Atomistry » Sodium » PDB 5en3-5f00 » 5etr
Atomistry »
  Sodium »
    PDB 5en3-5f00 »
      5etr »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy