Fluorine in PDB 6nah: Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)

All present enzymatic activity of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14):
3.4.21.92;

The structure of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14), PDB code: 6nah was solved by M.F.Mabanglo, W.A.Houry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.63 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	117.238, 195.976, 139.894, 90.00, 97.42, 90.00
R / Rfree (%)	19.2 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 56;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) (pdb code 6nah). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 56 binding sites of Fluorine where determined in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14), PDB code: 6nah:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ c:F2 b:49.0 occ:1.00 F1 c:WFP2 0.0 49.0 1.0 CE1 c:WFP2 1.4 44.1 1.0 CD1 c:WFP2 2.4 46.6 1.0 CZ c:WFP2 2.4 38.0 1.0 CB G:PHE87 3.2 47.7 1.0 CA G:THR84 3.3 37.1 1.0 O G:ASP83 3.4 41.0 1.0 CG G:PHE87 3.6 52.0 1.0 CG c:WFP2 3.6 42.7 1.0 CE2 c:WFP2 3.7 50.7 1.0 CD1 A:LEU119 3.7 43.7 1.0 CD2 G:PHE87 3.7 48.4 1.0 N G:THR84 3.8 37.6 1.0 C G:ASP83 3.8 38.4 1.0 CD2 A:LEU119 3.9 44.9 1.0 OG1 G:THR84 3.9 42.8 1.0 CB G:THR84 4.0 38.6 1.0 CD2 c:WFP2 4.1 46.4 1.0 O G:THR84 4.2 42.1 1.0 C G:THR84 4.2 39.2 1.0 CG2 G:THR84 4.2 38.4 1.0 CG A:LEU119 4.4 42.5 1.0 CA G:PHE87 4.5 42.4 1.0 CD1 G:PHE87 4.6 45.5 1.0 CE2 G:PHE87 4.8 47.6 1.0 N G:PHE87 4.8 45.0 1.0 F2 c:WFP2 4.8 50.3 1.0 CB c:WFP2 4.9 48.7 1.0 O G:HOH309 5.0 36.3 1.0

Fluorine binding site 2 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ c:F2 b:50.3 occ:1.00 F2 c:WFP2 0.0 50.3 1.0 CE2 c:WFP2 1.4 50.7 1.0 CD2 c:WFP2 2.4 46.4 1.0 CZ c:WFP2 2.4 38.0 1.0 CE2 A:TYR67 3.6 45.1 1.0 CG1 G:VAL49 3.7 37.9 1.0 CG c:WFP2 3.7 42.7 1.0 CD1 G:LEU53 3.7 40.0 1.0 CE1 c:WFP2 3.7 44.1 1.0 CD1 A:LEU97 3.8 38.0 1.0 CD2 A:TYR67 3.8 47.5 1.0 CD1 c:WFP2 4.2 46.6 1.0 CZ A:TYR67 4.4 50.6 1.0 CG G:LEU53 4.5 47.8 1.0 CD2 G:LEU53 4.6 41.5 1.0 OG1 G:THR84 4.7 42.8 1.0 CD2 A:LEU95 4.7 44.5 1.0 CG A:TYR67 4.7 48.6 1.0 CZ A:PHE35 4.8 49.3 1.0 F1 c:WFP2 4.8 49.0 1.0 CG A:LEU97 4.8 40.4 1.0 OH A:TYR67 4.9 50.0 1.0 CB c:WFP2 4.9 48.7 1.0 CD2 A:LEU97 5.0 41.6 1.0

Fluorine binding site 3 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ e:F2 b:44.4 occ:1.00 F1 e:WFP2 0.0 44.4 1.0 CE1 e:WFP2 1.4 42.7 1.0 CD1 e:WFP2 2.4 41.6 1.0 CZ e:WFP2 2.4 44.2 1.0 CB A:PHE87 3.2 40.8 1.0 CA A:THR84 3.3 40.4 1.0 CD1 B:LEU119 3.6 44.9 1.0 O A:ASP83 3.6 41.2 1.0 CG A:PHE87 3.6 42.0 1.0 CG e:WFP2 3.7 41.4 1.0 OG1 A:THR84 3.7 43.3 1.0 CE2 e:WFP2 3.7 45.1 1.0 N A:THR84 3.8 38.2 1.0 CB A:THR84 3.9 38.5 1.0 C A:ASP83 3.9 42.7 1.0 CD1 A:PHE87 3.9 36.4 1.0 CD2 B:LEU119 4.0 43.6 1.0 CG2 A:THR84 4.0 33.6 1.0 CD2 e:WFP2 4.2 43.0 1.0 O A:THR84 4.2 44.2 1.0 C A:THR84 4.3 40.9 1.0 CD2 A:PHE87 4.4 43.1 1.0 CG B:LEU119 4.4 46.9 1.0 CA A:PHE87 4.6 42.7 1.0 F2 e:WFP2 4.8 41.4 1.0 CE1 A:PHE87 4.8 33.5 1.0 CB e:WFP2 4.9 45.3 1.0 N A:PHE87 4.9 40.6 1.0

Fluorine binding site 4 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ e:F2 b:41.4 occ:1.00 F2 e:WFP2 0.0 41.4 1.0 CE2 e:WFP2 1.4 45.1 1.0 CD2 e:WFP2 2.4 43.0 1.0 CZ e:WFP2 2.4 44.2 1.0 CE2 B:TYR67 3.4 41.2 1.0 CD2 B:TYR67 3.6 46.9 1.0 CG e:WFP2 3.7 41.4 1.0 CE1 e:WFP2 3.7 42.7 1.0 CD1 A:LEU53 3.8 38.9 1.0 CG1 A:VAL49 3.8 40.0 1.0 CD1 B:LEU97 3.9 43.1 1.0 CD2 B:LEU97 4.0 46.9 1.0 CD1 e:WFP2 4.2 41.6 1.0 CZ B:TYR67 4.3 41.4 1.0 CG B:LEU97 4.5 48.2 1.0 CG A:LEU53 4.5 40.1 1.0 CD2 A:LEU53 4.6 41.8 1.0 CG B:TYR67 4.6 41.7 1.0 OG1 A:THR84 4.7 43.3 1.0 CD2 B:LEU95 4.7 40.7 1.0 F1 e:WFP2 4.8 44.4 1.0 OH B:TYR67 4.8 44.0 1.0 CB e:WFP2 4.9 45.3 1.0

Fluorine binding site 5 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ f:F2 b:48.4 occ:1.00 F1 f:WFP2 0.0 48.4 1.0 CE1 f:WFP2 1.4 48.7 1.0 CD1 f:WFP2 2.4 48.6 1.0 CZ f:WFP2 2.4 44.3 1.0 CA B:THR84 3.0 42.6 1.0 CB B:PHE87 3.1 38.4 1.0 OG1 B:THR84 3.4 38.5 1.0 O B:ASP83 3.5 44.1 1.0 N B:THR84 3.6 38.9 1.0 CG B:PHE87 3.6 43.7 1.0 CB B:THR84 3.6 42.7 1.0 CG f:WFP2 3.6 46.8 1.0 CE2 f:WFP2 3.6 47.0 1.0 C B:ASP83 3.7 42.4 1.0 CG2 B:THR84 3.8 41.0 1.0 CD2 C:LEU119 3.9 41.6 1.0 CD2 B:PHE87 3.9 43.8 1.0 C B:THR84 4.0 41.8 1.0 O B:THR84 4.1 46.8 1.0 CD2 f:WFP2 4.1 47.0 1.0 CG C:LEU119 4.2 42.6 1.0 CD1 B:PHE87 4.4 43.8 1.0 CA B:PHE87 4.5 38.3 1.0 CD1 C:LEU119 4.5 40.1 1.0 N B:PHE87 4.7 36.3 1.0 F2 f:WFP2 4.8 50.9 1.0 CB f:WFP2 4.9 50.7 1.0 CE2 B:PHE87 4.9 43.4 1.0 CB B:ASP83 5.0 36.3 1.0 CA B:ASP83 5.0 39.4 1.0

Fluorine binding site 6 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ f:F2 b:50.9 occ:1.00 F2 f:WFP2 0.0 50.9 1.0 CE2 f:WFP2 1.4 47.0 1.0 CZ f:WFP2 2.4 44.3 1.0 CD2 f:WFP2 2.4 47.0 1.0 CE2 C:TYR67 3.4 46.0 1.0 CD1 B:LEU53 3.6 51.1 1.0 CD2 C:TYR67 3.6 43.4 1.0 CG1 B:VAL49 3.7 41.8 1.0 CE1 f:WFP2 3.7 48.7 1.0 CG f:WFP2 3.7 46.8 1.0 CD1 C:LEU97 3.7 45.4 1.0 CD1 f:WFP2 4.2 48.6 1.0 CZ C:TYR67 4.3 48.2 1.0 CG B:LEU53 4.4 47.3 1.0 CD2 B:LEU53 4.4 51.4 1.0 CD2 C:LEU95 4.4 46.5 1.0 OG1 B:THR84 4.4 38.5 1.0 CG C:TYR67 4.6 49.1 1.0 OH C:TYR67 4.7 49.3 1.0 CG C:LEU97 4.7 51.2 1.0 F1 f:WFP2 4.8 48.4 1.0 CD2 C:LEU97 4.9 45.4 1.0 CB C:LEU97 4.9 41.5 1.0 CB f:WFP2 4.9 50.7 1.0 N f:WFP2 5.0 46.3 1.0

Fluorine binding site 7 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ g:F2 b:40.7 occ:1.00 F1 g:WFP2 0.0 40.7 1.0 CE1 g:WFP2 1.4 39.1 1.0 CD1 g:WFP2 2.4 41.1 1.0 CZ g:WFP2 2.4 37.9 1.0 CA C:THR84 3.3 41.0 1.0 CB C:PHE87 3.3 37.5 1.0 OG1 C:THR84 3.5 37.0 1.0 CG C:PHE87 3.6 44.8 1.0 CD1 D:LEU119 3.6 37.0 1.0 CE2 g:WFP2 3.7 36.4 1.0 CG g:WFP2 3.7 41.3 1.0 O C:ASP83 3.7 44.1 1.0 N C:THR84 3.7 41.1 1.0 CB C:THR84 3.8 40.2 1.0 CD2 C:PHE87 3.9 45.4 1.0 C C:ASP83 3.9 42.4 1.0 CD2 D:LEU119 4.0 44.9 1.0 CG2 C:THR84 4.1 40.2 1.0 CD2 g:WFP2 4.1 40.3 1.0 C C:THR84 4.3 43.3 1.0 O C:THR84 4.4 43.4 1.0 CD1 C:PHE87 4.4 49.3 1.0 CG D:LEU119 4.5 43.1 1.0 CA C:PHE87 4.7 43.0 1.0 F2 g:WFP2 4.8 43.5 1.0 CE2 C:PHE87 4.8 40.4 1.0 CB g:WFP2 4.9 43.0 1.0 CB C:ASP83 5.0 33.2 1.0

Fluorine binding site 8 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ g:F2 b:43.5 occ:1.00 F2 g:WFP2 0.0 43.5 1.0 CE2 g:WFP2 1.4 36.4 1.0 CD2 g:WFP2 2.4 40.3 1.0 CZ g:WFP2 2.4 37.9 1.0 CE2 D:TYR67 3.3 45.2 1.0 CD2 D:TYR67 3.5 41.7 1.0 CD1 C:LEU53 3.5 39.3 1.0 CG g:WFP2 3.6 41.3 1.0 CE1 g:WFP2 3.7 39.1 1.0 CD1 D:LEU97 3.8 44.3 1.0 CG1 C:VAL49 3.8 39.7 1.0 CZ D:TYR67 4.1 47.8 1.0 CD1 g:WFP2 4.1 41.1 1.0 CG D:TYR67 4.5 41.7 1.0 CG C:LEU53 4.5 39.0 1.0 CD2 D:LEU95 4.5 37.9 1.0 OH D:TYR67 4.6 48.0 1.0 CD2 C:LEU53 4.6 43.1 1.0 OG1 C:THR84 4.7 37.0 1.0 CG D:LEU97 4.8 47.7 1.0 F1 g:WFP2 4.8 40.7 1.0 CB g:WFP2 4.9 43.0 1.0 CD2 D:LEU97 5.0 44.2 1.0 CE1 D:TYR67 5.0 42.4 1.0

Fluorine binding site 9 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ h:F2 b:48.8 occ:1.00 F1 h:WFP2 0.0 48.8 1.0 CE1 h:WFP2 1.4 46.1 1.0 CZ h:WFP2 2.4 45.4 1.0 CD1 h:WFP2 2.4 42.7 1.0 CA D:THR84 3.0 43.3 1.0 CB D:PHE87 3.3 41.8 1.0 OG1 D:THR84 3.4 42.1 1.0 O D:ASP83 3.5 42.8 1.0 CD1 E:LEU119 3.5 46.3 1.0 N D:THR84 3.6 41.3 1.0 CE2 h:WFP2 3.6 45.4 1.0 CB D:THR84 3.7 41.7 1.0 CG h:WFP2 3.7 45.0 1.0 CG D:PHE87 3.7 45.4 1.0 C D:ASP83 3.8 44.2 1.0 CG2 D:THR84 3.9 43.9 1.0 CD2 D:PHE87 4.0 43.8 1.0 C D:THR84 4.1 46.1 1.0 CD2 h:WFP2 4.1 44.5 1.0 O D:THR84 4.2 47.2 1.0 CD2 E:LEU119 4.2 45.3 1.0 CG E:LEU119 4.5 49.1 1.0 CD1 D:PHE87 4.5 47.3 1.0 CA D:PHE87 4.6 40.2 1.0 F2 h:WFP2 4.8 46.2 1.0 N D:PHE87 4.8 41.2 1.0 CB h:WFP2 4.9 47.7 1.0 CE2 D:PHE87 5.0 44.4 1.0 CB D:ASP83 5.0 42.7 1.0 CA D:ASP83 5.0 43.6 1.0

Fluorine binding site 10 out of 56 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Neisseria Meningitidis Clpp Protease in Complex with Acyldepsipeptide-14 (Adep-14) within 5.0Å range: probe atom residue distance (Å) B Occ h:F2 b:46.2 occ:1.00 F2 h:WFP2 0.0 46.2 1.0 CE2 h:WFP2 1.4 45.4 1.0 CZ h:WFP2 2.4 45.4 1.0 CD2 h:WFP2 2.4 44.5 1.0 CD1 D:LEU53 3.2 42.9 1.0 CG1 D:VAL49 3.5 38.5 1.0 CD1 E:LEU97 3.5 43.8 1.0 CE1 h:WFP2 3.7 46.1 1.0 CG h:WFP2 3.7 45.0 1.0 CE2 E:TYR67 3.8 45.1 1.0 CD2 E:TYR67 3.8 45.7 1.0 CD1 h:WFP2 4.2 42.7 1.0 CG D:LEU53 4.4 44.4 1.0 OG1 D:THR84 4.5 42.1 1.0 CG E:LEU97 4.6 43.4 1.0 CD2 D:LEU53 4.7 35.6 1.0 CD2 E:LEU97 4.7 46.3 1.0 CD2 E:LEU95 4.7 43.9 1.0 F1 h:WFP2 4.8 48.8 1.0 CZ E:TYR67 4.8 45.2 1.0 CG E:TYR67 4.9 45.6 1.0 CB D:VAL49 4.9 39.2 1.0 CE1 E:PHE35 5.0 64.8 1.0 CB h:WFP2 5.0 47.7 1.0

M.F.Mabanglo, W.A.Houry. Molecular Basis of Clpp Activation By Small Molecules To Be Published.