Fluorine in PDB 6bba: Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28

Enzymatic activity of Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28

All present enzymatic activity of Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28, PDB code: 6bba 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) 46.74 / 2.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 172.399, 172.399, 135.963, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 23.5

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 (pdb code 6bba). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 14 binding sites of Fluorine where determined in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28, PDB code: 6bba:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 14 in 6bba

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Fluorine binding site 1 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F2

b:56.9
occ:1.00
 F1 H:WFP2 0.0 56.9 1.0
CE1 H:WFP2 1.4 59.5 1.0
CZ H:WFP2 2.4 54.3 1.0
CD1 H:WFP2 2.4 66.3 1.0
CD2 A:TYR161 3.2 65.3 1.0
CE2 A:TYR161 3.4 68.9 1.0
CE2 H:WFP2 3.6 53.2 1.0
CD1 G:LEU147 3.7 59.9 1.0
CG H:WFP2 3.7 65.0 1.0
CG2 G:ILE143 3.9 51.7 1.0
CG A:TYR161 4.0 63.5 1.0
CD1 A:TRP189 4.0 60.6 1.0
CD2 H:WFP2 4.2 55.9 1.0
CZ A:TYR161 4.2 66.6 1.0
NE1 A:TRP189 4.3 62.0 1.0
CG2 A:VAL191 4.4 58.5 1.0
CB A:VAL191 4.4 57.5 1.0
CB A:TYR161 4.6 58.3 1.0
CD1 A:TYR161 4.7 66.8 1.0
CG2 G:THR178 4.7 49.8 1.0
F2 H:WFP2 4.7 60.8 1.0
CG G:LEU147 4.8 53.8 1.0
CE1 A:TYR161 4.8 67.0 1.0
CG1 A:VAL191 4.9 54.8 1.0
CG A:TRP189 4.9 57.5 1.0
OH A:TYR161 4.9 66.8 1.0
CB H:WFP2 5.0 62.5 1.0

Fluorine binding site 2 out of 14 in 6bba

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Fluorine binding site 2 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F2

b:60.8
occ:1.00
 F2 H:WFP2 0.0 60.8 1.0
CE2 H:WFP2 1.4 53.2 1.0
CD2 H:WFP2 2.4 55.9 1.0
CZ H:WFP2 2.4 54.3 1.0
CG2 G:THR178 3.2 49.8 1.0
CB G:THR178 3.2 54.3 1.0
CA G:THR178 3.2 57.4 1.0
CB G:TYR181 3.3 58.0 1.0
CG H:WFP2 3.6 65.0 1.0
CE1 H:WFP2 3.6 59.5 1.0
CD1 A:LEU213 3.7 57.7 1.0
CG G:TYR181 3.8 61.0 1.0
CD2 A:LEU213 4.0 59.6 1.0
CD2 G:TYR181 4.0 60.8 1.0
CD1 H:WFP2 4.1 66.3 1.0
N G:THR178 4.2 57.2 1.0
O G:THR178 4.2 60.1 1.0
C G:THR178 4.3 59.9 1.0
CG A:LEU213 4.4 61.3 1.0
O G:ASP177 4.4 59.7 1.0
CD2 G:LEU147 4.5 50.5 1.0
C G:ASP177 4.6 60.8 1.0
OG1 G:THR178 4.6 61.3 1.0
CD1 G:TYR181 4.7 61.8 1.0
CA G:TYR181 4.7 60.8 1.0
NE1 A:TRP189 4.7 62.0 1.0
F1 H:WFP2 4.7 56.9 1.0
CB H:WFP2 4.9 62.5 1.0
CE2 G:TYR181 5.0 60.8 1.0
CG2 G:ILE182 5.0 51.0 1.0

Fluorine binding site 3 out of 14 in 6bba

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Fluorine binding site 3 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F2

b:63.5
occ:1.00
 F1 I:WFP2 0.0 63.5 1.0
CE1 I:WFP2 1.4 68.0 1.0
CZ I:WFP2 2.4 67.8 1.0
CD1 I:WFP2 2.4 67.8 1.0
CG2 B:VAL191 3.2 64.3 1.0
CD2 B:TYR161 3.5 52.4 1.0
CE2 I:WFP2 3.6 68.1 1.0
CG I:WFP2 3.7 66.0 1.0
CD1 B:TRP189 3.7 63.3 1.0
NE1 B:TRP189 3.8 67.8 1.0
CE2 B:TYR161 3.8 60.7 1.0
CG2 A:ILE143 4.0 56.9 1.0
CG B:TYR161 4.1 59.7 1.0
CD2 I:WFP2 4.1 67.4 1.0
CD1 A:LEU147 4.1 65.6 1.0
CB B:VAL191 4.2 62.8 1.0
CZ B:TYR161 4.6 68.1 1.0
CB B:TYR161 4.6 53.9 1.0
CG1 B:VAL191 4.7 63.3 1.0
F2 I:WFP2 4.7 66.0 1.0
CG B:TRP189 4.8 62.8 1.0
CD1 B:TYR161 4.8 56.5 1.0
OG1 A:THR178 4.9 55.8 1.0
CE2 B:TRP189 4.9 69.6 1.0
CB I:WFP2 5.0 66.7 1.0

Fluorine binding site 4 out of 14 in 6bba

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Fluorine binding site 4 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F2

b:66.0
occ:1.00
 F2 I:WFP2 0.0 66.0 1.0
CE2 I:WFP2 1.4 68.1 1.0
CZ I:WFP2 2.4 67.8 1.0
CD2 I:WFP2 2.4 67.4 1.0
CB A:TYR181 3.3 65.9 1.0
CA A:THR178 3.3 62.7 1.0
CG2 A:THR178 3.4 57.8 1.0
OG1 A:THR178 3.6 55.8 1.0
CB A:THR178 3.6 56.6 1.0
CG A:TYR181 3.6 69.9 1.0
CE1 I:WFP2 3.7 68.0 1.0
CG I:WFP2 3.7 66.0 1.0
CD1 B:LEU213 3.7 63.7 1.0
CD1 A:TYR181 3.9 66.7 1.0
O A:THR178 4.1 65.2 1.0
CD1 I:WFP2 4.2 67.8 1.0
C A:THR178 4.2 62.5 1.0
N A:THR178 4.2 64.8 1.0
CD2 A:TYR181 4.4 66.2 1.0
CD2 A:LEU147 4.4 65.9 1.0
O A:ASP177 4.5 70.2 1.0
CD2 B:LEU213 4.5 64.2 1.0
CA A:TYR181 4.6 66.2 1.0
CG B:LEU213 4.7 61.0 1.0
C A:ASP177 4.7 61.9 1.0
F1 I:WFP2 4.7 63.5 1.0
CE1 A:TYR181 4.8 68.9 1.0
CG2 A:ILE182 4.9 61.6 1.0
NE1 B:TRP189 4.9 67.8 1.0
N A:ILE182 5.0 68.7 1.0
CB I:WFP2 5.0 66.7 1.0

Fluorine binding site 5 out of 14 in 6bba

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Fluorine binding site 5 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F2

b:66.8
occ:1.00
 F1 J:WFP2 0.0 66.8 1.0
CE1 J:WFP2 1.4 64.0 1.0
CD1 J:WFP2 2.4 67.2 1.0
CZ J:WFP2 2.4 67.7 1.0
CD2 C:TYR161 3.6 62.1 1.0
CG J:WFP2 3.6 71.0 1.0
CE2 J:WFP2 3.6 65.0 1.0
CG2 C:VAL191 3.6 63.8 1.0
CG2 B:ILE143 3.7 51.2 1.0
CD1 B:LEU147 3.8 53.6 1.0
CE2 C:TYR161 3.8 61.0 1.0
CD1 C:TRP189 3.9 68.8 1.0
CD2 J:WFP2 4.1 69.1 1.0
CG C:TYR161 4.1 64.3 1.0
NE1 C:TRP189 4.1 68.4 1.0
CZ C:TYR161 4.6 63.7 1.0
CB C:VAL191 4.6 57.7 1.0
CB C:TYR161 4.6 57.9 1.0
F2 J:WFP2 4.7 70.9 1.0
CG B:LEU147 4.8 56.0 1.0
CD1 C:TYR161 4.8 63.6 1.0
CG1 C:VAL191 4.8 59.6 1.0
CB J:WFP2 4.9 64.0 1.0
OG1 B:THR178 4.9 57.0 1.0
CG C:TRP189 4.9 67.9 1.0

Fluorine binding site 6 out of 14 in 6bba

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Fluorine binding site 6 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F2

b:70.9
occ:1.00
 F2 J:WFP2 0.0 70.9 1.0
CE2 J:WFP2 1.4 65.0 1.0
CZ J:WFP2 2.4 67.7 1.0
CD2 J:WFP2 2.4 69.1 1.0
CA B:THR178 3.3 56.9 1.0
CB B:TYR181 3.3 67.7 1.0
CD1 C:LEU213 3.6 65.0 1.0
CG2 B:THR178 3.6 55.1 1.0
CE1 J:WFP2 3.6 64.0 1.0
CG J:WFP2 3.7 71.0 1.0
CG B:TYR181 3.7 66.8 1.0
OG1 B:THR178 3.7 57.0 1.0
CB B:THR178 3.7 62.0 1.0
CD2 B:TYR181 3.9 65.6 1.0
O B:THR178 4.0 69.2 1.0
O B:ASP177 4.1 70.9 1.0
CD1 J:WFP2 4.1 67.2 1.0
C B:THR178 4.2 62.8 1.0
N B:THR178 4.2 57.2 1.0
CD2 C:LEU213 4.3 67.8 1.0
CD1 B:TYR181 4.5 68.2 1.0
CD2 B:LEU147 4.5 55.8 1.0
CG C:LEU213 4.5 64.5 1.0
C B:ASP177 4.5 63.1 1.0
CA B:TYR181 4.7 70.8 1.0
NE1 C:TRP189 4.7 68.4 1.0
F1 J:WFP2 4.7 66.8 1.0
N B:ILE182 4.9 69.7 1.0
CE2 B:TYR181 4.9 67.2 1.0
CB J:WFP2 5.0 64.0 1.0

Fluorine binding site 7 out of 14 in 6bba

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Fluorine binding site 7 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F2

b:60.0
occ:1.00
 F1 K:WFP2 0.0 60.0 1.0
CE1 K:WFP2 1.4 60.3 1.0
CZ K:WFP2 2.4 54.6 1.0
CD1 K:WFP2 2.4 61.0 1.0
CG2 C:ILE143 3.5 44.6 1.0
CD2 D:TYR161 3.5 48.3 1.0
CE2 K:WFP2 3.6 56.7 1.0
CG K:WFP2 3.7 59.3 1.0
CE2 D:TYR161 3.9 56.1 1.0
CD1 C:LEU147 4.0 56.7 1.0
CG D:TYR161 4.1 48.2 1.0
CD2 K:WFP2 4.1 58.1 1.0
CD1 D:TRP189 4.2 59.4 1.0
CB D:VAL191 4.3 51.9 1.0
NE1 D:TRP189 4.3 56.5 1.0
CG1 D:VAL191 4.4 50.4 1.0
CB D:TYR161 4.5 49.6 1.0
CG2 D:VAL191 4.6 62.7 1.0
F2 K:WFP2 4.7 63.5 1.0
CZ D:TYR161 4.8 59.1 1.0
CD1 C:ILE143 4.8 47.0 1.0
OG1 C:THR178 4.8 56.7 1.0
CB C:ILE143 4.9 46.9 1.0
CG C:LEU147 4.9 51.1 1.0
CD1 D:TYR161 4.9 49.4 1.0
CB K:WFP2 5.0 56.9 1.0

Fluorine binding site 8 out of 14 in 6bba

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Fluorine binding site 8 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F2

b:63.5
occ:1.00
 F2 K:WFP2 0.0 63.5 1.0
CE2 K:WFP2 1.4 56.7 1.0
CZ K:WFP2 2.4 54.6 1.0
CD2 K:WFP2 2.4 58.1 1.0
CA C:THR178 3.3 56.2 1.0
CB C:TYR181 3.4 55.5 1.0
CG2 C:THR178 3.6 51.7 1.0
CD1 D:LEU213 3.6 55.0 1.0
OG1 C:THR178 3.6 56.7 1.0
CE1 K:WFP2 3.6 60.3 1.0
CG K:WFP2 3.7 59.3 1.0
CB C:THR178 3.7 52.4 1.0
CG C:TYR181 3.7 53.3 1.0
CD2 C:TYR181 3.9 52.9 1.0
O C:THR178 4.0 54.2 1.0
N C:THR178 4.1 54.7 1.0
CD1 K:WFP2 4.1 61.0 1.0
O C:ASP177 4.2 61.3 1.0
C C:THR178 4.2 59.4 1.0
CD2 D:LEU213 4.2 56.0 1.0
C C:ASP177 4.5 55.2 1.0
CG D:LEU213 4.5 50.9 1.0
CD2 C:LEU147 4.5 50.0 1.0
CD1 C:TYR181 4.6 50.2 1.0
F1 K:WFP2 4.7 60.0 1.0
CA C:TYR181 4.7 57.0 1.0
NE1 D:TRP189 4.8 56.5 1.0
CE2 C:TYR181 4.9 56.0 1.0
CB K:WFP2 4.9 56.9 1.0

Fluorine binding site 9 out of 14 in 6bba

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Fluorine binding site 9 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:F2

b:49.8
occ:1.00
 F1 L:WFP2 0.0 49.8 1.0
CE1 L:WFP2 1.4 49.2 1.0
CZ L:WFP2 2.4 47.9 1.0
CD1 L:WFP2 2.4 54.6 1.0
CD2 E:TYR161 3.3 46.1 1.0
CE2 L:WFP2 3.6 44.2 1.0
CG L:WFP2 3.7 50.7 1.0
CG2 D:ILE143 3.7 38.8 1.0
CG1 E:VAL191 3.7 58.3 1.0
CE2 E:TYR161 3.8 50.6 1.0
CG E:TYR161 3.9 52.7 1.0
CD1 D:LEU147 3.9 45.3 1.0
CD1 E:TRP189 4.0 50.3 1.0
CD2 L:WFP2 4.1 46.0 1.0
NE1 E:TRP189 4.2 53.7 1.0
CB E:TYR161 4.3 45.3 1.0
CG2 E:VAL191 4.4 46.7 1.0
CZ E:TYR161 4.6 55.0 1.0
CB E:VAL191 4.7 48.9 1.0
CD1 E:TYR161 4.7 51.7 1.0
F2 L:WFP2 4.7 50.2 1.0
OG1 D:THR178 4.8 48.1 1.0
CD1 D:ILE143 4.8 40.3 1.0
CG D:LEU147 5.0 44.5 1.0
CG E:TRP189 5.0 52.6 1.0
CB L:WFP2 5.0 46.0 1.0

Fluorine binding site 10 out of 14 in 6bba

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Fluorine binding site 10 out of 14 in the Crystal Structure of Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28


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 Human Mitochondrial Clpp Complex with Acyldepsipeptide Adep-28 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:F2

b:50.2
occ:1.00
 F2 L:WFP2 0.0 50.2 1.0
CE2 L:WFP2 1.4 44.2 1.0
CZ L:WFP2 2.4 47.9 1.0
CD2 L:WFP2 2.4 46.0 1.0
CA D:THR178 3.2 48.6 1.0
OG1 D:THR178 3.4 48.1 1.0
CG2 D:THR178 3.4 38.6 1.0
CB D:TYR181 3.5 49.6 1.0
CB D:THR178 3.5 47.2 1.0
CE1 L:WFP2 3.6 49.2 1.0
CG L:WFP2 3.7 50.7 1.0
CD1 E:LEU213 3.8 44.2 1.0
CG D:TYR181 3.8 41.7 1.0
CD2 D:TYR181 3.9 40.8 1.0
O D:THR178 3.9 48.5 1.0
C D:THR178 4.1 50.0 1.0
CD1 L:WFP2 4.2 54.6 1.0
CD2 E:LEU213 4.2 50.6 1.0
N D:THR178 4.2 47.7 1.0
O D:ASP177 4.4 48.5 1.0
CD2 D:LEU147 4.4 45.8 1.0
CG E:LEU213 4.6 49.9 1.0
C D:ASP177 4.6 47.3 1.0
F1 L:WFP2 4.7 49.8 1.0
NE1 E:TRP189 4.7 53.7 1.0
CD1 D:TYR181 4.7 41.7 1.0
CA D:TYR181 4.8 44.7 1.0
CE2 D:TYR181 4.8 44.3 1.0
CB L:WFP2 5.0 46.0 1.0

Reference:

K.S.Wong, M.F.Mabanglo, T.V.Seraphim, A.Mollica, Y.Q.Mao, K.Rizzolo, E.Leung, M.T.Moutaoufik, L.Hoell, S.Phanse, J.Goodreid, L.R.S.Barbosa, C.H.I.Ramos, M.Babu, V.Mennella, R.A.Batey, A.D.Schimmer, W.A.Houry. Acyldepsipeptide Analogs Dysregulate Human Mitochondrial Clpp Protease Activity and Cause Apoptotic Cell Death. Cell Chem Biol V. 25 1017 2018.
ISSN: ESSN 2451-9448
PubMed: 30126533
DOI: 10.1016/J.CHEMBIOL.2018.05.014
Page generated: Sun Dec 13 12:45:25 2020

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