Fluorine in PDB 6cfd: ADEP4 Bound to E. Faecium Clpp

All present enzymatic activity of ADEP4 Bound to E. Faecium Clpp:
3.4.21.92;

The structure of ADEP4 Bound to E. Faecium Clpp, PDB code: 6cfd was solved by R.E.Lee, E.C.Griffith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	101.08 / 2.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.395, 202.166, 97.385, 90.00, 102.69, 90.00
R / Rfree (%)	17.5 / 20.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Fluorine atom in the ADEP4 Bound to E. Faecium Clpp (pdb code 6cfd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 22 binding sites of Fluorine where determined in the ADEP4 Bound to E. Faecium Clpp, PDB code: 6cfd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:68.9 occ:1.00 F1 A:EZA402 0.0 68.9 1.0 C12 A:EZA402 1.3 67.3 1.0 C13 A:EZA402 2.3 65.5 1.0 C11 A:EZA402 2.4 65.5 1.0 CB B:PHE83 3.2 51.7 1.0 CA B:THR80 3.3 49.5 1.0 CG B:PHE83 3.5 51.5 1.0 OG1 B:THR80 3.5 40.8 1.0 C14 A:EZA402 3.6 71.2 1.0 CD1 A:LEU115 3.6 47.3 1.0 C10 A:EZA402 3.7 66.9 1.0 CD2 A:LEU115 3.7 54.6 1.0 CB B:THR80 3.8 47.1 1.0 CG2 B:THR80 3.8 44.1 1.0 O B:ASP79 3.9 59.5 1.0 CD2 B:PHE83 4.0 52.0 1.0 CD1 B:PHE83 4.0 55.6 1.0 N B:THR80 4.0 51.0 1.0 C15 A:EZA402 4.1 70.9 1.0 C B:ASP79 4.2 47.4 1.0 O B:THR80 4.3 50.5 1.0 C B:THR80 4.3 48.1 1.0 CG A:LEU115 4.3 48.6 1.0 F2 A:EZA402 4.6 78.9 1.0 CA B:PHE83 4.6 53.7 1.0 CD2 B:LEU49 4.7 53.1 1.0 CE2 B:PHE83 4.9 56.2 1.0 CE1 B:PHE83 4.9 57.1 1.0 C9 A:EZA402 4.9 72.3 1.0 N B:PHE83 5.0 51.3 1.0

Fluorine binding site 2 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:78.9 occ:1.00 F2 A:EZA402 0.0 78.9 1.0 C14 A:EZA402 1.3 71.2 1.0 C13 A:EZA402 2.3 65.5 1.0 C15 A:EZA402 2.3 70.9 1.0 CE A:MET93 2.4 72.5 1.0 CD2 A:TYR63 3.4 61.4 1.0 C12 A:EZA402 3.5 67.3 1.0 C10 A:EZA402 3.6 66.9 1.0 CE2 A:TYR63 3.6 57.6 1.0 SD A:MET93 3.7 72.0 1.0 CG A:TYR63 3.8 53.1 1.0 CD1 B:LEU49 3.9 56.0 1.0 CG2 B:ILE45 4.0 49.2 1.0 C11 A:EZA402 4.0 65.5 1.0 CZ A:TYR63 4.2 61.0 1.0 CD1 A:TYR63 4.4 57.9 1.0 CB A:TYR63 4.4 50.4 1.0 CE1 A:TYR63 4.6 62.1 1.0 F1 A:EZA402 4.6 68.9 1.0 CG A:MET93 4.7 60.0 1.0 C9 A:EZA402 4.8 72.3 1.0 CG B:LEU49 4.8 57.9 1.0 CB A:MET93 4.8 55.3 1.0 OG1 B:THR80 4.9 40.8 1.0 CD1 A:LEU115 4.9 47.3 1.0 CD2 B:LEU49 4.9 53.1 1.0

Fluorine binding site 3 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ C:F402 b:0.8 occ:1.00 F1 C:EZA402 0.0 0.8 1.0 C12 C:EZA402 1.3 0.8 1.0 C11 C:EZA402 2.4 0.4 1.0 C13 C:EZA402 2.4 0.1 1.0 CB D:PHE83 3.2 73.3 1.0 CG D:PHE83 3.2 81.4 1.0 C10 C:EZA402 3.6 0.5 1.0 C14 C:EZA402 3.7 0.3 1.0 CD1 D:PHE83 3.7 81.9 1.0 CD1 C:LEU115 3.7 47.4 1.0 CD2 D:PHE83 3.8 89.1 1.0 CA D:THR80 3.8 49.0 1.0 CD2 C:LEU115 3.8 50.0 1.0 CG2 D:THR80 3.9 47.2 1.0 OG1 D:THR80 4.0 51.7 1.0 CB D:THR80 4.1 47.0 1.0 C15 C:EZA402 4.1 0.1 1.0 CD2 D:LEU49 4.3 62.9 1.0 CG C:LEU115 4.4 44.7 1.0 N D:THR80 4.5 43.8 1.0 O D:ASP79 4.5 53.0 1.0 CE1 D:PHE83 4.5 92.7 1.0 CE2 D:PHE83 4.5 96.8 1.0 O D:THR80 4.6 52.1 1.0 CA D:PHE83 4.7 62.8 1.0 C D:THR80 4.7 52.8 1.0 C D:ASP79 4.8 47.8 1.0 F2 C:EZA402 4.8 0.9 1.0 CZ D:PHE83 4.9 98.9 1.0 C9 C:EZA402 4.9 0.1 1.0

Fluorine binding site 4 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ C:F402 b:0.9 occ:1.00 F2 C:EZA402 0.0 0.9 1.0 C14 C:EZA402 1.3 0.3 1.0 C15 C:EZA402 2.3 0.1 1.0 C13 C:EZA402 2.4 0.1 1.0 CE C:MET93 2.8 80.7 1.0 CG C:TYR63 2.9 59.4 1.0 CD2 C:TYR63 3.0 75.9 1.0 CD1 C:TYR63 3.0 70.3 1.0 CE2 C:TYR63 3.2 76.3 1.0 CE1 C:TYR63 3.3 75.4 1.0 CZ C:TYR63 3.4 75.4 1.0 C10 C:EZA402 3.6 0.5 1.0 CB C:TYR63 3.7 46.8 1.0 C12 C:EZA402 3.7 0.8 1.0 CG2 C:ILE91 3.9 42.9 1.0 SD C:MET93 4.1 80.1 1.0 CB C:ILE91 4.1 44.3 1.0 C11 C:EZA402 4.1 0.4 1.0 OH C:TYR63 4.3 94.3 1.0 CD1 D:LEU49 4.5 62.2 1.0 CG1 C:ILE91 4.6 54.7 1.0 CG C:MET93 4.6 59.4 1.0 CA C:TYR63 4.7 47.7 1.0 C9 C:EZA402 4.8 0.1 1.0 F1 C:EZA402 4.8 0.8 1.0

Fluorine binding site 5 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ D:F402 b:0.7 occ:1.00 F1 D:EZA402 0.0 0.7 1.0 C12 D:EZA402 1.3 0.6 1.0 C11 D:EZA402 2.4 0.5 1.0 C13 D:EZA402 2.4 0.4 1.0 CB E:PHE83 3.1 63.2 1.0 CG E:PHE83 3.3 69.6 1.0 CA E:THR80 3.5 48.5 1.0 C10 D:EZA402 3.6 0.5 1.0 C14 D:EZA402 3.7 0.3 1.0 CD1 D:LEU115 3.7 51.9 1.0 CD1 E:PHE83 3.7 74.6 1.0 CG2 E:THR80 3.8 47.5 1.0 OG1 E:THR80 3.8 48.1 1.0 CD2 E:PHE83 3.9 78.7 1.0 CD2 D:LEU115 3.9 55.7 1.0 CB E:THR80 3.9 47.7 1.0 O E:ASP79 4.1 48.9 1.0 C15 D:EZA402 4.1 0.6 1.0 N E:THR80 4.2 47.8 1.0 CD2 E:LEU49 4.3 51.2 1.0 O E:THR80 4.4 50.0 1.0 C E:THR80 4.5 47.2 1.0 C E:ASP79 4.5 48.8 1.0 CG D:LEU115 4.5 48.6 1.0 CA E:PHE83 4.6 59.9 1.0 CE1 E:PHE83 4.6 81.7 1.0 CE2 E:PHE83 4.7 89.3 1.0 F2 D:EZA402 4.8 0.7 1.0 C9 D:EZA402 4.9 0.4 1.0

Fluorine binding site 6 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ D:F402 b:0.7 occ:1.00 F2 D:EZA402 0.0 0.7 1.0 C14 D:EZA402 1.3 0.3 1.0 C15 D:EZA402 2.3 0.6 1.0 C13 D:EZA402 2.4 0.4 1.0 CD2 D:TYR63 2.8 71.7 1.0 CE D:MET93 2.9 75.8 1.0 CE2 D:TYR63 2.9 74.2 1.0 CG D:TYR63 3.2 62.6 1.0 CZ D:TYR63 3.4 80.6 1.0 CD1 D:TYR63 3.6 76.8 1.0 C10 D:EZA402 3.6 0.5 1.0 C12 D:EZA402 3.7 0.6 1.0 CE1 D:TYR63 3.7 82.0 1.0 CD1 E:LEU49 3.7 52.1 1.0 CB D:TYR63 4.0 57.6 1.0 C11 D:EZA402 4.1 0.5 1.0 SD D:MET93 4.1 79.7 1.0 OH D:TYR63 4.3 85.8 1.0 CG2 E:ILE45 4.6 48.5 1.0 C9 D:EZA402 4.8 0.4 1.0 F1 D:EZA402 4.8 0.7 1.0 CG E:LEU49 4.8 52.8 1.0 CG2 D:ILE91 4.8 51.8 1.0 CD2 E:LEU49 4.8 51.2 1.0 CG D:MET93 4.9 61.9 1.0 CB D:ILE91 5.0 53.3 1.0

Fluorine binding site 7 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ E:F402 b:92.5 occ:1.00 F1 E:EZA402 0.0 92.5 1.0 C12 E:EZA402 1.3 94.1 1.0 C11 E:EZA402 2.3 99.3 1.0 C13 E:EZA402 2.4 92.7 1.0 CB F:PHE83 3.1 56.6 1.0 CG F:PHE83 3.2 67.5 1.0 CD2 E:LEU115 3.5 49.2 1.0 C10 E:EZA402 3.6 0.5 1.0 CD1 E:LEU115 3.6 47.9 1.0 C14 E:EZA402 3.6 0.5 1.0 CD2 F:PHE83 3.7 75.9 1.0 CA F:THR80 3.7 41.8 1.0 CD1 F:PHE83 3.8 75.6 1.0 OG1 F:THR80 4.0 37.1 1.0 C15 E:EZA402 4.1 0.9 1.0 CG2 F:THR80 4.1 39.6 1.0 CB F:THR80 4.2 40.0 1.0 CG E:LEU115 4.2 49.7 1.0 O F:ASP79 4.3 44.4 1.0 N F:THR80 4.3 42.1 1.0 CE2 F:PHE83 4.5 75.9 1.0 C F:ASP79 4.6 46.0 1.0 CE1 F:PHE83 4.6 74.6 1.0 O F:THR80 4.6 48.9 1.0 CD2 F:LEU49 4.6 51.8 1.0 CA F:PHE83 4.6 52.2 1.0 C F:THR80 4.7 45.7 1.0 F2 E:EZA402 4.8 0.4 1.0 C9 E:EZA402 4.8 0.7 1.0 CZ F:PHE83 4.9 74.1 1.0

Fluorine binding site 8 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ E:F402 b:0.4 occ:1.00 F2 E:EZA402 0.0 0.4 1.0 C14 E:EZA402 1.3 0.5 1.0 C15 E:EZA402 2.3 0.9 1.0 C13 E:EZA402 2.4 92.7 1.0 CE E:MET93 2.7 74.8 1.0 CD2 E:TYR63 2.8 68.0 1.0 CE2 E:TYR63 2.9 74.8 1.0 CG E:TYR63 3.1 58.4 1.0 CZ E:TYR63 3.3 73.0 1.0 CD1 E:TYR63 3.4 72.0 1.0 CE1 E:TYR63 3.5 74.4 1.0 C10 E:EZA402 3.6 0.5 1.0 C12 E:EZA402 3.7 94.1 1.0 CB E:TYR63 3.9 51.4 1.0 CD1 F:LEU49 3.9 56.2 1.0 SD E:MET93 4.0 75.3 1.0 C11 E:EZA402 4.1 99.3 1.0 OH E:TYR63 4.2 86.0 1.0 CG2 E:ILE91 4.6 51.4 1.0 CG2 F:ILE45 4.7 48.1 1.0 F1 E:EZA402 4.8 92.5 1.0 C9 E:EZA402 4.8 0.7 1.0 CB E:ILE91 4.8 48.1 1.0 CG E:MET93 4.8 54.3 1.0 CG F:LEU49 5.0 56.4 1.0 CD2 F:LEU49 5.0 51.8 1.0

Fluorine binding site 9 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ F:F402 b:92.1 occ:1.00 F1 F:EZA402 0.0 92.1 1.0 C12 F:EZA402 1.3 95.4 1.0 C13 F:EZA402 2.4 91.9 1.0 C11 F:EZA402 2.4 92.5 1.0 CA G:THR80 3.3 42.9 1.0 OG1 G:THR80 3.4 41.5 1.0 CB G:PHE83 3.4 59.4 1.0 CG2 G:THR80 3.5 44.5 1.0 CB G:THR80 3.6 42.7 1.0 CG G:PHE83 3.6 69.1 1.0 C10 F:EZA402 3.6 97.7 1.0 C14 F:EZA402 3.6 0.4 1.0 CD1 F:LEU115 3.7 45.7 1.0 N G:THR80 4.1 41.7 1.0 CD1 G:PHE83 4.1 73.8 1.0 CD2 F:LEU115 4.1 47.0 1.0 C15 F:EZA402 4.1 93.2 1.0 CD2 G:PHE83 4.2 69.5 1.0 O G:ASP79 4.2 42.7 1.0 CD2 G:LEU49 4.2 48.9 1.0 O G:THR80 4.3 44.1 1.0 C G:THR80 4.3 43.3 1.0 C G:ASP79 4.4 43.4 1.0 CG F:LEU115 4.6 46.5 1.0 F2 F:EZA402 4.7 0.8 1.0 CA G:PHE83 4.9 56.0 1.0 C9 F:EZA402 4.9 99.7 1.0 CE1 G:PHE83 4.9 82.1 1.0

Fluorine binding site 10 out of 22 in the ADEP4 Bound to E. Faecium Clpp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of ADEP4 Bound to E. Faecium Clpp within 5.0Å range: probe atom residue distance (Å) B Occ F:F402 b:0.8 occ:1.00 F2 F:EZA402 0.0 0.8 1.0 C14 F:EZA402 1.3 0.4 1.0 C15 F:EZA402 2.3 93.2 1.0 C13 F:EZA402 2.4 91.9 1.0 CE F:MET93 2.7 83.1 1.0 CD2 F:TYR63 2.8 61.2 1.0 CG F:TYR63 3.0 57.7 1.0 CE2 F:TYR63 3.0 61.5 1.0 CD1 F:TYR63 3.4 66.6 1.0 CZ F:TYR63 3.5 67.3 1.0 C10 F:EZA402 3.6 97.7 1.0 CE1 F:TYR63 3.6 68.7 1.0 C12 F:EZA402 3.7 95.4 1.0 CB F:TYR63 3.7 51.8 1.0 SD F:MET93 4.1 78.3 1.0 C11 F:EZA402 4.1 92.5 1.0 CD1 G:LEU49 4.2 48.0 1.0 OH F:TYR63 4.4 77.3 1.0 CG F:MET93 4.6 62.7 1.0 CG2 F:ILE91 4.6 45.1 1.0 CB F:ILE91 4.7 46.0 1.0 F1 F:EZA402 4.7 92.1 1.0 CG2 G:ILE45 4.8 43.1 1.0 C9 F:EZA402 4.8 99.7 1.0 CA F:TYR63 4.9 46.9 1.0 CB F:MET93 5.0 55.9 1.0

A.Brown Gandt, E.C.Griffith, I.M.Lister, L.L.Billings, A.Han, R.Tangallapally, Y.Zhao, A.P.Singh, R.E.Lee, M.D.Lafleur. In Vivoandin Vitroeffects of A Clpp-Activating Antibiotic Against Vancomycin-Resistant Enterococci. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 29784838
DOI: 10.1128/AAC.00424-18