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Chlorine 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
Sodium (Na) 3 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 5etr

Go back to Chlorine Binding Sites List in 5etr
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl207

b:16.2
occ:1.00
 O B:HOH475 3.1 23.4 1.0
N B:ILE84 3.2 10.6 1.0
N B:THR93 3.3 7.7 1.0
CA B:ARG92 3.5 8.1 1.0
O B:PRO91 3.7 10.2 1.0
CG2 B:THR93 3.8 9.5 1.0
CB B:ILE84 3.8 14.6 1.0
CA B:ARG83 3.8 9.8 1.0
C B:ARG92 3.9 8.0 1.0
CG1 B:ILE84 3.9 14.6 1.0
OG1 B:THR93 4.0 8.2 1.0
O B:HOH353 4.0 18.4 1.0
C B:ARG83 4.0 9.8 1.0
CA B:ILE84 4.1 10.9 1.0
O B:HOH354 4.1 16.5 1.0
CG2 B:ILE12 4.2 10.7 1.0
CD1 B:ILE84 4.2 18.4 1.0
CB B:THR93 4.2 7.8 1.0
CB B:ARG92 4.3 9.0 1.0
CA B:THR93 4.3 7.1 1.0
O B:HIS82 4.3 11.4 1.0
CG B:ARG83 4.3 9.5 1.0
N B:ARG92 4.4 8.0 1.0
C B:PRO91 4.4 9.3 1.0
O B:ILE84 4.4 12.9 1.0
CB B:ARG83 4.6 9.2 1.0
C B:ILE84 4.8 11.7 1.0
N B:ARG83 4.8 8.9 1.0
C B:HIS82 5.0 10.1 1.0

Chlorine binding site 2 out of 2 in 5etr

Go back to Chlorine Binding Sites List in 5etr
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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
A:Cl206

b:27.1
occ:1.00
 N A:ILE84 3.1 19.5 1.0
N A:THR93 3.2 7.2 1.0
O A:HOH448 3.3 26.7 1.0
CA A:ARG92 3.4 8.9 1.0
O A:PRO91 3.6 12.5 1.0
CA A:ARG83 3.7 13.3 1.0
C A:ARG92 3.8 7.9 1.0
CG2 A:THR93 3.8 10.0 1.0
CB A:ILE84 3.8 28.9 1.0
OG1 A:THR93 3.9 9.4 1.0
C A:ARG83 3.9 16.0 1.0
CG1 A:ILE84 4.0 28.7 1.0
CA A:ILE84 4.0 24.4 1.0
O A:ILE84 4.0 35.1 1.0
O A:HIS82 4.0 14.7 1.0
CG A:ARG83 4.1 13.6 1.0
CB A:ARG92 4.2 10.2 1.0
CB A:THR93 4.2 9.0 1.0
CA A:THR93 4.3 7.8 1.0
O A:HOH314 4.3 24.8 1.0
CG2 A:ILE12 4.3 12.6 1.0
N A:ARG92 4.3 8.7 1.0
C A:PRO91 4.3 10.1 1.0
C A:ILE84 4.5 27.1 1.0
CB A:ARG83 4.5 12.7 1.0
O A:HOH349 4.6 22.9 1.0
N A:ARG83 4.7 11.4 1.0
C A:HIS82 4.8 12.9 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: Sat Jul 12 01:50:00 2025

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