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Fluorine 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:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 2 in 5etr

Go back to Fluorine Binding Sites List in 5etr
Fluorine 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 Fluorine with other atoms in the F 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:F202

b:11.8
occ:1.00
 F19 B:5RW202 0.0 11.8 1.0
C6 B:5RW202 1.4 10.9 1.0
C3 B:5RW202 2.3 10.9 1.0
C4 B:5RW202 2.3 10.9 1.0
ND2 B:ASN11 3.1 8.2 1.0
C B:GLY90 3.4 9.9 1.0
O B:GLY90 3.4 9.9 1.0
N B:PRO91 3.5 9.4 1.0
C1 B:5RW202 3.6 10.9 1.0
CG B:GLN51 3.6 11.3 1.0
C2 B:5RW202 3.6 10.4 1.0
CA B:PRO91 3.7 9.4 1.0
CB B:GLN51 3.8 10.2 1.0
OE1 B:GLN51 3.9 14.6 1.0
CD B:GLN51 3.9 12.2 1.0
CG B:ASN11 4.1 7.6 1.0
C5 B:5RW202 4.1 10.0 1.0
CA B:GLY90 4.1 10.4 1.0
CZ B:PHE54 4.2 9.7 1.0
OD1 B:ASN11 4.2 8.3 1.0
CD B:PRO91 4.3 10.9 1.0
NE B:ARG92 4.3 10.0 1.0
CG B:PRO91 4.4 11.2 1.0
CE1 B:PHE54 4.5 10.0 1.0
CB B:PRO91 4.6 10.7 1.0
CD2 B:TYR48 4.7 12.8 1.0
C B:PRO91 4.8 9.3 1.0
NE2 B:GLN51 4.8 15.0 1.0
N B:GLY90 4.8 10.8 1.0
CD B:ARG92 4.9 10.3 1.0
CZ B:ARG92 5.0 9.8 1.0

Fluorine binding site 2 out of 2 in 5etr

Go back to Fluorine Binding Sites List in 5etr
Fluorine 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 Fluorine with other atoms in the F 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:F202

b:13.9
occ:1.00
 F19 A:5RW202 0.0 13.9 1.0
C6 A:5RW202 1.4 11.3 1.0
C4 A:5RW202 2.3 10.1 1.0
C3 A:5RW202 2.4 11.0 1.0
ND2 A:ASN11 3.3 9.3 1.0
O A:GLY90 3.4 11.0 1.0
C A:GLY90 3.4 11.3 1.0
CG A:GLN51 3.5 13.5 1.0
C2 A:5RW202 3.6 11.2 1.0
C1 A:5RW202 3.6 12.1 1.0
N A:PRO91 3.6 11.8 1.0
CB A:GLN51 3.7 12.3 1.0
CA A:PRO91 3.8 10.8 1.0
CD A:GLN51 3.8 15.7 1.0
OE1 A:GLN51 3.9 19.6 1.0
CZ A:PHE54 4.1 8.9 1.0
C5 A:5RW202 4.1 10.6 1.0
CA A:GLY90 4.1 13.4 1.0
CG A:ASN11 4.2 7.7 1.0
OD1 A:ASN11 4.2 9.4 1.0
NE A:ARG92 4.3 12.1 1.0
CD A:PRO91 4.4 13.8 1.0
CE1 A:PHE54 4.4 8.9 1.0
CG A:PRO91 4.6 14.9 1.0
NE2 A:GLN51 4.7 19.9 1.0
CB A:PRO91 4.7 13.0 1.0
N A:GLY90 4.8 13.2 1.0
CD2 A:TYR48 4.8 14.7 1.0
C A:PRO91 4.9 10.1 1.0
CD A:ARG92 4.9 12.5 1.0
CZ A:ARG92 4.9 11.5 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: Tue Jul 15 03:24:15 2025

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