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Sodium in PDB 5ets: S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.95 Angstrom Resolution

Enzymatic activity of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.95 Angstrom Resolution

All present enzymatic activity of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.95 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 1.95 Angstrom Resolution, PDB code: 5ets 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) 40.90 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.790, 68.580, 52.990, 90.00, 105.94, 90.00
R / Rfree (%) 18.9 / 21.8

Other elements in 5ets:

The structure of S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.95 Angstrom Resolution also contains other interesting chemical elements:

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 1.95 Angstrom Resolution (pdb code 5ets). 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 1.95 Angstrom Resolution, PDB code: 5ets:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5ets

Go back to Sodium Binding Sites List in 5ets
Sodium binding site 1 out of 3 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.95 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 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:15.6
occ:1.00
 O B:ILE32 2.2 8.9 1.0
O B:HOH372 2.3 21.1 1.0
O B:HOH320 2.4 11.3 1.0
O B:ASN27 2.4 5.3 1.0
O B:TYR29 2.5 9.4 1.0
C B:ILE32 3.4 8.7 1.0
C B:ASN27 3.5 6.3 1.0
C B:TYR29 3.5 9.1 1.0
N B:ILE32 4.1 8.0 1.0
C B:GLU28 4.1 7.5 1.0
N B:TYR29 4.1 8.2 1.0
OG B:SER33 4.2 10.4 1.0
CA B:ILE32 4.3 8.2 1.0
N B:SER33 4.3 8.2 1.0
N B:ASP30 4.3 10.6 1.0
CA B:GLU28 4.3 8.2 1.0
N B:GLU28 4.3 7.2 1.0
CA B:ASP30 4.3 11.7 1.0
O B:GLU28 4.3 6.3 1.0
CA B:SER33 4.4 8.9 1.0
CA B:ASN27 4.4 6.2 1.0
CA B:TYR29 4.5 9.3 1.0
N B:GLY31 4.6 9.2 1.0
OD1 B:ASN27 4.7 5.1 1.0
CB B:ILE32 4.7 7.9 1.0
C B:ASP30 4.7 10.2 1.0
OD1 B:ASP30 4.8 20.0 1.0
O B:LEU26 4.8 6.5 1.0
CG B:ASN27 4.9 5.6 1.0
CB B:SER33 4.9 9.0 1.0

Sodium binding site 2 out of 3 in 5ets

Go back to Sodium Binding Sites List in 5ets
Sodium binding site 2 out of 3 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.95 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 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:42.3
occ:1.00
 OD1 A:ASP107 2.3 28.0 1.0
OD1 B:ASP107 2.3 27.1 1.0
CG B:ASP107 3.3 22.7 1.0
CG A:ASP107 3.4 23.8 1.0
OD2 B:ASP107 3.5 26.9 1.0
OD2 A:ASP107 3.7 30.4 1.0
O A:LEU108 4.1 9.9 1.0
O B:LEU108 4.3 11.2 1.0
OG A:SER112 4.4 11.9 1.0
C A:LEU108 4.5 11.1 1.0
C B:LEU108 4.5 10.5 1.0
CB B:ASP107 4.7 17.4 1.0
CB A:ASP107 4.7 19.6 1.0
C B:ASP107 4.7 12.6 1.0
C A:ASP107 4.8 15.8 1.0
N A:LEU108 4.8 11.8 1.0
OG B:SER112 4.8 12.3 1.0
N B:LEU108 4.9 10.8 1.0
O B:ASP107 4.9 11.6 1.0
N B:PRO109 4.9 11.0 1.0
CA A:PRO109 5.0 11.8 1.0
CA B:PRO109 5.0 10.8 1.0

Sodium binding site 3 out of 3 in 5ets

Go back to Sodium Binding Sites List in 5ets
Sodium binding site 3 out of 3 in the S. Aureus 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.95 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 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:22.4
occ:1.00
 O A:ILE32 2.3 8.6 1.0
O A:HOH356 2.4 13.7 1.0
O A:ASN27 2.4 5.8 1.0
O A:TYR29 2.6 10.2 1.0
C A:ILE32 3.5 9.4 1.0
C A:ASN27 3.5 6.3 1.0
C A:TYR29 3.7 10.6 1.0
C A:GLU28 4.1 8.7 1.0
N A:TYR29 4.2 9.1 1.0
OG A:SER33 4.3 10.3 1.0
N A:ILE32 4.3 9.0 1.0
CA A:GLU28 4.3 9.1 1.0
N A:GLU28 4.3 7.4 1.0
N A:SER33 4.3 9.0 1.0
O A:GLU28 4.4 7.1 1.0
CA A:SER33 4.4 9.2 1.0
CA A:ILE32 4.4 9.1 1.0
CA A:ASN27 4.4 5.7 1.0
N A:ASP30 4.5 11.0 1.0
CA A:ASP30 4.5 12.1 1.0
CA A:TYR29 4.6 10.7 1.0
OD1 A:ASN27 4.6 4.6 1.0
CB A:ILE32 4.9 9.5 1.0
CG A:ASN27 4.9 4.8 1.0
N A:GLY31 4.9 10.1 1.0
O A:LEU26 4.9 5.5 1.0
CB A:SER33 4.9 8.8 1.0
C A:ASP30 5.0 10.8 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 20:51:22 2024

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