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

Sodium binding site 1 out of 3 in 5ett

Go back to Sodium Binding Sites List in 5ett
Sodium binding site 1 out of 3 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 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 1.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:11.8
occ:1.00
 O B:ILE32 2.2 11.8 1.0
O B:HOH414 2.4 13.5 1.0
O B:HOH399 2.4 14.6 1.0
O B:ASN27 2.4 10.2 1.0
O B:HOH349 2.4 13.1 1.0
O B:TYR29 2.4 13.0 1.0
C B:ILE32 3.4 11.3 1.0
C B:TYR29 3.4 13.1 1.0
C B:ASN27 3.5 10.6 1.0
N B:TYR29 4.0 11.2 1.0
N B:ILE32 4.0 12.5 1.0
C B:GLU28 4.0 11.8 1.0
CA B:ASP30 4.2 18.7 1.0
N B:ASP30 4.2 16.4 1.0
OG B:SER33 4.2 15.7 1.0
CA B:ILE32 4.3 12.2 1.0
N B:GLU28 4.3 11.9 1.0
CA B:TYR29 4.3 12.3 1.0
N B:SER33 4.3 11.6 1.0
O B:GLU28 4.3 12.7 1.0
CA B:GLU28 4.3 12.4 1.0
CA B:ASN27 4.4 10.2 1.0
CA B:SER33 4.4 12.9 1.0
N B:GLY31 4.6 15.2 1.0
OD1 B:ASN27 4.6 8.5 1.0
C B:ASP30 4.7 16.1 1.0
OD1 B:ASP30 4.7 23.4 1.0
CB B:ILE32 4.7 11.7 1.0
O B:LEU26 4.7 10.2 1.0
CG B:ASN27 4.8 9.4 1.0
CB B:SER33 5.0 13.2 1.0

Sodium binding site 2 out of 3 in 5ett

Go back to Sodium Binding Sites List in 5ett
Sodium binding site 2 out of 3 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 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 1.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:26.9
occ:1.00
 O A:HOH349 2.0 22.2 1.0
O A:HOH327 2.1 28.8 1.0
O B:HOH328 2.1 29.3 1.0
OD1 B:ASP107 2.1 27.4 1.0
OD1 A:ASP107 2.3 34.3 1.0
CG B:ASP107 3.2 26.2 1.0
CG A:ASP107 3.4 30.1 1.0
OD2 B:ASP107 3.5 31.1 1.0
OD2 A:ASP107 3.6 35.1 1.0
OG A:SER112 4.0 19.8 1.0
O B:LEU108 4.1 15.7 1.0
O A:LEU108 4.2 16.8 1.0
O B:HOH420 4.3 32.3 1.0
O A:ASP107 4.4 27.3 1.0
OG B:SER112 4.5 22.5 1.0
C B:LEU108 4.5 16.9 1.0
CB B:ASP107 4.6 21.6 1.0
O B:HOH423 4.6 26.5 1.0
C B:ASP107 4.6 20.6 1.0
O A:HOH340 4.7 33.1 1.0
N B:LEU108 4.7 17.2 1.0
C A:ASP107 4.7 24.0 1.0
C A:LEU108 4.7 19.1 1.0
CB A:ASP107 4.8 26.5 1.0
O B:ASP107 4.9 20.4 1.0
CA B:ASP107 4.9 17.9 1.0
N B:PRO109 5.0 15.3 1.0

Sodium binding site 3 out of 3 in 5ett

Go back to Sodium Binding Sites List in 5ett
Sodium binding site 3 out of 3 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 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 1.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:13.8
occ:1.00
 O A:ILE32 2.2 15.4 1.0
O A:ASN27 2.4 10.9 1.0
O A:TYR29 2.4 15.4 1.0
C A:ILE32 3.4 14.6 1.0
C A:TYR29 3.4 14.1 1.0
C A:ASN27 3.5 12.0 1.0
N A:TYR29 4.0 13.1 1.0
C A:GLU28 4.1 14.5 1.0
N A:ILE32 4.1 16.0 1.0
OG A:SER33 4.3 22.5 1.0
N A:SER33 4.3 13.7 1.0
CA A:ILE32 4.3 16.2 1.0
N A:GLU28 4.3 12.4 1.0
CA A:TYR29 4.3 14.4 1.0
N A:ASP30 4.4 18.6 1.0
CA A:GLU28 4.4 12.9 1.0
CA A:SER33 4.4 16.1 1.0
CA A:ASN27 4.4 10.0 1.0
O A:GLU28 4.4 15.0 1.0
CA A:ASP30 4.5 20.6 1.0
OD1 A:ASN27 4.5 9.8 1.0
N A:GLY31 4.7 16.7 1.0
CB A:ILE32 4.7 14.8 1.0
O A:LEU26 4.8 10.4 1.0
CG A:ASN27 4.8 9.8 1.0
C A:ASP30 4.9 15.7 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 20:51:38 2024

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