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Sodium 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
Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 5etr

Go back to Sodium Binding Sites List in 5etr
Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na203

b:10.3
occ:1.00
 O B:ILE32 2.2 11.0 1.0
O B:TYR29 2.3 12.0 1.0
O B:ASN27 2.4 9.2 1.0
O B:HOH436 2.4 14.3 1.0
O B:HOH407 2.4 15.1 1.0
C B:TYR29 3.4 11.8 1.0
C B:ILE32 3.4 9.5 1.0
C B:ASN27 3.4 8.5 1.0
N B:TYR29 3.9 10.0 1.0
C B:GLU28 4.0 10.2 1.0
N B:ILE32 4.0 10.7 1.0
CA B:ASP30 4.2 17.5 1.0
N B:ASP30 4.2 15.2 1.0
CA B:ILE32 4.2 10.0 1.0
N B:GLU28 4.3 8.9 1.0
CA B:TYR29 4.3 10.5 1.0
OG B:SER33 4.3 13.7 1.0
CA B:GLU28 4.3 10.4 1.0
N B:SER33 4.3 8.9 1.0
O B:GLU28 4.4 13.0 1.0
CA B:ASN27 4.4 8.2 1.0
CA B:SER33 4.5 9.4 1.0
N B:GLY31 4.5 13.8 1.0
C B:ASP30 4.6 14.7 1.0
OD1 B:ASN27 4.6 8.8 1.0
CB B:ILE32 4.7 9.8 1.0
OD1 B:ASP30 4.7 24.8 1.0
O B:LEU26 4.8 9.1 1.0
CG B:ASN27 4.8 8.8 1.0
CB B:SER33 5.0 11.4 1.0

Sodium binding site 2 out of 3 in 5etr

Go back to Sodium Binding Sites List in 5etr
Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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:Na204

b:18.4
occ:1.00
 O A:HOH351 2.0 22.3 1.0
O B:HOH347 2.0 23.2 1.0
O A:HOH355 2.0 19.7 1.0
OD1 B:ASP107 2.1 20.0 1.0
OD1 A:ASP107 2.3 28.2 1.0
CG B:ASP107 3.1 19.2 1.0
CG A:ASP107 3.3 28.1 1.0
OD2 B:ASP107 3.5 23.6 1.0
OD2 A:ASP107 3.7 30.8 1.0
OG A:SER112 4.0 11.1 0.5
O B:LEU108 4.2 12.4 1.0
O A:LEU108 4.2 14.5 1.0
O B:HOH429 4.3 23.5 1.0
OG B:SER112 4.3 10.5 0.5
O A:ASP107 4.3 21.1 1.0
CB B:ASP107 4.5 16.7 1.0
O A:HOH325 4.5 30.7 1.0
C B:LEU108 4.5 11.7 1.0
C A:ASP107 4.6 16.9 1.0
C B:ASP107 4.6 14.2 1.0
O B:HOH447 4.6 27.9 1.0
CB A:ASP107 4.6 21.2 1.0
N B:LEU108 4.6 12.4 1.0
CA B:ASP107 4.8 13.7 1.0
CA A:ASP107 4.8 17.1 1.0
C A:LEU108 4.8 15.4 1.0
O B:ASP107 4.9 17.1 1.0

Sodium binding site 3 out of 3 in 5etr

Go back to Sodium Binding Sites List in 5etr
Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na 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:Na203

b:12.0
occ:1.00
 O A:ILE32 2.2 16.2 1.0
O A:ASN27 2.4 10.1 1.0
O A:TYR29 2.4 14.1 1.0
O A:HOH353 2.5 12.4 1.0
C A:ILE32 3.4 12.0 1.0
C A:TYR29 3.4 14.3 1.0
C A:ASN27 3.5 9.7 1.0
N A:TYR29 4.0 11.9 1.0
C A:GLU28 4.0 11.6 1.0
N A:ILE32 4.1 14.9 1.0
OG A:SER33 4.3 19.2 1.0
CA A:ILE32 4.3 13.6 1.0
N A:SER33 4.3 12.4 1.0
N A:GLU28 4.3 9.7 1.0
CA A:TYR29 4.3 13.0 1.0
N A:ASP30 4.3 17.1 1.0
CA A:GLU28 4.3 10.2 1.0
O A:HOH305 4.3 28.8 1.0
CA A:ASN27 4.4 9.1 1.0
CA A:SER33 4.4 12.6 1.0
O A:GLU28 4.4 14.8 1.0
OD1 A:ASN27 4.5 9.7 1.0
CA A:ASP30 4.6 18.3 1.0
N A:GLY31 4.7 16.3 1.0
CB A:ILE32 4.7 12.9 1.0
O A:LEU26 4.8 10.4 1.0
CG A:ASN27 4.8 9.6 1.0
C A:ASP30 4.8 16.1 1.0
CB A:SER33 4.9 15.5 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: Mon Oct 7 20:51:21 2024

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