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Fluorine in PDB 2i80: Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies

Enzymatic activity of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies

All present enzymatic activity of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies:
6.3.2.4;

Protein crystallography data

The structure of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies, PDB code: 2i80 was solved by S.Liu, J.S.Chang, J.T.Herberg, M.-M.Horng, P.K.Tomich, A.H.Lin, K.R.Marotti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.06 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.730, 66.082, 78.789, 90.00, 96.57, 90.00
R / Rfree (%) 18.8 / 25.1

Other elements in 2i80:

The structure of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies (pdb code 2i80). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies, PDB code: 2i80:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 2i80

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Fluorine binding site 1 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:36.8
occ:0.50
 F23 A:G1L400 0.0 36.8 0.5
F23 A:G1L400 1.1 24.5 0.5
C20 A:G1L400 1.3 39.1 0.5
C20 A:G1L400 1.4 28.0 0.5
F22 A:G1L400 1.4 32.4 0.5
F21 A:G1L400 2.1 37.8 0.5
F22 A:G1L400 2.2 40.5 0.5
C3 A:G1L400 2.3 39.2 0.5
F21 A:G1L400 2.4 26.9 0.5
C3 A:G1L400 2.6 28.3 0.5
C4 A:G1L400 2.8 39.6 0.5
C4 A:G1L400 3.2 27.9 0.5
CD2 A:LEU289 3.2 34.6 1.0
CG1 A:VAL117 3.3 31.7 1.0
C2 A:G1L400 3.6 39.5 0.5
CD1 A:LEU289 3.6 29.4 1.0
C2 A:G1L400 3.8 27.8 0.5
CD2 A:LEU337 4.0 33.4 1.0
CG A:LEU289 4.0 33.5 1.0
CA A:GLY118 4.1 36.2 1.0
CD1 A:LEU337 4.1 30.5 1.0
C5 A:G1L400 4.2 39.5 0.5
N A:GLY118 4.4 35.3 1.0
O A:HOH414 4.4 31.1 1.0
CB A:VAL117 4.5 36.4 1.0
C5 A:G1L400 4.5 28.7 0.5
C A:VAL117 4.6 36.1 1.0
CG A:LEU337 4.6 35.3 1.0
C1 A:G1L400 4.7 39.4 0.5
O A:VAL117 4.8 37.2 1.0
CD1 A:PHE92 4.9 40.2 1.0
C1 A:G1L400 5.0 26.8 0.5

Fluorine binding site 2 out of 9 in 2i80

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Fluorine binding site 2 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:24.5
occ:0.50
 F23 A:G1L400 0.0 24.5 0.5
F23 A:G1L400 1.1 36.8 0.5
C20 A:G1L400 1.3 28.0 0.5
C20 A:G1L400 1.4 39.1 0.5
F21 A:G1L400 1.7 37.8 0.5
C3 A:G1L400 2.0 39.2 0.5
F21 A:G1L400 2.1 26.9 0.5
F22 A:G1L400 2.2 32.4 0.5
C3 A:G1L400 2.3 28.3 0.5
C4 A:G1L400 2.5 39.6 0.5
C4 A:G1L400 2.6 27.9 0.5
F22 A:G1L400 2.7 40.5 0.5
C2 A:G1L400 3.2 39.5 0.5
CG1 A:VAL117 3.5 31.7 1.0
C2 A:G1L400 3.6 27.8 0.5
C5 A:G1L400 3.8 39.5 0.5
CD1 A:LEU337 3.9 30.5 1.0
C5 A:G1L400 4.0 28.7 0.5
CD1 A:LEU289 4.1 29.4 1.0
CD1 A:PHE92 4.1 40.2 1.0
CD2 A:LEU289 4.2 34.6 1.0
C1 A:G1L400 4.3 39.4 0.5
CE1 A:PHE92 4.3 38.6 1.0
CD2 A:LEU337 4.4 33.4 1.0
CZ A:PHE313 4.5 41.2 1.0
C6 A:G1L400 4.6 38.7 0.5
CB A:VAL117 4.6 36.4 1.0
CE1 A:PHE313 4.6 42.4 1.0
CD2 A:LEU94 4.6 37.1 1.0
C1 A:G1L400 4.7 26.8 0.5
CG A:LEU337 4.7 35.3 1.0
CE2 A:PHE313 4.7 42.8 1.0
CG A:LEU289 4.8 33.5 1.0
C6 A:G1L400 4.9 27.1 0.5
CD1 A:PHE313 5.0 41.0 1.0

Fluorine binding site 3 out of 9 in 2i80

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Fluorine binding site 3 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:37.8
occ:0.50
 F21 A:G1L400 0.0 37.8 0.5
F21 A:G1L400 0.5 26.9 0.5
C20 A:G1L400 1.2 28.0 0.5
C20 A:G1L400 1.3 39.1 0.5
F23 A:G1L400 1.7 24.5 0.5
F23 A:G1L400 2.1 36.8 0.5
F22 A:G1L400 2.1 32.4 0.5
F22 A:G1L400 2.2 40.5 0.5
C3 A:G1L400 2.3 39.2 0.5
C3 A:G1L400 2.3 28.3 0.5
C2 A:G1L400 2.8 39.5 0.5
C2 A:G1L400 3.1 27.8 0.5
CG1 A:VAL117 3.1 31.7 1.0
C4 A:G1L400 3.3 27.9 0.5
C4 A:G1L400 3.4 39.6 0.5
CD1 A:PHE92 3.5 40.2 1.0
CB A:VAL117 3.6 36.4 1.0
CD A:PRO93 4.0 39.1 1.0
C1 A:G1L400 4.1 39.4 0.5
CD2 A:LEU94 4.1 37.1 1.0
CE1 A:PHE92 4.1 38.6 1.0
O A:VAL117 4.2 37.2 1.0
C A:VAL117 4.3 36.1 1.0
CG A:PHE92 4.3 39.5 1.0
C1 A:G1L400 4.4 26.8 0.5
CB A:PHE92 4.4 39.6 1.0
CA A:PHE92 4.5 39.4 1.0
C5 A:G1L400 4.5 28.7 0.5
N A:PRO93 4.5 39.3 1.0
C5 A:G1L400 4.6 39.5 0.5
CA A:VAL117 4.6 35.9 1.0
CG2 A:VAL117 4.7 35.0 1.0
N A:GLY118 4.7 35.3 1.0
O A:PRO93 4.8 34.9 1.0
CA A:GLY118 4.8 36.2 1.0
C6 A:G1L400 4.8 38.7 0.5
C A:PHE92 4.9 40.1 1.0
CG A:PRO93 4.9 38.3 1.0
C6 A:G1L400 5.0 27.1 0.5

Fluorine binding site 4 out of 9 in 2i80

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Fluorine binding site 4 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:26.9
occ:0.50
 F21 A:G1L400 0.0 26.9 0.5
F21 A:G1L400 0.5 37.8 0.5
C20 A:G1L400 1.3 28.0 0.5
C20 A:G1L400 1.4 39.1 0.5
F22 A:G1L400 2.0 40.5 0.5
F23 A:G1L400 2.1 24.5 0.5
F22 A:G1L400 2.1 32.4 0.5
C3 A:G1L400 2.3 28.3 0.5
C3 A:G1L400 2.3 39.2 0.5
F23 A:G1L400 2.4 36.8 0.5
C2 A:G1L400 2.6 39.5 0.5
C2 A:G1L400 2.8 27.8 0.5
CG1 A:VAL117 3.3 31.7 1.0
C4 A:G1L400 3.4 27.9 0.5
C4 A:G1L400 3.6 39.6 0.5
CD A:PRO93 3.6 39.1 1.0
CB A:VAL117 3.7 36.4 1.0
CD1 A:PHE92 3.7 40.2 1.0
C1 A:G1L400 3.9 39.4 0.5
O A:VAL117 4.0 37.2 1.0
CD2 A:LEU94 4.0 37.1 1.0
C1 A:G1L400 4.1 26.8 0.5
N A:PRO93 4.1 39.3 1.0
C A:VAL117 4.2 36.1 1.0
CA A:PHE92 4.3 39.4 1.0
CB A:PHE92 4.4 39.6 1.0
O A:PRO93 4.4 34.9 1.0
CG A:PHE92 4.4 39.5 1.0
CE1 A:PHE92 4.4 38.6 1.0
CG A:PRO93 4.5 38.3 1.0
C5 A:G1L400 4.5 28.7 0.5
CA A:VAL117 4.6 35.9 1.0
C A:PHE92 4.6 40.1 1.0
C5 A:G1L400 4.6 39.5 0.5
C A:PRO93 4.7 39.2 1.0
N A:GLY118 4.7 35.3 1.0
C6 A:G1L400 4.8 38.7 0.5
CA A:GLY118 4.8 36.2 1.0
CG2 A:VAL117 4.8 35.0 1.0
C6 A:G1L400 4.8 27.1 0.5
O A:HOH414 4.9 31.1 1.0
CA A:PRO93 5.0 38.8 1.0

Fluorine binding site 5 out of 9 in 2i80

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Fluorine binding site 5 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:40.5
occ:0.50
 F22 A:G1L400 0.0 40.5 0.5
F22 A:G1L400 0.9 32.4 0.5
C20 A:G1L400 1.3 39.1 0.5
C20 A:G1L400 1.6 28.0 0.5
F21 A:G1L400 2.0 26.9 0.5
F21 A:G1L400 2.2 37.8 0.5
F23 A:G1L400 2.2 36.8 0.5
C3 A:G1L400 2.2 39.2 0.5
C3 A:G1L400 2.3 28.3 0.5
C2 A:G1L400 2.6 27.8 0.5
C2 A:G1L400 2.7 39.5 0.5
F23 A:G1L400 2.7 24.5 0.5
O A:HOH414 3.0 31.1 1.0
C4 A:G1L400 3.4 39.6 0.5
O A:VAL117 3.4 37.2 1.0
CA A:GLY118 3.5 36.2 1.0
C4 A:G1L400 3.6 27.9 0.5
C A:VAL117 3.8 36.1 1.0
CD2 A:LEU289 3.8 34.6 1.0
O A:HOH403 3.9 34.2 1.0
C1 A:G1L400 3.9 26.8 0.5
N A:GLY118 4.0 35.3 1.0
C1 A:G1L400 4.0 39.4 0.5
CG1 A:VAL117 4.0 31.7 1.0
CE A:MET310 4.1 58.4 1.0
CD A:PRO93 4.2 39.1 1.0
CB A:VAL117 4.5 36.4 1.0
C5 A:G1L400 4.5 39.5 0.5
CG A:PRO93 4.5 38.3 1.0
C A:GLY118 4.6 36.8 1.0
N A:ASN119 4.6 36.8 1.0
C5 A:G1L400 4.6 28.7 0.5
O A:ALA309 4.7 37.2 1.0
O A:PRO93 4.7 34.9 1.0
C6 A:G1L400 4.8 38.7 0.5
C6 A:G1L400 4.8 27.1 0.5
CA A:VAL117 4.8 35.9 1.0

Fluorine binding site 6 out of 9 in 2i80

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Fluorine binding site 6 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:32.4
occ:0.50
 F22 A:G1L400 0.0 32.4 0.5
F22 A:G1L400 0.9 40.5 0.5
C20 A:G1L400 1.0 39.1 0.5
C20 A:G1L400 1.3 28.0 0.5
F23 A:G1L400 1.4 36.8 0.5
F21 A:G1L400 2.1 37.8 0.5
F21 A:G1L400 2.1 26.9 0.5
F23 A:G1L400 2.2 24.5 0.5
C3 A:G1L400 2.2 39.2 0.5
C3 A:G1L400 2.4 28.3 0.5
C2 A:G1L400 3.1 27.8 0.5
C2 A:G1L400 3.1 39.5 0.5
C4 A:G1L400 3.1 39.6 0.5
CD2 A:LEU289 3.2 34.6 1.0
O A:HOH414 3.2 31.1 1.0
CA A:GLY118 3.3 36.2 1.0
C4 A:G1L400 3.5 27.9 0.5
CG1 A:VAL117 3.6 31.7 1.0
O A:VAL117 3.8 37.2 1.0
N A:GLY118 3.8 35.3 1.0
C A:VAL117 3.9 36.1 1.0
C1 A:G1L400 4.3 39.4 0.5
CD1 A:LEU289 4.4 29.4 1.0
C1 A:G1L400 4.4 26.8 0.5
CB A:VAL117 4.4 36.4 1.0
C5 A:G1L400 4.4 39.5 0.5
CG A:LEU289 4.4 33.5 1.0
O A:HOH403 4.6 34.2 1.0
C A:GLY118 4.6 36.8 1.0
C5 A:G1L400 4.7 28.7 0.5
N A:ASN119 4.7 36.8 1.0
O A:ALA309 4.7 37.2 1.0
CE A:MET310 4.8 58.4 1.0
CA A:VAL117 4.8 35.9 1.0
CD A:PRO93 4.9 39.1 1.0
C6 A:G1L400 4.9 38.7 0.5
CD2 A:LEU337 5.0 33.4 1.0

Fluorine binding site 7 out of 9 in 2i80

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Fluorine binding site 7 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F400

b:44.7
occ:1.00
 F23 B:G1L400 0.0 44.7 1.0
C20 B:G1L400 1.3 45.1 1.0
F21 B:G1L400 2.1 48.8 1.0
F22 B:G1L400 2.1 48.1 1.0
C3 B:G1L400 2.3 44.6 1.0
C4 B:G1L400 2.7 45.2 1.0
CG1 B:VAL117 3.3 34.0 1.0
C2 B:G1L400 3.5 45.1 1.0
CD1 B:LEU337 3.8 34.9 1.0
CD2 B:LEU289 3.8 32.2 1.0
CD1 B:LEU289 4.0 31.7 1.0
C5 B:G1L400 4.1 44.9 1.0
CD1 B:PHE92 4.3 42.8 1.0
CB B:VAL117 4.4 37.8 1.0
CE1 B:PHE92 4.4 40.6 1.0
CD2 B:LEU337 4.4 33.6 1.0
CG B:LEU289 4.6 30.4 1.0
CZ B:PHE313 4.6 42.9 1.0
C1 B:G1L400 4.6 45.7 1.0
CG B:LEU337 4.7 35.8 1.0
CE1 B:PHE313 4.7 42.8 1.0
CA B:GLY118 4.7 36.2 1.0
N B:GLY118 4.8 36.8 1.0
C6 B:G1L400 4.9 43.4 1.0
CE2 B:PHE313 4.9 42.5 1.0
C B:VAL117 4.9 37.1 1.0

Fluorine binding site 8 out of 9 in 2i80

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Fluorine binding site 8 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F400

b:48.8
occ:1.00
 F21 B:G1L400 0.0 48.8 1.0
C20 B:G1L400 1.3 45.1 1.0
F23 B:G1L400 2.1 44.7 1.0
F22 B:G1L400 2.1 48.1 1.0
C3 B:G1L400 2.3 44.6 1.0
C2 B:G1L400 2.7 45.1 1.0
CG1 B:VAL117 3.3 34.0 1.0
C4 B:G1L400 3.4 45.2 1.0
CD1 B:PHE92 3.5 42.8 1.0
CB B:VAL117 3.6 37.8 1.0
CD B:PRO93 3.8 39.5 1.0
C1 B:G1L400 4.0 45.7 1.0
CD2 B:LEU94 4.0 38.4 1.0
O B:VAL117 4.1 37.8 1.0
C B:VAL117 4.2 37.1 1.0
CE1 B:PHE92 4.3 40.6 1.0
CG B:PHE92 4.4 41.3 1.0
CB B:PHE92 4.4 41.5 1.0
CA B:PHE92 4.4 40.7 1.0
N B:PRO93 4.4 39.8 1.0
O B:PRO93 4.5 40.0 1.0
C5 B:G1L400 4.5 44.9 1.0
CA B:VAL117 4.6 37.3 1.0
CG2 B:VAL117 4.7 34.9 1.0
CG B:PRO93 4.7 38.1 1.0
N B:GLY118 4.7 36.8 1.0
C6 B:G1L400 4.8 43.4 1.0
C B:PHE92 4.8 40.9 1.0
C B:PRO93 4.8 40.9 1.0
CA B:GLY118 4.8 36.2 1.0
CE B:MET310 4.9 57.1 1.0

Fluorine binding site 9 out of 9 in 2i80

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Fluorine binding site 9 out of 9 in the Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F400

b:48.1
occ:1.00
 F22 B:G1L400 0.0 48.1 1.0
C20 B:G1L400 1.3 45.1 1.0
F23 B:G1L400 2.1 44.7 1.0
F21 B:G1L400 2.1 48.8 1.0
C3 B:G1L400 2.4 44.6 1.0
C2 B:G1L400 3.2 45.1 1.0
CA B:GLY118 3.2 36.2 1.0
O B:HOH436 3.3 35.2 1.0
CD2 B:LEU289 3.3 32.2 1.0
C4 B:G1L400 3.3 45.2 1.0
O B:VAL117 3.6 37.8 1.0
CG1 B:VAL117 3.6 34.0 1.0
N B:GLY118 3.7 36.8 1.0
C B:VAL117 3.7 37.1 1.0
CE B:MET310 4.0 57.1 1.0
CB B:VAL117 4.2 37.8 1.0
C1 B:G1L400 4.4 45.7 1.0
C B:GLY118 4.5 36.2 1.0
O B:HOH403 4.5 37.6 1.0
C5 B:G1L400 4.5 44.9 1.0
CG B:LEU289 4.6 30.4 1.0
CA B:VAL117 4.6 37.3 1.0
CD1 B:LEU289 4.7 31.7 1.0
N B:ASN119 4.7 36.5 1.0
O B:ALA309 4.8 37.6 1.0
CD B:PRO93 4.8 39.5 1.0

Reference:

S.Liu, J.S.Chang, J.T.Herberg, M.M.Horng, P.K.Tomich, A.H.Lin, K.R.Marotti. Allosteric Inhibition of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies. Proc.Natl.Acad.Sci.Usa V. 103 15178 2006.
ISSN: ISSN 0027-8424
PubMed: 17015835
DOI: 10.1073/PNAS.0604905103
Page generated: Wed Jul 31 14:50:57 2024

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