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Fluorine in PDB 6w9t: Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06

Enzymatic activity of Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06

All present enzymatic activity of Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06, PDB code: 6w9t 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) 97.33 / 1.64
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.328, 119.150, 127.763, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.2

Other elements in 6w9t:

The structure of Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06 also contains other interesting chemical elements:

Potassium (K) 7 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06 (pdb code 6w9t). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06, PDB code: 6w9t:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6w9t

Go back to Fluorine Binding Sites List in 6w9t
Fluorine binding site 1 out of 6 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:73.8
occ:0.56
 FAA F:KHS301 0.0 73.8 0.6
FAA F:KHS301 0.7 74.2 0.4
CAC F:KHS301 1.4 75.7 0.6
CAC F:KHS301 1.7 75.8 0.4
CAF F:KHS301 2.2 76.0 0.4
FAD F:KHS301 2.2 75.2 0.6
FAB F:KHS301 2.2 75.9 0.6
CAF F:KHS301 2.3 76.9 0.6
H16 F:KHS301 2.4 91.4 0.4
FAB F:KHS301 2.5 77.4 0.4
CAE F:KHS301 2.5 76.1 0.4
O F:HOH480 2.6 56.9 1.0
OD2 F:ASP63 2.7 26.0 1.0
FAD F:KHS301 2.8 75.3 0.4
HE2 F:LYS115 3.1 50.9 1.0
CAE F:KHS301 3.1 76.8 0.6
H16 F:KHS301 3.1 92.2 0.6
CAG F:KHS301 3.3 78.0 0.6
CAG F:KHS301 3.3 78.3 0.4
H17 F:KHS301 3.4 93.7 0.6
HE1 F:PHE65 3.6 34.4 1.0
HZ3 F:LYS115 3.6 39.5 1.0
H17 F:KHS301 3.6 94.0 0.4
HD3 F:LYS115 3.7 65.1 1.0
NAI F:KHS301 3.7 77.8 0.4
CE F:LYS115 3.8 42.4 1.0
CG F:ASP63 3.9 35.4 1.0
NZ F:LYS115 4.1 32.9 1.0
CD F:LYS115 4.2 54.2 1.0
CAH F:KHS301 4.3 78.0 0.4
NAI F:KHS301 4.3 79.0 0.6
HB2 F:ASP63 4.4 63.0 1.0
HZ1 F:LYS115 4.4 39.5 1.0
CAJ F:KHS301 4.4 76.6 0.4
CAH F:KHS301 4.5 77.7 0.6
CE1 F:PHE65 4.5 28.6 1.0
HB3 F:ASP63 4.6 63.0 1.0
CB F:ASP63 4.6 52.5 1.0
HG2 F:LYS115 4.6 63.8 1.0
HE3 F:LYS115 4.6 50.9 1.0
HZ F:PHE65 4.8 59.1 1.0
HB2 F:SER93 4.8 44.6 1.0
CAJ F:KHS301 4.9 75.2 0.6
OD1 F:ASP63 4.9 35.6 1.0
HB3 F:LYS115 4.9 56.9 1.0
HZ2 F:LYS115 4.9 39.5 1.0
CG F:LYS115 5.0 53.1 1.0

Fluorine binding site 2 out of 6 in 6w9t

Go back to Fluorine Binding Sites List in 6w9t
Fluorine binding site 2 out of 6 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:74.2
occ:0.44
 FAA F:KHS301 0.0 74.2 0.4
FAA F:KHS301 0.7 73.8 0.6
CAC F:KHS301 1.3 75.7 0.6
CAC F:KHS301 1.4 75.8 0.4
FAD F:KHS301 1.8 75.2 0.6
FAB F:KHS301 2.1 75.9 0.6
FAB F:KHS301 2.2 77.4 0.4
FAD F:KHS301 2.2 75.3 0.4
CAF F:KHS301 2.4 76.0 0.4
HE2 F:LYS115 2.4 50.9 1.0
H16 F:KHS301 2.6 91.4 0.4
CAF F:KHS301 2.7 76.9 0.6
CAE F:KHS301 2.8 76.1 0.4
OD2 F:ASP63 2.9 26.0 1.0
CE F:LYS115 3.2 42.4 1.0
HZ3 F:LYS115 3.3 39.5 1.0
O F:HOH480 3.3 56.9 1.0
HD3 F:LYS115 3.3 65.1 1.0
H16 F:KHS301 3.3 92.2 0.6
CAE F:KHS301 3.4 76.8 0.6
CAG F:KHS301 3.5 78.3 0.4
CAG F:KHS301 3.6 78.0 0.6
NZ F:LYS115 3.7 32.9 1.0
H17 F:KHS301 3.7 93.7 0.6
H17 F:KHS301 3.8 94.0 0.4
CD F:LYS115 3.8 54.2 1.0
HZ1 F:LYS115 3.9 39.5 1.0
HE3 F:LYS115 4.0 50.9 1.0
HG2 F:LYS115 4.0 63.8 1.0
CG F:ASP63 4.1 35.4 1.0
NAI F:KHS301 4.1 77.8 0.4
HE1 F:PHE65 4.2 34.4 1.0
CG F:LYS115 4.5 53.1 1.0
HZ2 F:LYS115 4.5 39.5 1.0
HD2 F:LYS115 4.6 65.1 1.0
HB3 F:LYS115 4.6 56.9 1.0
CAH F:KHS301 4.6 78.0 0.4
O F:HOH425 4.7 44.8 1.0
NAI F:KHS301 4.7 79.0 0.6
HB2 F:ASP63 4.8 63.0 1.0
CAJ F:KHS301 4.8 76.6 0.4
CAH F:KHS301 4.9 77.7 0.6
HB3 F:ASP63 4.9 63.0 1.0
HB2 F:SER93 4.9 44.6 1.0
OD1 F:ASP63 4.9 35.6 1.0
CB F:ASP63 4.9 52.5 1.0

Fluorine binding site 3 out of 6 in 6w9t

Go back to Fluorine Binding Sites List in 6w9t
Fluorine binding site 3 out of 6 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:75.2
occ:0.56
 FAD F:KHS301 0.0 75.2 0.6
FAD F:KHS301 1.0 75.3 0.4
CAC F:KHS301 1.4 75.8 0.4
CAC F:KHS301 1.4 75.7 0.6
FAA F:KHS301 1.8 74.2 0.4
CAF F:KHS301 2.0 76.0 0.4
H16 F:KHS301 2.1 91.4 0.4
FAA F:KHS301 2.2 73.8 0.6
FAB F:KHS301 2.2 75.9 0.6
CAE F:KHS301 2.3 76.1 0.4
CAF F:KHS301 2.4 76.9 0.6
HE2 F:LYS115 2.5 50.9 1.0
H16 F:KHS301 2.5 92.2 0.6
FAB F:KHS301 2.6 77.4 0.4
HG2 F:LYS115 2.7 63.8 1.0
HD3 F:LYS115 2.7 65.1 1.0
CAE F:KHS301 2.8 76.8 0.6
HB3 F:LYS115 3.1 56.9 1.0
CD F:LYS115 3.1 54.2 1.0
CE F:LYS115 3.2 42.4 1.0
CG F:LYS115 3.2 53.1 1.0
CAG F:KHS301 3.2 78.3 0.4
O F:HOH425 3.3 44.8 1.0
CAG F:KHS301 3.6 78.0 0.6
NAI F:KHS301 3.6 77.8 0.4
H17 F:KHS301 3.6 94.0 0.4
HZ F:PHE117 3.6 43.7 1.0
CB F:LYS115 3.6 47.4 1.0
HE2 F:PHE117 3.7 40.5 1.0
HE3 F:LYS115 3.8 50.9 1.0
H17 F:KHS301 3.8 93.7 0.6
HA F:LYS115 3.9 31.2 1.0
OD2 F:ASP63 4.0 26.0 1.0
HZ3 F:LYS115 4.1 39.5 1.0
NAI F:KHS301 4.1 79.0 0.6
HD2 F:LYS115 4.1 65.1 1.0
HG3 F:LYS115 4.1 63.8 1.0
HB2 F:SER93 4.1 44.6 1.0
NZ F:LYS115 4.2 32.9 1.0
CAH F:KHS301 4.3 78.0 0.4
CZ F:PHE117 4.3 36.4 1.0
CE2 F:PHE117 4.3 33.8 1.0
CA F:LYS115 4.4 26.0 1.0
CAJ F:KHS301 4.4 76.6 0.4
HB2 F:LYS115 4.4 56.9 1.0
HG F:SER93 4.5 40.1 1.0
HE1 F:PHE65 4.7 34.4 1.0
CAH F:KHS301 4.7 77.7 0.6
HZ1 F:LYS115 4.7 39.5 1.0
OG F:SER93 4.7 33.4 1.0
O F:HOH480 4.8 56.9 1.0
CAJ F:KHS301 4.8 75.2 0.6
CB F:SER93 4.9 37.2 1.0
HZ2 F:LYS115 4.9 39.5 1.0

Fluorine binding site 4 out of 6 in 6w9t

Go back to Fluorine Binding Sites List in 6w9t
Fluorine binding site 4 out of 6 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:75.3
occ:0.44
 FAD F:KHS301 0.0 75.3 0.4
FAD F:KHS301 1.0 75.2 0.6
CAC F:KHS301 1.4 75.8 0.4
CAC F:KHS301 1.7 75.7 0.6
FAB F:KHS301 1.9 75.9 0.6
FAB F:KHS301 2.2 77.4 0.4
FAA F:KHS301 2.2 74.2 0.4
CAF F:KHS301 2.4 76.0 0.4
O F:HOH425 2.5 44.8 1.0
HE2 F:LYS115 2.6 50.9 1.0
HG2 F:LYS115 2.6 63.8 1.0
FAA F:KHS301 2.8 73.8 0.6
CAF F:KHS301 2.9 76.9 0.6
H16 F:KHS301 3.1 91.4 0.4
CAE F:KHS301 3.1 76.1 0.4
CAG F:KHS301 3.3 78.3 0.4
HD3 F:LYS115 3.4 65.1 1.0
HZ F:PHE117 3.4 43.7 1.0
CG F:LYS115 3.4 53.1 1.0
CE F:LYS115 3.4 42.4 1.0
H16 F:KHS301 3.4 92.2 0.6
H17 F:KHS301 3.4 94.0 0.4
CAE F:KHS301 3.5 76.8 0.6
CD F:LYS115 3.5 54.2 1.0
HB3 F:LYS115 3.6 56.9 1.0
HE3 F:LYS115 3.8 50.9 1.0
CAG F:KHS301 3.8 78.0 0.6
H17 F:KHS301 3.9 93.7 0.6
HA F:LYS115 3.9 31.2 1.0
CB F:LYS115 4.0 47.4 1.0
HE2 F:PHE117 4.1 40.5 1.0
HG3 F:LYS115 4.1 63.8 1.0
CZ F:PHE117 4.2 36.4 1.0
NAI F:KHS301 4.3 77.8 0.4
CA F:LYS115 4.5 26.0 1.0
CAH F:KHS301 4.5 78.0 0.4
HZ3 F:LYS115 4.5 39.5 1.0
HD2 F:LYS115 4.5 65.1 1.0
NZ F:LYS115 4.5 32.9 1.0
CE2 F:PHE117 4.5 33.8 1.0
O F:GLY114 4.6 30.1 1.0
OD2 F:ASP63 4.7 26.0 1.0
NAI F:KHS301 4.7 79.0 0.6
HZ1 F:LYS115 4.9 39.5 1.0
HB2 F:LYS115 4.9 56.9 1.0
CAJ F:KHS301 4.9 76.6 0.4

Fluorine binding site 5 out of 6 in 6w9t

Go back to Fluorine Binding Sites List in 6w9t
Fluorine binding site 5 out of 6 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:75.9
occ:0.56
 FAB F:KHS301 0.0 75.9 0.6
FAB F:KHS301 0.6 77.4 0.4
CAC F:KHS301 1.0 75.8 0.4
CAC F:KHS301 1.4 75.7 0.6
CAF F:KHS301 1.8 76.0 0.4
FAD F:KHS301 1.9 75.3 0.4
FAA F:KHS301 2.1 74.2 0.4
H17 F:KHS301 2.1 94.0 0.4
CAG F:KHS301 2.2 78.3 0.4
FAD F:KHS301 2.2 75.2 0.6
FAA F:KHS301 2.2 73.8 0.6
CAF F:KHS301 2.4 76.9 0.6
H17 F:KHS301 2.4 93.7 0.6
CAG F:KHS301 2.7 78.0 0.6
CAE F:KHS301 3.1 76.1 0.4
H16 F:KHS301 3.5 91.4 0.4
CAH F:KHS301 3.6 78.0 0.4
CAE F:KHS301 3.6 76.8 0.6
HE2 F:LYS115 3.7 50.9 1.0
O F:HOH425 3.9 44.8 1.0
H16 F:KHS301 3.9 92.2 0.6
CAH F:KHS301 4.1 77.7 0.6
NAI F:KHS301 4.1 77.8 0.4
H18 F:KHS301 4.2 93.7 0.4
O F:HOH480 4.3 56.9 1.0
CAJ F:KHS301 4.4 76.6 0.4
HZ F:PHE117 4.4 43.7 1.0
HG2 F:LYS115 4.5 63.8 1.0
H18 F:KHS301 4.6 93.3 0.6
CE F:LYS115 4.6 42.4 1.0
NAI F:KHS301 4.7 79.0 0.6
HD3 F:LYS115 4.8 65.1 1.0
HE2 F:PHE117 4.9 40.5 1.0
CAJ F:KHS301 4.9 75.2 0.6
OD2 F:ASP63 4.9 26.0 1.0

Fluorine binding site 6 out of 6 in 6w9t

Go back to Fluorine Binding Sites List in 6w9t
Fluorine binding site 6 out of 6 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:77.4
occ:0.44
 FAB F:KHS301 0.0 77.4 0.4
FAB F:KHS301 0.6 75.9 0.6
CAC F:KHS301 1.4 75.8 0.4
CAC F:KHS301 1.8 75.7 0.6
FAD F:KHS301 2.2 75.3 0.4
FAA F:KHS301 2.2 74.2 0.4
H17 F:KHS301 2.3 94.0 0.4
CAF F:KHS301 2.4 76.0 0.4
FAA F:KHS301 2.5 73.8 0.6
FAD F:KHS301 2.6 75.2 0.6
CAG F:KHS301 2.7 78.3 0.4
H17 F:KHS301 2.7 93.7 0.6
CAF F:KHS301 2.9 76.9 0.6
CAG F:KHS301 3.1 78.0 0.6
CAE F:KHS301 3.6 76.1 0.4
HE2 F:LYS115 3.8 50.9 1.0
H16 F:KHS301 4.0 91.4 0.4
O F:HOH425 4.0 44.8 1.0
CAH F:KHS301 4.1 78.0 0.4
CAE F:KHS301 4.2 76.8 0.6
O F:HOH480 4.4 56.9 1.0
H16 F:KHS301 4.4 92.2 0.6
CAH F:KHS301 4.5 77.7 0.6
H18 F:KHS301 4.6 93.7 0.4
NAI F:KHS301 4.7 77.8 0.4
CE F:LYS115 4.7 42.4 1.0
HG2 F:LYS115 4.7 63.8 1.0
HZ F:PHE117 4.8 43.7 1.0
CAJ F:KHS301 4.9 76.6 0.4

Reference:

G.Binepal, M.F.Mabanglo, J.D.Goodreid, E.Leung, M.M.Barghash, K.S.Wong, F.Lin, M.Cossette, J.Bansagi, B.Song, V.H.Balasco Serrao, E.F.Pai, R.A.Batey, S.D.Gray-Owen, W.A.Houry. Development of Antibiotics That Dysregulate the Neisserial Clpp Protease. Acs Infect Dis. 2020.
ISSN: ESSN 2373-8227
PubMed: 33237740
DOI: 10.1021/ACSINFECDIS.0C00599
Page generated: Fri Aug 2 03:39:57 2024

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