7.4 1.0
O B:HOH387 2.1 8.4 1.0
O B:HOH362 2.1 8.6 1.0
O1B B:APC201 2.1 8.7 1.0
CG B:ASP97 3.0 7.9 1.0
CG B:ASP95 3.1 8.5 1.0
PB B:APC201 3.2 8.6 1.0
PG B:APC201 3.2 9.4 1.0
OD1 B:ASP97 3.3 8.2 1.0
O3B B:APC201 3.4 8.2 1.0
MG B:MG204 3.5 7.6 1.0
OD1 B:ASP95 3.6 7.6 1.0
O2B B:APC201 3.8 8.6 1.0
O B:HOH358 3.9 9.2 1.0
O2G B:APC201 4.0 11.9 1.0
O B:HOH402 4.0 13.2 1.0
O B:HOH393 4.1 18.9 1.0
N18 B:5RY202 4.2 12.0 1.0
NH1 B:ARG121 4.3 8.7 1.0
CB B:ASP97 4.4 8.0 1.0
O3G B:APC201 4.4 10.0 1.0
CB B:ASP95 4.4 7.4 1.0
O B:HOH368 4.6 8.9 1.0
C3A B:APC201 4.7 8.0 1.0
NH1 B:ARG92 4.7 15.6 1.0
NE2 B:HIS115 4.8 8.3 1.0
S22 B:5RY202 4.8 14.6 1.0
C12 B:5RY202 4.8 12.0 1.0
O1A B:APC201 4.9 8.3 1.0

Magnesium binding site 3 out of 4 in 5ett

Go back to Magnesium Binding Sites List in 5ett
Magnesium binding site 3 out of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.55 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 1.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:7.6
occ:1.00
 O2G A:APC201 2.0 8.6 1.0
OD2 A:ASP97 2.1 7.6 1.0
OD2 A:ASP95 2.1 8.2 1.0
O A:HOH375 2.1 7.5 1.0
O A:HOH351 2.1 9.3 1.0
O1B A:APC201 2.2 8.2 1.0
CG A:ASP97 3.0 7.1 1.0
CG A:ASP95 3.1 7.5 1.0
PB A:APC201 3.2 9.0 1.0
PG A:APC201 3.2 8.6 1.0
OD1 A:ASP97 3.2 7.7 1.0
O3B A:APC201 3.4 9.0 1.0
MG A:MG205 3.5 8.5 1.0
OD1 A:ASP95 3.6 7.3 1.0
O2B A:APC201 3.8 8.9 1.0
O A:HOH352 3.8 9.8 1.0
O A:HOH396 4.0 13.0 1.0
O A:HOH379 4.0 18.1 1.0
O3G A:APC201 4.1 10.1 1.0
N18 A:5RY202 4.2 10.9 1.0
NH1 A:ARG121 4.3 8.8 1.0
O1G A:APC201 4.4 8.7 1.0
CB A:ASP95 4.4 7.9 1.0
CB A:ASP97 4.4 6.8 1.0
O A:HOH373 4.6 8.1 1.0
C3A A:APC201 4.7 8.6 1.0
NE2 A:HIS115 4.7 9.6 1.0
NH1 A:ARG92 4.8 15.8 1.0
S22 A:5RY202 4.9 14.5 1.0
O2A A:APC201 4.9 10.1 1.0
C12 A:5RY202 4.9 11.7 1.0

Magnesium binding site 4 out of 4 in 5ett

Go back to Magnesium Binding Sites List in 5ett
Magnesium binding site 4 out of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.55 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 1.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:8.5
occ:1.00
 OD1 A:ASP95 2.0 7.3 1.0
OD1 A:ASP97 2.1 7.7 1.0
O A:HOH319 2.1 8.4 1.0
O2A A:APC201 2.1 10.1 1.0
O1B A:APC201 2.1 8.2 1.0
O A:HOH373 2.2 8.1 1.0
CG A:ASP95 3.0 7.5 1.0
CG A:ASP97 3.2 7.1 1.0
PB A:APC201 3.2 9.0 1.0
PA A:APC201 3.3 9.5 1.0
OD2 A:ASP95 3.4 8.2 1.0
C3A A:APC201 3.5 8.6 1.0
MG A:MG204 3.5 7.6 1.0
OD2 A:ASP97 3.6 7.6 1.0
O5' A:APC201 3.8 11.7 1.0
OE2 A:GLU78 4.0 10.2 1.0
O2B A:APC201 4.0 8.9 1.0
O A:VAL96 4.2 7.5 1.0
O A:HOH320 4.2 15.6 1.0
NH1 A:ARG83 4.3 14.4 1.0
CB A:ASP95 4.4 7.9 1.0
O3B A:APC201 4.5 9.0 1.0
CB A:ASP97 4.5 6.8 1.0
C A:VAL96 4.5 7.1 1.0
O A:HOH314 4.5 13.3 1.0
O1A A:APC201 4.5 10.9 1.0
N A:VAL96 4.6 7.7 1.0
C2 A:APC201 4.6 9.9 1.0
N3 A:APC201 4.6 9.5 1.0
CA A:ASP97 4.6 7.1 1.0
O A:HOH351 4.7 9.3 1.0
O2G A:APC201 4.7 8.6 1.0
N A:ASP97 4.7 7.2 1.0
CA A:ASP95 4.8 7.4 1.0
O3G A:APC201 4.9 10.1 1.0
C A:ASP95 4.9 8.3 1.0
NH2 A:ARG83 5.0 14.9 1.0
PG A:APC201 5.0 8.6 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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