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Calcium in PDB 6y0u: Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution

Protein crystallography data

The structure of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution, PDB code: 6y0u was solved by S.Baeriswyl, A.Stocker, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.29 / 1.49
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 122.821, 56.6, 70.452, 90, 90, 90
R / Rfree (%) 16.8 / 19.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution (pdb code 6y0u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution, PDB code: 6y0u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6y0u

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Calcium binding site 1 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:15.0
occ:1.00
 OD2 A:ASP99 2.3 17.8 1.0
OD2 A:ASP104 2.4 15.2 1.0
OD1 A:ASP101 2.4 16.6 1.0
OE2 A:GLU95 2.4 17.3 1.0
OE1 A:GLU95 2.5 16.8 1.0
O3 E:ZDC101 2.5 16.4 1.0
O4 E:ZDC101 2.5 17.2 1.0
OD1 A:ASP104 2.6 16.0 1.0
CD A:GLU95 2.8 16.6 1.0
CG A:ASP104 2.9 13.8 1.0
C4 E:ZDC101 3.3 16.6 1.0
CG A:ASP99 3.3 22.4 1.0
C3 E:ZDC101 3.4 15.4 1.0
CG A:ASP101 3.4 17.0 1.0
OD1 A:ASP99 3.6 19.4 1.0
CA A:CA302 3.7 14.2 1.0
OD2 A:ASP101 3.9 15.0 1.0
N A:ASP101 4.1 15.8 1.0
O A:HOH449 4.1 26.4 1.0
OD1 A:ASP96 4.2 16.8 1.0
CG A:GLU95 4.3 16.1 1.0
CB A:ASP104 4.4 14.6 1.0
N A:ASN100 4.4 19.5 1.0
N A:TYR102 4.4 14.5 1.0
N A:ASP96 4.5 14.5 1.0
N A:GLY97 4.6 15.8 1.0
CB A:ASP101 4.6 15.3 1.0
CA A:GLU95 4.7 14.0 1.0
OD1 A:ASN103 4.7 14.7 1.0
C2 E:ZDC101 4.7 16.2 1.0
CB A:ASP99 4.7 19.9 1.0
CA A:ASP101 4.7 15.3 1.0
C5 E:ZDC101 4.7 17.8 1.0
O2 E:ZDC101 4.8 13.7 1.0
N A:ASP99 4.8 17.8 1.0
CB A:GLU95 4.9 14.9 1.0
CG A:ASP96 4.9 16.6 1.0
C A:ASP99 4.9 17.5 1.0
C A:ASP101 5.0 17.3 1.0

Calcium binding site 2 out of 8 in 6y0u

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Calcium binding site 2 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:14.2
occ:1.00
 OD1 A:ASN103 2.3 14.7 1.0
OD1 A:ASP104 2.3 16.0 1.0
O A:ASN21 2.3 17.5 1.0
OD2 A:ASP101 2.4 15.0 1.0
O B:GLY114 2.5 15.1 1.0
O2 E:ZDC101 2.5 13.7 1.0
O3 E:ZDC101 2.5 16.4 1.0
CG A:ASP101 3.1 17.0 1.0
OD1 A:ASP101 3.1 16.6 1.0
CG A:ASN103 3.3 15.4 1.0
C3 E:ZDC101 3.4 15.4 1.0
C2 E:ZDC101 3.4 16.2 1.0
C B:GLY114 3.5 14.2 1.0
C A:ASN21 3.5 14.8 1.0
CG A:ASP104 3.6 13.8 1.0
OXT B:GLY114 3.7 18.4 1.0
CA A:CA301 3.7 15.0 1.0
ND2 A:ASN103 3.7 13.8 1.0
C4 E:ZDC101 3.8 16.6 1.0
CB A:ASN21 4.1 16.0 1.0
CA A:ASP104 4.2 14.4 1.0
N A:ASP104 4.3 13.0 1.0
CA A:SER22 4.4 14.6 1.0
N A:SER22 4.4 14.7 1.0
OD2 A:ASP104 4.4 15.2 1.0
O A:HOH434 4.4 30.6 1.0
OD1 A:ASP99 4.4 19.4 1.0
CB A:ASP104 4.4 14.6 1.0
C A:ASN103 4.5 12.9 1.0
O4 E:ZDC101 4.5 17.2 1.0
CA A:ASN21 4.5 14.8 1.0
CB A:ASP101 4.5 15.3 1.0
CB A:SER22 4.6 14.4 1.0
CB A:ASN103 4.7 13.2 1.0
C1 E:ZDC101 4.8 16.1 1.0
O A:ASN103 4.8 14.3 1.0
CA B:GLY114 4.8 17.6 1.0
N A:ASN103 4.9 13.4 1.0
CA A:ASN103 4.9 13.7 1.0
O B:HOH495 5.0 38.9 1.0
O5 E:ZDC101 5.0 16.0 1.0
OD2 A:ASP99 5.0 17.8 1.0

Calcium binding site 3 out of 8 in 6y0u

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Calcium binding site 3 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:17.7
occ:1.00
 OD1 B:ASP104 2.4 17.3 1.0
OD1 B:ASP99 2.4 21.4 1.0
OE1 B:GLU95 2.4 19.2 1.0
OD1 B:ASP101 2.4 18.4 1.0
OE2 B:GLU95 2.5 18.8 1.0
O3 F:ZDC101 2.5 19.2 1.0
O4 F:ZDC101 2.6 23.0 1.0
OD2 B:ASP104 2.6 16.9 1.0
CD B:GLU95 2.8 17.7 1.0
CG B:ASP104 2.9 19.1 1.0
C4 F:ZDC101 3.3 20.1 1.0
C3 F:ZDC101 3.4 16.9 1.0
CG B:ASP99 3.4 27.2 1.0
CG B:ASP101 3.5 19.0 1.0
OD2 B:ASP99 3.7 21.4 1.0
CA B:CA302 3.7 17.0 1.0
OD2 B:ASP101 4.0 17.4 1.0
O B:HOH467 4.0 26.1 1.0
N B:ASP101 4.1 18.3 1.0
OD1 B:ASP96 4.2 21.2 1.0
CG B:GLU95 4.3 19.1 1.0
CB B:ASP104 4.4 17.9 1.0
N B:ASN100 4.5 20.7 1.0
N B:ASP96 4.5 17.2 1.0
N B:TYR102 4.5 17.0 1.0
N B:GLY97 4.5 19.6 1.0
CB B:ASP101 4.6 20.6 1.0
CA B:GLU95 4.6 17.7 1.0
C2 F:ZDC101 4.7 18.3 1.0
OD1 B:ASN103 4.7 16.5 1.0
C5 F:ZDC101 4.7 21.7 1.0
CA B:ASP101 4.8 19.1 1.0
CB B:ASP99 4.8 20.2 1.0
O2 F:ZDC101 4.8 19.2 1.0
N B:ASP99 4.9 25.9 1.0
CB B:GLU95 4.9 16.8 1.0
CG B:ASP96 4.9 20.8 1.0
C B:ASP99 5.0 22.9 1.0

Calcium binding site 4 out of 8 in 6y0u

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Calcium binding site 4 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:17.0
occ:1.00
 OD1 B:ASN103 2.3 16.5 1.0
O B:ASN21 2.3 16.7 1.0
OD2 B:ASP104 2.4 16.9 1.0
OD2 B:ASP101 2.4 17.4 1.0
O A:GLY114 2.4 18.8 1.0
O3 F:ZDC101 2.4 19.2 1.0
O2 F:ZDC101 2.5 19.2 1.0
OD1 B:ASP101 3.1 18.4 1.0
CG B:ASP101 3.1 19.0 1.0
CG B:ASN103 3.4 16.2 1.0
C3 F:ZDC101 3.4 16.9 1.0
C A:GLY114 3.4 20.1 1.0
C2 F:ZDC101 3.4 18.3 1.0
C B:ASN21 3.5 18.1 1.0
OXT A:GLY114 3.6 22.0 1.0
CG B:ASP104 3.6 19.1 1.0
ND2 B:ASN103 3.7 15.4 1.0
CA B:CA301 3.7 17.7 1.0
C4 F:ZDC101 3.8 20.1 1.0
CB B:ASN21 4.1 15.7 1.0
CA B:ASP104 4.2 16.4 1.0
N B:ASP104 4.2 14.6 1.0
CA B:SER22 4.4 17.4 1.0
N B:SER22 4.4 19.4 1.0
C B:ASN103 4.5 17.0 1.0
CB B:ASP104 4.5 17.9 1.0
OD1 B:ASP104 4.5 17.3 1.0
CA B:ASN21 4.5 17.0 1.0
O4 F:ZDC101 4.5 23.0 1.0
OD2 B:ASP99 4.6 21.4 1.0
CB B:ASP101 4.6 20.6 1.0
CB B:SER22 4.6 18.7 1.0
O B:HOH459 4.7 33.7 1.0
CB B:ASN103 4.7 14.9 1.0
C1 F:ZDC101 4.8 19.9 1.0
CA A:GLY114 4.8 16.8 1.0
O B:ASN103 4.8 17.0 1.0
N B:ASN103 4.9 17.4 1.0
CA B:ASN103 4.9 17.3 1.0

Calcium binding site 5 out of 8 in 6y0u

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Calcium binding site 5 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:15.6
occ:1.00
 OD1 C:ASP99 2.3 17.9 1.0
OD1 C:ASP101 2.3 14.6 1.0
OD2 C:ASP104 2.4 16.1 1.0
OE2 C:GLU95 2.4 17.1 1.0
OE1 C:GLU95 2.4 16.1 1.0
O3 C:ZDC303 2.5 14.5 1.0
O4 C:ZDC303 2.6 15.1 1.0
OD1 C:ASP104 2.7 15.8 1.0
CD C:GLU95 2.7 16.3 1.0
CG C:ASP104 2.9 16.2 1.0
C4 C:ZDC303 3.3 13.5 1.0
CG C:ASP99 3.4 19.2 1.0
C3 C:ZDC303 3.4 13.4 1.0
CG C:ASP101 3.4 16.7 1.0
OD2 C:ASP99 3.7 17.6 1.0
CA C:CA302 3.7 15.3 1.0
O C:HOH465 3.9 19.3 1.0
OD2 C:ASP101 3.9 16.6 1.0
OD1 C:ASP96 4.1 18.2 1.0
N C:ASP101 4.1 15.2 1.0
CG C:GLU95 4.2 16.8 1.0
CB C:ASP104 4.4 14.7 1.0
N C:TYR102 4.4 13.5 1.0
N C:ASN100 4.4 16.5 1.0
N C:ASP96 4.5 15.7 1.0
CB C:ASP101 4.5 16.2 1.0
N C:GLY97 4.5 14.8 1.0
OD1 C:ASN103 4.6 14.8 1.0
CA C:ASP101 4.7 15.8 1.0
CA C:GLU95 4.7 14.4 1.0
N C:ASP99 4.7 18.5 1.0
CB C:ASP99 4.7 19.5 1.0
C2 C:ZDC303 4.7 14.8 1.0
C5 C:ZDC303 4.8 17.4 1.0
O2 C:ZDC303 4.9 15.1 1.0
CB C:GLU95 4.9 14.3 1.0
C C:ASP99 4.9 19.7 1.0
C C:ASP101 4.9 17.5 1.0
CA C:ASP99 5.0 19.1 1.0
CA C:GLY97 5.0 17.1 1.0

Calcium binding site 6 out of 8 in 6y0u

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Calcium binding site 6 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:15.3
occ:1.00
 OD1 C:ASN103 2.3 14.8 1.0
O C:ASN21 2.4 17.2 1.0
OD1 C:ASP104 2.4 15.8 1.0
O D:GLY114 2.4 16.0 1.0
OD2 C:ASP101 2.4 16.6 1.0
O3 C:ZDC303 2.5 14.5 1.0
O2 C:ZDC303 2.5 15.1 1.0
OD1 C:ASP101 3.0 14.6 1.0
CG C:ASP101 3.1 16.7 1.0
CG C:ASN103 3.3 14.9 1.0
C3 C:ZDC303 3.3 13.4 1.0
C2 C:ZDC303 3.4 14.8 1.0
C D:GLY114 3.4 18.7 1.0
C C:ASN21 3.6 15.1 1.0
CG C:ASP104 3.6 16.2 1.0
OXT D:GLY114 3.7 21.5 1.0
ND2 C:ASN103 3.7 13.6 1.0
CA C:CA301 3.7 15.6 1.0
C4 C:ZDC303 3.7 13.5 1.0
CB C:ASN21 4.1 15.7 1.0
CA C:ASP104 4.3 14.8 1.0
N C:ASP104 4.3 14.5 1.0
OD2 C:ASP104 4.4 16.1 1.0
N C:SER22 4.4 17.4 1.0
CA C:SER22 4.4 15.8 1.0
O4 C:ZDC303 4.4 15.1 1.0
CB C:ASP104 4.5 14.7 1.0
CA C:ASN21 4.5 15.5 1.0
OD2 C:ASP99 4.5 17.6 1.0
C C:ASN103 4.5 16.0 1.0
CB C:ASP101 4.5 16.2 1.0
O C:HOH432 4.6 26.6 1.0
CB C:SER22 4.7 15.4 1.0
CB C:ASN103 4.7 14.3 1.0
C1 C:ZDC303 4.7 17.9 1.0
CA D:GLY114 4.8 17.9 1.0
O C:ASN103 4.9 13.8 1.0
N C:ASN103 4.9 14.6 1.0
OD1 C:ASP99 5.0 17.9 1.0
CA C:ASN103 5.0 15.7 1.0
O5 C:ZDC303 5.0 16.9 1.0

Calcium binding site 7 out of 8 in 6y0u

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Calcium binding site 7 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:16.6
occ:1.00
 OD2 D:ASP104 2.4 17.2 1.0
OD1 D:ASP101 2.4 17.9 1.0
OD1 D:ASP99 2.4 18.9 1.0
OE1 D:GLU95 2.4 18.0 1.0
OE2 D:GLU95 2.4 18.4 1.0
O3 H:ZDC101 2.5 17.1 1.0
O4 H:ZDC101 2.6 16.8 1.0
OD1 D:ASP104 2.6 16.9 1.0
CD D:GLU95 2.8 18.0 1.0
CG D:ASP104 2.8 18.1 1.0
C4 H:ZDC101 3.4 16.6 1.0
C3 H:ZDC101 3.4 16.8 1.0
CG D:ASP101 3.5 20.4 1.0
CG D:ASP99 3.5 22.0 1.0
CA D:CA302 3.7 16.0 1.0
OD2 D:ASP99 3.8 20.3 1.0
O D:HOH445 4.0 22.9 1.0
OD2 D:ASP101 4.0 16.7 1.0
N D:ASP101 4.1 17.5 1.0
OD1 D:ASP96 4.2 16.6 1.0
CG D:GLU95 4.3 19.5 1.0
CB D:ASP104 4.4 14.6 1.0
N D:TYR102 4.4 15.8 1.0
N D:ASN100 4.4 19.7 1.0
N D:ASP96 4.5 16.4 1.0
N D:GLY97 4.6 19.7 1.0
CB D:ASP101 4.6 18.5 1.0
CA D:GLU95 4.7 17.5 1.0
CA D:ASP101 4.7 16.6 1.0
OD1 D:ASN103 4.7 15.2 1.0
C2 H:ZDC101 4.7 16.1 1.0
C5 H:ZDC101 4.8 20.2 1.0
CB D:ASP99 4.8 20.9 1.0
N D:ASP99 4.8 24.9 1.0
O2 H:ZDC101 4.8 14.9 1.0
CB D:GLU95 4.9 17.1 1.0
C D:ASP101 5.0 19.9 1.0
C D:ASP99 5.0 26.5 1.0
CG D:ASP96 5.0 18.8 1.0

Calcium binding site 8 out of 8 in 6y0u

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Calcium binding site 8 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:16.0
occ:1.00
 OD1 D:ASP104 2.3 16.9 1.0
O C:GLY114 2.4 14.7 1.0
O D:ASN21 2.4 16.8 1.0
OD1 D:ASN103 2.4 15.2 1.0
OD2 D:ASP101 2.4 16.7 1.0
O2 H:ZDC101 2.4 14.9 1.0
O3 H:ZDC101 2.5 17.1 1.0
OD1 D:ASP101 3.0 17.9 1.0
CG D:ASP101 3.1 20.4 1.0
C C:GLY114 3.4 18.1 1.0
C3 H:ZDC101 3.4 16.8 1.0
C2 H:ZDC101 3.4 16.1 1.0
CG D:ASN103 3.4 15.7 1.0
CG D:ASP104 3.6 18.1 1.0
C D:ASN21 3.6 17.6 1.0
OXT C:GLY114 3.6 17.9 1.0
CA D:CA301 3.7 16.6 1.0
C4 H:ZDC101 3.8 16.6 1.0
ND2 D:ASN103 3.8 15.9 1.0
CB D:ASN21 4.1 16.7 1.0
CA D:ASP104 4.2 14.1 1.0
N D:ASP104 4.3 14.1 1.0
OD2 D:ASP104 4.4 17.2 1.0
O4 H:ZDC101 4.4 16.8 1.0
CA D:SER22 4.4 15.3 1.0
CB D:ASP104 4.4 14.6 1.0
N D:SER22 4.4 17.0 1.0
C D:ASN103 4.5 14.8 1.0
CA D:ASN21 4.5 15.9 1.0
OD2 D:ASP99 4.5 20.3 1.0
CB D:ASP101 4.5 18.5 1.0
CB D:SER22 4.7 17.5 1.0
O D:HOH461 4.7 34.2 1.0
C1 H:ZDC101 4.7 16.7 1.0
CA C:GLY114 4.8 16.9 1.0
CB D:ASN103 4.8 14.5 1.0
O D:ASN103 4.8 15.2 1.0
N D:ASN103 4.9 15.0 1.0
O5 H:ZDC101 5.0 20.6 1.0
CA D:ASN103 5.0 18.1 1.0
OD1 D:ASP99 5.0 18.9 1.0

Reference:

S.Baeriswyl, A.Stocker, J.-L.Reymond. Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.5 Angstrom Resolution To Be Published.
Page generated: Tue Jul 16 18:20:27 2024

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