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Magnesium in PDB 5etr: S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.32 Angstrom Resolution

Enzymatic activity of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.32 Angstrom Resolution

All present enzymatic activity of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.32 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 1.32 Angstrom Resolution, PDB code: 5etr 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) 45.71 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.582, 68.110, 53.227, 90.00, 106.12, 90.00
R / Rfree (%) 12.4 / 15.2

Other elements in 5etr:

The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.32 Angstrom Resolution also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 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 1.32 Angstrom Resolution (pdb code 5etr). 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 1.32 Angstrom Resolution, PDB code: 5etr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5etr

Go back to Magnesium Binding Sites List in 5etr
Magnesium binding site 1 out of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.32 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 1.32 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:6.3
occ:1.00
 OD1 B:ASP97 2.1 6.3 1.0
OD1 B:ASP95 2.1 6.2 1.0
O1B B:APC201 2.1 6.4 1.0
O B:HOH331 2.1 6.8 1.0
O1A B:APC201 2.1 6.2 1.0
O B:HOH391 2.1 6.8 1.0
CG B:ASP95 3.0 6.5 1.0
CG B:ASP97 3.2 6.2 1.0
PB B:APC201 3.2 6.7 1.0
PA B:APC201 3.2 6.8 1.0
OD2 B:ASP95 3.4 7.3 1.0
MG B:MG206 3.5 6.7 1.0
C3A B:APC201 3.5 6.9 1.0
OD2 B:ASP97 3.6 6.0 1.0
O5' B:APC201 3.8 7.6 1.0
O2B B:APC201 4.0 7.8 1.0
OE2 B:GLU78 4.1 7.4 1.0
O B:VAL96 4.2 6.1 1.0
O B:HOH324 4.3 11.0 1.0
NH1 B:ARG83 4.3 8.8 1.0
CB B:ASP95 4.4 6.5 1.0
CB B:ASP97 4.4 6.0 1.0
O3B B:APC201 4.5 6.8 1.0
C B:VAL96 4.5 5.3 1.0
O B:HOH319 4.5 11.1 1.0
O2A B:APC201 4.5 7.7 1.0
N B:VAL96 4.6 5.5 1.0
C2 B:APC201 4.6 6.9 1.0
CA B:ASP97 4.7 5.6 1.0
N3 B:APC201 4.7 7.7 1.0
O1G B:APC201 4.7 6.8 1.0
O B:HOH343 4.7 7.8 1.0
N B:ASP97 4.8 6.1 1.0
CA B:ASP95 4.8 6.2 1.0
NH2 B:ARG83 4.8 9.3 1.0
O2G B:APC201 4.9 8.0 1.0
C B:ASP95 5.0 5.8 1.0
PG B:APC201 5.0 7.1 1.0

Magnesium binding site 2 out of 4 in 5etr

Go back to Magnesium Binding Sites List in 5etr
Magnesium binding site 2 out of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.32 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 1.32 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:6.7
occ:1.00
 O1G B:APC201 2.0 6.8 1.0
OD2 B:ASP95 2.1 7.3 1.0
OD2 B:ASP97 2.1 6.0 1.0
O B:HOH343 2.1 7.8 1.0
O B:HOH394 2.1 7.6 1.0
O1B B:APC201 2.1 6.4 1.0
CG B:ASP97 3.0 6.2 1.0
CG B:ASP95 3.1 6.5 1.0
PB B:APC201 3.2 6.7 1.0
PG B:APC201 3.2 7.1 1.0
OD1 B:ASP97 3.3 6.3 1.0
O3B B:APC201 3.4 6.8 1.0
MG B:MG205 3.5 6.3 1.0
OD1 B:ASP95 3.6 6.2 1.0
O2B B:APC201 3.8 7.8 1.0
O B:HOH370 3.8 8.0 1.0
O2G B:APC201 4.0 8.0 1.0
O B:HOH418 4.0 9.5 1.0
O B:HOH424 4.1 12.1 1.0
N13 B:5RW202 4.2 8.7 1.0
NH1 B:ARG121 4.3 7.7 1.0
CB B:ASP97 4.4 6.0 1.0
O3G B:APC201 4.4 7.9 1.0
CB B:ASP95 4.4 6.5 1.0
O B:HOH391 4.6 6.8 1.0
NH1 B:ARG92 4.7 10.3 1.0
C3A B:APC201 4.7 6.9 1.0
NE2 B:HIS115 4.8 8.2 1.0
O1A B:APC201 4.9 6.2 1.0
O18 B:5RW202 4.9 8.6 1.0

Magnesium binding site 3 out of 4 in 5etr

Go back to Magnesium Binding Sites List in 5etr
Magnesium binding site 3 out of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.32 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 1.32 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:6.7
occ:1.00
 O3G A:APC201 2.0 7.4 1.0
OD2 A:ASP95 2.1 7.3 1.0
OD2 A:ASP97 2.1 6.4 1.0
O A:HOH390 2.1 7.8 1.0
O A:HOH344 2.1 7.8 1.0
O1B A:APC201 2.2 6.5 1.0
CG A:ASP97 3.0 6.2 1.0
CG A:ASP95 3.1 6.8 1.0
PB A:APC201 3.2 7.3 1.0
PG A:APC201 3.2 7.1 1.0
OD1 A:ASP97 3.3 6.7 1.0
O3B A:APC201 3.4 7.2 1.0
MG A:MG205 3.6 7.1 1.0
OD1 A:ASP95 3.6 6.7 1.0
O2B A:APC201 3.8 7.5 1.0
O A:HOH354 3.8 8.3 1.0
O2G A:APC201 4.0 8.0 1.0
O A:HOH404 4.1 9.6 1.0
O A:HOH410 4.1 11.6 1.0
N13 A:5RW202 4.2 9.1 1.0
NH1 A:ARG121 4.3 7.6 1.0
CB A:ASP97 4.4 6.8 1.0
O1G A:APC201 4.4 7.7 1.0
CB A:ASP95 4.4 6.1 1.0
O A:HOH377 4.7 7.8 1.0
C3A A:APC201 4.7 8.0 1.0
NE2 A:HIS115 4.8 8.1 1.0
NH1 A:ARG92 4.8 11.5 1.0
O18 A:5RW202 4.8 9.1 1.0
O2A A:APC201 4.9 7.3 1.0

Magnesium binding site 4 out of 4 in 5etr

Go back to Magnesium Binding Sites List in 5etr
Magnesium binding site 4 out of 4 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.32 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 1.32 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:7.1
occ:1.00
 OD1 A:ASP97 2.0 6.7 1.0
O A:HOH333 2.1 6.9 1.0
OD1 A:ASP95 2.1 6.7 1.0
O A:HOH377 2.1 7.8 1.0
O2A A:APC201 2.1 7.3 1.0
O1B A:APC201 2.1 6.5 1.0
CG A:ASP95 3.0 6.8 1.0
CG A:ASP97 3.1 6.2 1.0
PB A:APC201 3.2 7.3 1.0
PA A:APC201 3.3 8.2 1.0
OD2 A:ASP95 3.4 7.3 1.0
C3A A:APC201 3.5 8.0 1.0
MG A:MG204 3.6 6.7 1.0
OD2 A:ASP97 3.7 6.4 1.0
O5' A:APC201 3.8 9.6 1.0
O2B A:APC201 4.0 7.5 1.0
OE2 A:GLU78 4.0 8.5 1.0
O A:VAL96 4.2 6.8 1.0
NH1 A:ARG83 4.3 13.4 1.0
O A:HOH312 4.3 15.9 1.0
CB A:ASP95 4.4 6.1 1.0
CB A:ASP97 4.4 6.8 1.0
O A:HOH316 4.5 9.9 1.0
C A:VAL96 4.5 6.4 1.0
O3B A:APC201 4.5 7.2 1.0
O1A A:APC201 4.5 9.0 1.0
N A:VAL96 4.6 6.1 1.0
C2 A:APC201 4.6 8.9 1.0
N3 A:APC201 4.6 8.6 1.0
CA A:ASP97 4.6 6.6 1.0
O3G A:APC201 4.7 7.4 1.0
O A:HOH344 4.7 7.8 1.0
N A:ASP97 4.7 6.0 1.0
CA A:ASP95 4.8 6.0 1.0
O2G A:APC201 4.9 8.0 1.0
NH2 A:ARG83 4.9 13.5 1.0
C A:ASP95 5.0 5.8 1.0
PG A:APC201 5.0 7.1 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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