Fluorine in PDB 6pka: Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide

All present enzymatic activity of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide:
3.4.21.92;

The structure of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide, PDB code: 6pka was solved by E.C.Griffith, R.E.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.61 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.957, 126.681, 146.776, 90.00, 93.36, 90.00
R / Rfree (%)	19.4 / 21.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Fluorine atom in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide (pdb code 6pka). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 28 binding sites of Fluorine where determined in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide, PDB code: 6pka:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ H:F2 b:29.8 occ:1.00 F1 H:WFP2 0.0 29.8 1.0 CE1 H:WFP2 1.3 29.4 1.0 CZ H:WFP2 2.3 27.6 1.0 CD1 H:WFP2 2.4 30.5 1.0 CB B:HIS83 3.2 29.5 1.0 CA B:THR80 3.3 27.2 1.0 OG1 B:THR80 3.5 23.1 1.0 CG B:HIS83 3.5 29.7 1.0 CE2 H:WFP2 3.6 28.5 1.0 CD2 A:LEU115 3.6 29.0 1.0 CG H:WFP2 3.6 27.5 1.0 CB B:THR80 3.7 25.1 1.0 CD1 A:LEU115 3.8 30.5 1.0 CG2 B:THR80 3.8 26.5 1.0 O B:ASP79 3.9 27.2 1.0 CD2 B:HIS83 3.9 29.9 1.0 N B:THR80 4.0 27.6 1.0 CD2 H:WFP2 4.1 28.2 1.0 O B:THR80 4.2 26.6 1.0 C B:ASP79 4.2 28.7 1.0 C B:THR80 4.3 26.2 1.0 CG A:LEU115 4.3 28.0 1.0 ND1 B:HIS83 4.4 30.3 1.0 CD2 B:LEU49 4.6 28.8 1.0 CA B:HIS83 4.6 28.8 1.0 F2 H:WFP2 4.7 29.4 1.0 NE2 B:HIS83 4.8 29.5 1.0 CB H:WFP2 4.9 27.8 1.0

Fluorine binding site 2 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ H:F2 b:29.4 occ:1.00 F2 H:WFP2 0.0 29.4 1.0 CE2 H:WFP2 1.3 28.5 1.0 CD2 H:WFP2 2.3 28.2 1.0 CZ H:WFP2 2.3 27.6 1.0 CG2 A:ILE93 3.4 39.8 1.0 CD1 B:LEU49 3.4 29.4 1.0 CE1 H:WFP2 3.6 29.4 1.0 CD2 A:TYR63 3.6 27.1 1.0 CG H:WFP2 3.6 27.5 1.0 CE2 A:TYR63 3.6 27.3 1.0 CG1 B:VAL45 3.7 25.1 1.0 CD1 H:WFP2 4.1 30.5 1.0 CD1 A:ILE93 4.2 44.3 1.0 CG A:TYR63 4.2 24.6 1.0 CZ A:TYR63 4.3 28.0 1.0 CB A:ILE93 4.5 36.9 1.0 CG B:LEU49 4.6 29.1 1.0 F1 H:WFP2 4.7 29.8 1.0 CD1 A:TYR63 4.7 24.6 1.0 OG1 B:THR80 4.8 23.1 1.0 CE1 A:TYR63 4.8 26.1 1.0 CD2 B:LEU49 4.8 28.8 1.0 CB H:WFP2 4.9 27.8 1.0 CB A:TYR63 4.9 24.1 1.0 OH A:TYR63 4.9 28.9 1.0 CG1 A:ILE93 4.9 38.2 1.0 CG2 A:ILE91 4.9 27.7 1.0 CD1 A:LEU115 5.0 30.5 1.0

Fluorine binding site 3 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ J:F2 b:37.9 occ:1.00 F1 J:WFP2 0.0 37.9 1.0 CE1 J:WFP2 1.3 33.2 1.0 CD1 J:WFP2 2.3 30.7 1.0 CZ J:WFP2 2.4 32.0 1.0 CB C:HIS83 3.2 30.5 1.0 CA C:THR80 3.4 25.8 1.0 CG C:HIS83 3.5 29.7 1.0 OG1 C:THR80 3.5 21.9 1.0 CG J:WFP2 3.6 30.9 1.0 CE2 J:WFP2 3.6 34.0 1.0 CD2 B:LEU115 3.7 34.5 1.0 CB C:THR80 3.8 24.4 1.0 CD2 C:HIS83 3.8 28.9 1.0 CG2 C:THR80 3.8 24.9 1.0 CD1 B:LEU115 3.9 34.5 1.0 O C:ASP79 4.0 24.9 1.0 N C:THR80 4.1 25.9 1.0 CD2 J:WFP2 4.1 31.2 1.0 O C:THR80 4.2 24.2 1.0 C C:ASP79 4.3 29.4 1.0 ND1 C:HIS83 4.3 29.8 1.0 C C:THR80 4.3 25.0 1.0 CG B:LEU115 4.4 35.8 1.0 CE B:MET190 4.5 55.8 1.0 CD2 C:LEU49 4.5 28.2 1.0 F2 J:WFP2 4.7 36.7 1.0 CA C:HIS83 4.7 32.2 1.0 NE2 C:HIS83 4.7 31.5 1.0 CB J:WFP2 4.8 28.4 1.0 CE1 C:HIS83 5.0 29.7 1.0

Fluorine binding site 4 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ J:F2 b:36.7 occ:1.00 F2 J:WFP2 0.0 36.7 1.0 CE2 J:WFP2 1.3 34.0 1.0 CZ J:WFP2 2.3 32.0 1.0 CD2 J:WFP2 2.4 31.2 1.0 CG2 B:ILE93 3.5 42.2 1.0 CD1 C:LEU49 3.5 25.7 1.0 CD2 B:TYR63 3.5 26.6 1.0 CE2 B:TYR63 3.5 29.5 1.0 CE1 J:WFP2 3.6 33.2 1.0 CG J:WFP2 3.6 30.9 1.0 CG1 C:VAL45 3.7 26.5 1.0 CD1 B:ILE93 4.1 43.8 1.0 CD1 J:WFP2 4.1 30.7 1.0 CG B:TYR63 4.1 26.2 1.0 CZ B:TYR63 4.2 27.2 1.0 CB B:ILE93 4.5 39.7 1.0 CG C:LEU49 4.6 26.9 1.0 F1 J:WFP2 4.7 37.9 1.0 CD1 B:TYR63 4.7 26.2 1.0 CE1 B:TYR63 4.7 25.8 1.0 OG1 C:THR80 4.8 21.9 1.0 CB B:TYR63 4.8 25.5 1.0 CD2 C:LEU49 4.8 28.2 1.0 OH B:TYR63 4.9 26.4 1.0 CG1 B:ILE93 4.9 39.7 1.0 CB J:WFP2 4.9 28.4 1.0

Fluorine binding site 5 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ O:F2 b:30.9 occ:1.00 F1 O:WFP2 0.0 30.9 1.0 CE1 O:WFP2 1.3 30.9 1.0 CD1 O:WFP2 2.4 31.9 1.0 CZ O:WFP2 2.4 29.0 1.0 CB D:HIS83 3.3 32.4 1.0 CA D:THR80 3.4 24.7 1.0 CG D:HIS83 3.5 35.7 1.0 OG1 D:THR80 3.5 24.1 1.0 CD2 C:LEU115 3.5 38.4 1.0 CG O:WFP2 3.6 30.7 1.0 CE2 O:WFP2 3.7 30.4 1.0 CD2 D:HIS83 3.7 34.5 1.0 CD1 C:LEU115 3.8 43.0 1.0 CB D:THR80 3.8 25.9 1.0 CG2 D:THR80 3.8 28.0 1.0 O D:ASP79 4.1 27.4 1.0 N D:THR80 4.1 27.0 1.0 CD2 O:WFP2 4.2 28.9 1.0 ND1 D:HIS83 4.3 35.2 1.0 CG C:LEU115 4.3 39.2 1.0 O D:THR80 4.4 24.5 1.0 C D:ASP79 4.4 28.8 1.0 C D:THR80 4.4 27.0 1.0 CD2 D:LEU49 4.5 29.6 1.0 NE2 D:HIS83 4.6 35.7 1.0 CA D:HIS83 4.8 31.6 1.0 F2 O:WFP2 4.8 34.0 1.0 CE1 D:HIS83 4.8 36.7 1.0 CB O:WFP2 4.9 32.2 1.0

Fluorine binding site 6 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ O:F2 b:34.0 occ:1.00 F2 O:WFP2 0.0 34.0 1.0 CE2 O:WFP2 1.3 30.4 1.0 CD2 O:WFP2 2.4 28.9 1.0 CZ O:WFP2 2.4 29.0 1.0 CG2 C:ILE93 3.3 41.7 1.0 CD1 D:LEU49 3.4 33.9 1.0 CD2 C:TYR63 3.5 27.2 1.0 CE2 C:TYR63 3.6 28.6 1.0 CG1 D:VAL45 3.6 25.8 1.0 CG O:WFP2 3.6 30.7 1.0 CE1 O:WFP2 3.6 30.9 1.0 CD1 C:ILE93 4.0 47.6 1.0 CG C:TYR63 4.1 26.7 1.0 CD1 O:WFP2 4.1 31.9 1.0 CZ C:TYR63 4.2 28.4 1.0 CB C:ILE93 4.4 42.2 1.0 CG D:LEU49 4.7 30.2 1.0 CD1 C:TYR63 4.7 27.9 1.0 CB C:TYR63 4.7 25.6 1.0 CG1 C:ILE93 4.8 43.0 1.0 CE1 C:TYR63 4.8 25.4 1.0 F1 O:WFP2 4.8 30.9 1.0 OG1 D:THR80 4.9 24.1 1.0 OH C:TYR63 4.9 29.4 1.0 CB O:WFP2 4.9 32.2 1.0 CG2 C:ILE91 5.0 31.1 1.0 CD2 D:LEU49 5.0 29.6 1.0

Fluorine binding site 7 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ P:F2 b:30.7 occ:1.00 F1 P:WFP2 0.0 30.7 1.0 CE1 P:WFP2 1.3 27.6 1.0 CD1 P:WFP2 2.3 26.8 1.0 CZ P:WFP2 2.3 28.0 1.0 CB E:HIS83 3.3 30.5 1.0 CA E:THR80 3.4 21.9 1.0 OG1 E:THR80 3.5 21.0 1.0 CD2 D:LEU115 3.6 32.6 1.0 CG E:HIS83 3.6 33.2 1.0 CE2 P:WFP2 3.6 30.1 1.0 CG P:WFP2 3.6 28.0 1.0 CD1 D:LEU115 3.7 32.5 1.0 CB E:THR80 3.8 21.2 1.0 CG2 E:THR80 3.9 23.0 1.0 CD2 E:HIS83 3.9 31.4 1.0 O E:ASP79 4.0 26.2 1.0 N E:THR80 4.1 21.9 1.0 CD2 P:WFP2 4.1 27.9 1.0 CG D:LEU115 4.3 30.9 1.0 C E:ASP79 4.3 24.6 1.0 O E:THR80 4.3 23.9 1.0 ND1 E:HIS83 4.4 33.1 1.0 C E:THR80 4.4 23.7 1.0 CD2 E:LEU49 4.6 27.8 1.0 F2 P:WFP2 4.7 32.2 1.0 NE2 E:HIS83 4.7 32.4 1.0 CA E:HIS83 4.8 31.1 1.0 CB P:WFP2 4.9 27.7 1.0 CE1 E:HIS83 5.0 33.5 1.0

Fluorine binding site 8 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ P:F2 b:32.2 occ:1.00 F2 P:WFP2 0.0 32.2 1.0 CE2 P:WFP2 1.3 30.1 1.0 CD2 P:WFP2 2.3 27.9 1.0 CZ P:WFP2 2.3 28.0 1.0 CD2 D:TYR63 3.4 23.1 1.0 CG2 D:ILE93 3.4 42.1 1.0 CD1 E:LEU49 3.4 28.8 1.0 CE2 D:TYR63 3.5 23.9 1.0 CE1 P:WFP2 3.6 27.6 1.0 CG P:WFP2 3.6 28.0 1.0 CG1 E:VAL45 3.7 24.8 1.0 CD1 D:ILE93 4.0 40.7 1.0 CG D:TYR63 4.0 21.7 1.0 CD1 P:WFP2 4.1 26.8 1.0 CZ D:TYR63 4.2 23.3 1.0 CB D:ILE93 4.5 37.6 1.0 CD1 D:TYR63 4.6 23.0 1.0 CG E:LEU49 4.6 27.5 1.0 CE1 D:TYR63 4.7 22.4 1.0 F1 P:WFP2 4.7 30.7 1.0 CB D:TYR63 4.7 21.5 1.0 OH D:TYR63 4.8 23.0 1.0 OG1 E:THR80 4.8 21.0 1.0 CG1 D:ILE93 4.9 39.1 1.0 CB P:WFP2 4.9 27.7 1.0 CD2 E:LEU49 4.9 27.8 1.0 CG2 D:ILE91 5.0 32.8 1.0

Fluorine binding site 9 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ Q:F2 b:23.1 occ:1.00 F1 Q:WFP2 0.0 23.1 1.0 CE1 Q:WFP2 1.3 21.2 1.0 CD1 Q:WFP2 2.4 20.6 1.0 CZ Q:WFP2 2.4 20.0 1.0 CB F:HIS83 3.2 25.3 1.0 CA F:THR80 3.3 20.4 1.0 CG F:HIS83 3.4 26.1 1.0 OG1 F:THR80 3.5 19.3 1.0 CE2 Q:WFP2 3.6 20.8 1.0 CG Q:WFP2 3.6 20.3 1.0 CD2 F:HIS83 3.7 25.0 1.0 CB F:THR80 3.7 20.1 1.0 CD2 E:LEU115 3.7 29.7 1.0 CG2 F:THR80 3.8 21.3 1.0 CD1 E:LEU115 3.9 30.7 1.0 O F:ASP79 3.9 19.1 1.0 N F:THR80 4.1 18.2 1.0 O F:THR80 4.1 20.6 1.0 CD2 Q:WFP2 4.1 19.6 1.0 C F:THR80 4.2 21.4 1.0 C F:ASP79 4.3 19.2 1.0 ND1 F:HIS83 4.3 27.6 1.0 CG E:LEU115 4.4 27.5 1.0 CD2 F:LEU49 4.4 21.1 1.0 CA F:HIS83 4.6 24.2 1.0 NE2 F:HIS83 4.7 25.1 1.0 F2 Q:WFP2 4.7 23.0 1.0 CB Q:WFP2 4.9 20.2 1.0

Fluorine binding site 10 out of 28 in the Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of Clpp From Staphylococcus Aureus in Complex with Ureadepsipeptide within 5.0Å range: probe atom residue distance (Å) B Occ Q:F2 b:23.0 occ:1.00 F2 Q:WFP2 0.0 23.0 1.0 CE2 Q:WFP2 1.3 20.8 1.0 CZ Q:WFP2 2.3 20.0 1.0 CD2 Q:WFP2 2.3 19.6 1.0 CG2 E:ILE93 3.2 32.8 1.0 CG Q:WFP2 3.6 20.3 1.0 CE1 Q:WFP2 3.6 21.2 1.0 CD1 F:LEU49 3.6 23.1 1.0 CD2 E:TYR63 3.6 21.7 1.0 CG1 F:VAL45 3.7 18.5 1.0 CE2 E:TYR63 3.7 22.1 1.0 CD1 E:ILE93 4.0 34.0 1.0 CD1 Q:WFP2 4.1 20.6 1.0 CG E:TYR63 4.2 22.0 1.0 CB E:ILE93 4.3 30.7 1.0 CZ E:TYR63 4.4 22.4 1.0 CG1 E:ILE93 4.7 30.8 1.0 F1 Q:WFP2 4.7 23.1 1.0 OG1 F:THR80 4.7 19.3 1.0 CD1 E:TYR63 4.8 22.0 1.0 CG F:LEU49 4.8 20.6 1.0 CG2 E:ILE91 4.8 28.8 1.0 CD1 E:LEU115 4.8 30.7 1.0 CB E:TYR63 4.8 23.1 1.0 CB Q:WFP2 4.9 20.2 1.0 CE1 E:TYR63 4.9 20.4 1.0 CD2 F:LEU49 5.0 21.1 1.0

E.C.Griffith, Y.Zhao, A.P.Singh, B.P.Conlon, R.Tangallapally, W.R.Shadrick, J.Liu, M.J.Wallace, L.Yang, J.M.Elmore, Y.Li, Z.Zheng, D.J.Miller, M.N.Cheramie, R.B.Lee, M.D.Lafleur, K.Lewis, R.E.Lee. Ureadepsipeptides As Clpp Activators. Acs Infect Dis. V. 5 1915 2019.
ISSN: ESSN 2373-8227
PubMed: 31588734
DOI: 10.1021/ACSINFECDIS.9B00245