Fluorine in PDB 6pmd: Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide

Enzymatic activity of Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide

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

Protein crystallography data

The structure of Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide, PDB code: 6pmd 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) 38.80 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.377, 125.972, 145.603, 90.00, 93.77, 90.00
R / Rfree (%) 20 / 22.7

Fluorine Binding Sites:

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 Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide (pdb code 6pmd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 22 binding sites of Fluorine where determined in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide, PDB code: 6pmd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 22 in 6pmd

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Fluorine binding site 1 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F2

b:24.2
occ:0.50
 F1 H:WFP2 0.0 24.2 0.5
CE1 H:WFP2 1.3 25.4 0.5
CD1 H:WFP2 2.3 25.4 0.5
CZ H:WFP2 2.4 24.4 0.5
CB B:HIS83 3.3 41.5 1.0
CA B:THR80 3.3 28.2 1.0
OG1 B:THR80 3.5 22.3 1.0
CG B:HIS83 3.6 44.2 1.0
CG H:WFP2 3.6 27.1 0.5
CE2 H:WFP2 3.6 26.8 0.5
CB B:THR80 3.7 27.2 1.0
CG2 B:THR80 3.7 29.8 1.0
CD2 B:HIS83 3.8 48.5 1.0
CD1 A:LEU115 3.9 44.0 1.0
O B:ASP79 4.0 28.1 1.0
N B:THR80 4.0 30.8 1.0
O B:THR80 4.1 29.8 1.0
CD2 H:WFP2 4.1 26.9 0.5
C B:THR80 4.2 30.8 1.0
C B:ASP79 4.3 29.9 1.0
CG A:LEU115 4.4 42.2 1.0
ND1 B:HIS83 4.5 44.6 1.0
CA B:HIS83 4.6 39.1 1.0
CD2 B:LEU49 4.7 38.8 1.0
F2 H:WFP2 4.7 26.7 0.5
NE2 B:HIS83 4.8 47.9 1.0
CB H:WFP2 4.8 29.8 0.5
CD2 A:LEU115 4.9 48.4 1.0
CG2 B:ILE84 5.0 37.1 1.0

Fluorine binding site 2 out of 22 in 6pmd

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Fluorine binding site 2 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F2

b:26.7
occ:0.50
 F2 H:WFP2 0.0 26.7 0.5
CE2 H:WFP2 1.3 26.8 0.5
CZ H:WFP2 2.3 24.4 0.5
CD2 H:WFP2 2.4 26.9 0.5
CD2 A:TYR63 3.0 53.8 1.0
CE2 A:TYR63 3.2 54.0 1.0
CD1 B:LEU49 3.5 36.9 1.0
CE1 H:WFP2 3.6 25.4 0.5
CG H:WFP2 3.6 27.1 0.5
CG1 B:VAL45 3.6 27.6 1.0
CG2 A:ILE93 3.7 45.5 1.0
CD1 A:ILE93 3.8 43.4 1.0
CG A:TYR63 3.9 48.3 1.0
CD1 H:WFP2 4.1 25.4 0.5
CZ A:TYR63 4.2 56.8 1.0
CG B:LEU49 4.5 38.0 1.0
CB A:TYR63 4.5 42.2 1.0
OG1 B:THR80 4.6 22.3 1.0
F1 H:WFP2 4.7 24.2 0.5
CD2 B:LEU49 4.7 38.8 1.0
CG1 A:ILE93 4.7 40.8 1.0
CD1 A:TYR63 4.8 53.0 1.0
CB A:ILE93 4.8 38.4 1.0
CE1 A:TYR63 4.9 53.4 1.0
CB H:WFP2 4.9 29.8 0.5
OH A:TYR63 4.9 54.5 1.0

Fluorine binding site 3 out of 22 in 6pmd

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Fluorine binding site 3 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F2

b:14.0
occ:0.50
 F1 J:WFP2 0.0 14.0 0.5
CE1 J:WFP2 1.3 15.7 0.5
CD1 J:WFP2 2.4 15.6 0.5
CZ J:WFP2 2.4 15.0 0.5
CA C:THR80 3.3 16.3 1.0
OG1 C:THR80 3.4 13.1 1.0
CB C:HIS83 3.4 24.9 1.0
CG2 C:THR80 3.6 14.9 1.0
CB C:THR80 3.6 16.2 1.0
CG J:WFP2 3.6 16.6 0.5
CE2 J:WFP2 3.7 17.1 0.5
CG C:HIS83 3.7 25.6 1.0
CD2 C:HIS83 3.9 26.4 1.0
CD1 B:LEU115 3.9 31.5 1.0
N C:THR80 4.1 16.8 1.0
O C:ASP79 4.1 14.4 1.0
O C:THR80 4.2 18.1 1.0
CD2 J:WFP2 4.2 16.8 0.5
C C:THR80 4.3 17.9 1.0
CG B:LEU115 4.3 30.4 1.0
C C:ASP79 4.4 16.6 1.0
CD2 C:LEU49 4.5 21.8 1.0
ND1 C:HIS83 4.7 28.3 1.0
CD2 B:LEU115 4.7 35.5 1.0
F2 J:WFP2 4.7 18.2 0.5
CA C:HIS83 4.8 22.3 1.0
NE2 C:HIS83 4.8 28.4 1.0
CB J:WFP2 4.8 17.1 0.5
CG2 C:ILE84 4.9 21.4 1.0

Fluorine binding site 4 out of 22 in 6pmd

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Fluorine binding site 4 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F2

b:18.2
occ:0.50
 F2 J:WFP2 0.0 18.2 0.5
CE2 J:WFP2 1.4 17.1 0.5
CZ J:WFP2 2.4 15.0 0.5
CD2 J:WFP2 2.4 16.8 0.5
CD2 B:TYR63 2.9 42.2 1.0
CE2 B:TYR63 3.2 41.7 1.0
CG2 B:ILE93 3.6 37.2 1.0
CD1 C:LEU49 3.6 24.5 1.0
CG B:TYR63 3.6 33.3 1.0
CE1 J:WFP2 3.6 15.7 0.5
CD1 B:ILE93 3.7 33.6 1.0
CG J:WFP2 3.7 16.6 0.5
CG1 C:VAL45 3.8 16.5 1.0
CB B:TYR63 4.2 31.1 1.0
CD1 J:WFP2 4.2 15.6 0.5
CZ B:TYR63 4.2 41.1 1.0
CD1 B:TYR63 4.5 35.9 1.0
CG1 B:ILE93 4.5 33.9 1.0
CG C:LEU49 4.6 21.3 1.0
CB B:ILE93 4.6 32.1 1.0
CE1 B:TYR63 4.7 38.4 1.0
F1 J:WFP2 4.7 14.0 0.5
CD2 C:LEU49 4.8 21.8 1.0
CG2 B:ILE91 4.8 26.4 1.0
OG1 C:THR80 4.9 13.1 1.0
CE B:MET31 5.0 56.3 1.0

Fluorine binding site 5 out of 22 in 6pmd

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Fluorine binding site 5 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
O:F2

b:24.9
occ:0.50
 F1 O:WFP2 0.0 24.9 0.5
CE1 O:WFP2 1.3 24.1 0.5
CD1 O:WFP2 2.3 22.2 0.5
CZ O:WFP2 2.4 24.9 0.5
CA D:THR80 3.2 16.7 1.0
OG1 D:THR80 3.3 15.7 1.0
CG2 D:THR80 3.5 15.6 1.0
CB D:THR80 3.5 16.4 1.0
CG O:WFP2 3.5 24.5 0.5
CB D:HIS83 3.6 25.8 1.0
CE2 O:WFP2 3.6 27.5 0.5
CG D:HIS83 3.9 27.1 1.0
N D:THR80 4.1 17.7 1.0
CD2 D:HIS83 4.1 28.5 1.0
CD2 O:WFP2 4.1 26.5 0.5
CD1 C:LEU115 4.1 25.9 1.0
O D:THR80 4.1 17.8 1.0
O D:ASP79 4.2 14.5 1.0
C D:THR80 4.2 18.7 1.0
CD2 D:LEU49 4.4 22.1 1.0
CG C:LEU115 4.4 23.5 1.0
C D:ASP79 4.5 16.4 1.0
CB O:WFP2 4.7 27.9 0.5
CD2 C:LEU115 4.8 26.6 1.0
F2 O:WFP2 4.8 27.3 0.5
CG2 D:ILE84 4.9 23.0 1.0
ND1 D:HIS83 4.9 31.0 1.0
CA D:HIS83 5.0 24.6 1.0

Fluorine binding site 6 out of 22 in 6pmd

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Fluorine binding site 6 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
O:F2

b:27.3
occ:0.50
 F2 O:WFP2 0.0 27.3 0.5
CE2 O:WFP2 1.3 27.5 0.5
CD2 C:TYR63 2.2 39.8 1.0
CD2 O:WFP2 2.4 26.5 0.5
CZ O:WFP2 2.5 24.9 0.5
CE2 C:TYR63 2.5 45.4 1.0
CG C:TYR63 2.8 30.0 1.0
CZ C:TYR63 3.3 48.4 1.0
CD1 C:TYR63 3.5 40.1 1.0
CB C:TYR63 3.6 21.9 1.0
CG O:WFP2 3.7 24.5 0.5
CE1 O:WFP2 3.7 24.1 0.5
CE1 C:TYR63 3.7 43.8 1.0
CD1 D:LEU49 3.8 21.9 1.0
CG2 C:ILE93 4.0 27.4 1.0
CD1 O:WFP2 4.2 22.2 0.5
OH C:TYR63 4.2 59.7 1.0
CG2 C:ILE91 4.3 20.2 1.0
CD1 C:ILE93 4.4 25.0 1.0
CD1 C:ILE91 4.5 26.6 1.0
CB C:ILE91 4.6 19.0 1.0
CG1 D:VAL45 4.6 18.4 1.0
CA C:TYR63 4.7 17.6 1.0
F1 O:WFP2 4.8 24.9 0.5
CG D:LEU49 4.9 21.9 1.0
CB O:WFP2 4.9 27.9 0.5
CD2 D:LEU49 5.0 22.1 1.0

Fluorine binding site 7 out of 22 in 6pmd

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Fluorine binding site 7 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F2

b:25.2
occ:0.50
 F1 P:WFP2 0.0 25.2 0.5
CE1 P:WFP2 1.3 22.3 0.5
CD1 P:WFP2 2.3 21.4 0.5
CZ P:WFP2 2.3 20.9 0.5
CB E:HIS83 3.2 34.6 1.0
CA E:THR80 3.3 24.3 1.0
OG1 E:THR80 3.5 20.5 1.0
CG P:WFP2 3.5 21.2 0.5
CG E:HIS83 3.5 32.4 1.0
CE2 P:WFP2 3.5 22.2 0.5
CD1 D:LEU115 3.6 26.9 1.0
CB E:THR80 3.8 20.4 1.0
CD2 E:HIS83 3.8 35.9 1.0
CG2 E:THR80 3.9 19.8 1.0
O E:ASP79 3.9 23.5 1.0
N E:THR80 4.0 21.8 1.0
CD2 P:WFP2 4.0 22.6 0.5
CG D:LEU115 4.1 25.4 1.0
C E:ASP79 4.2 22.5 1.0
O E:THR80 4.3 26.3 1.0
C E:THR80 4.3 25.9 1.0
ND1 E:HIS83 4.4 32.6 1.0
CD2 D:LEU115 4.6 28.8 1.0
F2 P:WFP2 4.6 23.1 0.5
CA E:HIS83 4.7 33.3 1.0
CB P:WFP2 4.7 22.1 0.5
NE2 E:HIS83 4.7 35.1 1.0
CD2 E:LEU49 4.9 32.2 1.0

Fluorine binding site 8 out of 22 in 6pmd

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Fluorine binding site 8 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F2

b:23.1
occ:0.50
 F2 P:WFP2 0.0 23.1 0.5
CE2 P:WFP2 1.3 22.2 0.5
CZ P:WFP2 2.3 20.9 0.5
CD2 P:WFP2 2.4 22.6 0.5
CD2 D:TYR63 3.0 41.4 1.0
CE2 D:TYR63 3.1 38.5 1.0
CE1 P:WFP2 3.5 22.3 0.5
CD1 E:LEU49 3.6 34.8 1.0
CG1 E:VAL45 3.6 22.3 1.0
CG P:WFP2 3.6 21.2 0.5
CG2 D:ILE93 3.7 34.4 1.0
CG D:TYR63 3.9 32.6 1.0
CD1 D:ILE93 3.9 33.7 1.0
CD1 P:WFP2 4.0 21.4 0.5
CZ D:TYR63 4.1 41.8 1.0
CB D:TYR63 4.5 26.0 1.0
CG E:LEU49 4.5 33.2 1.0
OG1 E:THR80 4.5 20.5 1.0
F1 P:WFP2 4.6 25.2 0.5
CD2 E:LEU49 4.7 32.2 1.0
CD1 D:TYR63 4.7 37.5 1.0
CG1 D:ILE93 4.7 31.8 1.0
CB D:ILE93 4.8 30.9 1.0
CE1 D:TYR63 4.8 43.8 1.0
OH D:TYR63 4.9 52.4 1.0
CB P:WFP2 5.0 22.1 0.5

Fluorine binding site 9 out of 22 in 6pmd

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Fluorine binding site 9 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:F2

b:26.9
occ:0.50
 F1 Q:WFP2 0.0 26.9 0.5
CE1 Q:WFP2 1.3 27.3 0.5
CD1 Q:WFP2 2.3 26.8 0.5
CZ Q:WFP2 2.4 25.3 0.5
CB F:HIS83 3.2 45.1 1.0
CA F:THR80 3.3 35.0 1.0
CG F:HIS83 3.5 42.2 1.0
OG1 F:THR80 3.5 32.1 1.0
CD1 E:LEU115 3.6 41.9 1.0
CG Q:WFP2 3.6 26.2 0.5
CE2 Q:WFP2 3.6 27.0 0.5
CB F:THR80 3.7 34.1 1.0
CG2 F:THR80 3.7 33.5 1.0
CD2 F:HIS83 3.7 41.3 1.0
CD2 E:LEU115 3.9 42.3 1.0
O F:ASP79 3.9 35.4 1.0
N F:THR80 4.0 35.5 1.0
O F:THR80 4.0 32.7 1.0
CD2 Q:WFP2 4.1 27.9 0.5
C F:THR80 4.2 34.9 1.0
C F:ASP79 4.3 34.3 1.0
CG E:LEU115 4.3 39.5 1.0
ND1 F:HIS83 4.5 46.9 1.0
CA F:HIS83 4.6 43.0 1.0
F2 Q:WFP2 4.7 27.1 0.5
CD2 F:LEU49 4.7 38.1 1.0
NE2 F:HIS83 4.7 42.7 1.0
CB Q:WFP2 4.8 26.8 0.5
CG2 F:ILE84 4.9 44.5 1.0
N F:HIS83 5.0 42.6 1.0

Fluorine binding site 10 out of 22 in 6pmd

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Fluorine binding site 10 out of 22 in the Structure of Clpp From Staphylococcus Aureus in Complex with Acyldepsipeptide


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 Acyldepsipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:F2

b:27.1
occ:0.50
 F2 Q:WFP2 0.0 27.1 0.5
CE2 Q:WFP2 1.3 27.0 0.5
CZ Q:WFP2 2.3 25.3 0.5
CD2 Q:WFP2 2.4 27.9 0.5
CD2 E:TYR63 3.1 52.5 1.0
CE2 E:TYR63 3.2 60.5 1.0
CD1 F:LEU49 3.3 39.1 1.0
CE1 Q:WFP2 3.6 27.3 0.5
CG1 F:VAL45 3.6 30.2 1.0
CG Q:WFP2 3.6 26.2 0.5
CG2 E:ILE93 3.8 43.6 1.0
CG E:TYR63 4.0 46.8 1.0
CD1 E:ILE93 4.0 43.1 1.0
CZ E:TYR63 4.1 64.1 1.0
CD1 Q:WFP2 4.1 26.8 0.5
CG F:LEU49 4.3 39.3 1.0
CD2 F:LEU49 4.4 38.1 1.0
CB E:TYR63 4.6 36.5 1.0
OG1 F:THR80 4.7 32.1 1.0
F1 Q:WFP2 4.7 26.9 0.5
CD1 E:TYR63 4.7 50.7 1.0
CE1 E:TYR63 4.8 57.1 1.0
OH E:TYR63 4.8 67.2 1.0
CB Q:WFP2 4.9 26.8 0.5
CB E:ILE93 4.9 38.3 1.0
CG1 E:ILE93 4.9 40.5 1.0

Reference:

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
Page generated: Sun Dec 13 13:06:57 2020

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