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Calcium in PDB 7c7r: Biofilm Associated Protein - B Domain

Protein crystallography data

The structure of Biofilm Associated Protein - B Domain, PDB code: 7c7r was solved by J.F.Ma, Z.H.Xu, Y.K.Zhang, X.Cheng, S.L.Fan, J.W.Wang, X.Y.Fang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.10 / 3.07
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 171.171, 171.171, 102.503, 90, 90, 90
R / Rfree (%) 19.2 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Biofilm Associated Protein - B Domain (pdb code 7c7r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Biofilm Associated Protein - B Domain, PDB code: 7c7r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7c7r

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Calcium binding site 1 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:65.7
occ:1.00
OD1 B:ASP614 2.4 63.7 1.0
OD1 B:ASN656 2.5 62.6 1.0
O B:TYR615 2.7 58.3 1.0
OE1 B:GLU661 2.7 86.1 1.0
CG B:ASP614 3.4 62.3 1.0
OD2 B:ASP614 3.6 71.7 1.0
CG B:ASN656 3.7 61.5 1.0
C B:TYR615 3.7 34.0 1.0
CD B:GLU661 3.7 85.3 1.0
OE2 B:GLU661 4.1 89.9 1.0
OE2 B:GLU654 4.1 84.1 1.0
N B:TYR615 4.3 61.0 1.0
CB B:ASN656 4.4 42.7 1.0
CA B:TYR615 4.5 34.0 1.0
N B:LYS616 4.6 28.1 1.0
CA B:LYS616 4.6 31.9 1.0
ND2 B:ASN656 4.7 68.9 1.0
CG B:GLU654 4.7 74.5 1.0
CD B:GLU654 4.8 86.2 1.0
CB B:ASP614 4.8 52.5 1.0
N B:GLY617 4.8 42.8 1.0
CB B:TYR615 4.8 36.9 1.0
CA B:ASN656 4.9 47.4 1.0
C B:ASP614 4.9 60.0 1.0
CD1 B:LEU659 4.9 55.6 1.0

Calcium binding site 2 out of 10 in 7c7r

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Calcium binding site 2 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:76.6
occ:1.00
O B:LEU735 2.4 82.3 1.0
OD1 B:ASP731 2.4 76.8 1.0
OE2 B:GLU740 2.4 80.1 1.0
OD1 B:ASP733 2.4 81.9 1.0
O B:HOH901 2.5 115.4 1.0
OD1 B:ASP729 2.6 72.1 1.0
CG B:ASP733 3.2 72.6 1.0
CG B:ASP731 3.3 66.9 1.0
OD2 B:ASP733 3.5 66.5 1.0
C B:LEU735 3.5 78.8 1.0
CD B:GLU740 3.5 78.0 1.0
OD2 B:ASP731 3.6 71.2 1.0
CG B:ASP729 3.8 80.2 1.0
CA B:LEU735 4.1 79.2 1.0
CB B:LEU735 4.2 69.8 1.0
CG B:GLU740 4.2 69.6 1.0
N B:LEU735 4.2 82.5 1.0
N B:ASP733 4.2 79.4 1.0
OD2 B:ASP737 4.3 106.0 1.0
CA B:CA803 4.3 76.3 1.0
C B:LEU736 4.4 66.6 1.0
CA B:ASP729 4.4 73.2 1.0
O B:ALA748 4.5 83.3 1.0
CB B:ASP733 4.5 72.1 1.0
N B:ASP731 4.5 82.4 1.0
O B:LEU736 4.5 55.3 1.0
OD2 B:ASP729 4.5 78.4 1.0
N B:LEU736 4.5 82.0 1.0
N B:ASP737 4.5 71.5 1.0
OE1 B:GLU740 4.6 74.1 1.0
N B:LYS732 4.6 80.9 1.0
N B:TYR730 4.6 82.5 1.0
C B:ASP729 4.6 77.6 1.0
CB B:ASP731 4.7 43.6 1.0
CB B:ASP729 4.7 81.7 1.0
CA B:LEU736 4.7 74.4 1.0
CA B:ASP733 4.8 81.2 1.0
CA B:ASP737 4.9 62.8 1.0
CA B:ASP731 4.9 71.9 1.0
C B:ASP731 5.0 86.9 1.0
CG B:ASP737 5.0 93.6 1.0

Calcium binding site 3 out of 10 in 7c7r

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Calcium binding site 3 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:76.3
occ:1.00
OE1 B:GLU740 2.4 74.1 1.0
O B:ASP747 2.4 70.4 1.0
OD2 B:ASP731 2.4 71.2 1.0
O B:ASN750 2.5 94.5 1.0
OD1 B:ASP760 2.5 108.9 1.0
OD2 B:ASP733 2.6 66.5 1.0
OE2 B:GLU740 2.7 80.1 1.0
CD B:GLU740 2.9 78.0 1.0
CG B:ASP760 3.5 103.8 1.0
C B:ASN750 3.6 97.1 1.0
CG B:ASP731 3.6 66.9 1.0
C B:ASP747 3.6 68.7 1.0
CG B:ASP733 3.8 72.6 1.0
CB B:ASP760 3.8 93.0 1.0
OD1 B:ASP731 4.2 76.8 1.0
N B:ASN750 4.2 104.6 1.0
OG1 B:THR753 4.3 69.6 1.0
CA B:CA802 4.3 76.6 1.0
CA B:ALA748 4.3 78.1 1.0
CG B:GLU740 4.4 69.6 1.0
OD1 B:ASP733 4.4 81.9 1.0
N B:ALA748 4.4 76.1 1.0
CA B:ASN750 4.4 103.1 1.0
C B:ALA748 4.5 85.5 1.0
N B:GLU751 4.5 91.6 1.0
OG B:SER746 4.5 69.5 1.0
CA B:GLU751 4.6 86.9 1.0
N B:ASP747 4.6 69.4 1.0
CB B:SER746 4.6 78.5 1.0
CA B:ASP747 4.6 63.8 1.0
OD2 B:ASP760 4.6 107.2 1.0
O B:ALA748 4.7 83.3 1.0
O B:HOH901 4.7 115.4 1.0
CB B:ASP731 4.8 43.6 1.0
CB B:ASP733 4.8 72.1 1.0
C B:GLU751 4.8 92.3 1.0
N B:GLU749 4.9 96.7 1.0
CB B:ASN750 4.9 103.7 1.0
C B:SER746 5.0 80.8 1.0

Calcium binding site 4 out of 10 in 7c7r

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Calcium binding site 4 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:89.0
occ:1.00
OD1 B:ASP752 2.3 76.5 1.0
OD1 B:ASP754 2.4 125.4 1.0
O B:LYS758 2.4 84.0 1.0
OD2 B:ASP756 2.5 101.5 1.0
OE1 B:GLU763 2.5 87.0 1.0
OD2 B:ASP754 2.8 130.3 1.0
CG B:ASP754 2.9 120.5 1.0
CG B:ASP756 3.5 102.6 1.0
CG B:ASP752 3.5 89.4 1.0
C B:LYS758 3.6 88.7 1.0
CD B:GLU763 3.6 88.8 1.0
CA B:CA805 3.8 88.6 1.0
CB B:LYS758 3.9 100.0 1.0
OD1 B:ASP756 4.1 105.5 1.0
OE2 B:GLU763 4.1 94.3 1.0
CA B:LYS758 4.1 90.9 1.0
N B:LYS758 4.1 83.3 1.0
OD2 B:ASP760 4.2 107.2 1.0
OD2 B:ASP752 4.3 93.4 1.0
CB B:ASP754 4.3 105.3 1.0
N B:ASP754 4.3 95.7 1.0
N B:ASP756 4.4 98.0 1.0
CA B:ASP752 4.5 86.9 1.0
N B:GLY755 4.5 80.6 1.0
O B:PRO771 4.6 91.9 1.0
CB B:ASP752 4.6 90.4 1.0
N B:THR753 4.6 72.5 1.0
CB B:ASP756 4.7 98.6 1.0
CA B:PRO771 4.7 95.7 1.0
N B:ASN759 4.7 91.7 1.0
CA B:ASP754 4.8 99.8 1.0
O B:ASN759 4.8 87.5 1.0
C B:ASN759 4.8 90.0 1.0
C B:ASP752 4.8 83.3 1.0
CG B:GLU763 4.8 84.0 1.0
C B:PRO771 4.8 93.5 1.0
CA B:ASP756 4.9 92.1 1.0
C B:ASP754 4.9 93.6 1.0
CB B:GLU763 5.0 75.9 1.0
CG B:LYS758 5.0 108.1 1.0

Calcium binding site 5 out of 10 in 7c7r

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Calcium binding site 5 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:88.6
occ:1.00
O B:VAL773 2.3 114.2 1.0
OE2 B:GLU763 2.3 94.3 1.0
O B:SER770 2.4 84.7 1.0
OD2 B:ASP754 2.6 130.3 1.0
CD B:GLU763 3.0 88.8 1.0
CG B:ASP754 3.2 120.5 1.0
OE1 B:GLU763 3.3 87.0 1.0
OD1 B:ASP756 3.4 105.5 1.0
C B:VAL773 3.5 109.8 1.0
OD1 B:ASP754 3.5 125.4 1.0
C B:SER770 3.6 91.4 1.0
N B:VAL773 3.7 112.4 1.0
CA B:PRO771 3.8 95.7 1.0
CA B:CA804 3.8 89.0 1.0
CG B:ASP756 3.9 102.6 1.0
C B:PRO771 4.0 93.5 1.0
OD2 B:ASP756 4.1 101.5 1.0
N B:LEU772 4.1 97.2 1.0
CG B:GLU763 4.1 84.0 1.0
N B:PRO771 4.2 100.8 1.0
CA B:VAL773 4.2 101.7 1.0
CB B:ASP754 4.3 105.3 1.0
N B:GLY774 4.5 111.2 1.0
O B:PRO771 4.7 91.9 1.0
C B:LEU772 4.7 113.6 1.0
CA B:SER770 4.7 85.1 1.0
CA B:GLY774 4.8 117.4 1.0
CB B:VAL773 4.8 86.8 1.0
N B:SER770 4.9 90.1 1.0
CA B:LEU772 4.9 102.3 1.0
OG1 B:THR769 5.0 111.8 1.0

Calcium binding site 6 out of 10 in 7c7r

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Calcium binding site 6 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:56.7
occ:1.00
OD1 A:ASN656 2.3 71.2 1.0
OD1 A:ASP614 2.4 63.6 1.0
O A:TYR615 2.5 56.0 1.0
OE1 A:GLU661 2.6 82.5 1.0
CG A:ASP614 3.4 50.3 1.0
CG A:ASN656 3.5 76.1 1.0
C A:TYR615 3.6 47.7 1.0
OD2 A:ASP614 3.7 64.5 1.0
CD A:GLU661 3.7 80.3 1.0
OE2 A:GLU661 4.0 86.2 1.0
N A:TYR615 4.1 47.7 1.0
CB A:ASN656 4.3 66.7 1.0
CA A:TYR615 4.4 44.8 1.0
OE1 A:GLU654 4.4 97.8 1.0
N A:LYS616 4.5 39.0 1.0
ND2 A:ASN656 4.5 79.1 1.0
CA A:LYS616 4.5 36.8 1.0
CB A:TYR615 4.7 53.1 1.0
CG A:GLU654 4.7 88.8 1.0
CD1 A:LEU659 4.7 59.9 1.0
CB A:ASP614 4.8 40.8 1.0
N A:GLY617 4.8 47.1 1.0
C A:ASP614 4.8 47.8 1.0
CA A:ASN656 4.8 59.7 1.0
CD A:GLU654 5.0 94.1 1.0
CG A:GLU661 5.0 68.8 1.0

Calcium binding site 7 out of 10 in 7c7r

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Calcium binding site 7 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:50.7
occ:1.00
OD1 A:ASP731 2.3 71.5 1.0
OD1 A:ASP733 2.3 79.7 1.0
OE2 A:GLU740 2.4 85.0 1.0
O A:LEU735 2.4 44.5 1.0
O A:HOH901 2.6 89.7 1.0
OD1 A:ASP729 2.6 49.5 1.0
CG A:ASP733 3.1 79.2 1.0
CG A:ASP731 3.2 68.0 1.0
OD2 A:ASP733 3.3 80.3 1.0
OD2 A:ASP731 3.4 67.3 1.0
C A:LEU735 3.5 52.9 1.0
CD A:GLU740 3.5 72.0 1.0
CG A:ASP729 3.7 58.6 1.0
CA A:CA803 4.1 62.6 1.0
CB A:LEU735 4.1 43.6 1.0
N A:LEU735 4.1 53.2 1.0
CA A:LEU735 4.1 51.6 1.0
CG A:GLU740 4.1 56.8 1.0
OD1 A:ASP737 4.1 82.1 1.0
N A:ASP733 4.2 71.6 1.0
O A:ALA748 4.3 76.2 1.0
CB A:ASP733 4.4 73.0 1.0
OD2 A:ASP729 4.4 56.3 1.0
CA A:ASP729 4.5 56.0 1.0
N A:ASP731 4.5 64.0 1.0
C A:LEU736 4.5 55.8 1.0
OE1 A:GLU740 4.5 79.0 1.0
N A:LEU736 4.6 46.9 1.0
O A:LEU736 4.6 61.9 1.0
CB A:ASP731 4.6 54.7 1.0
CB A:ASP729 4.6 61.8 1.0
N A:LYS732 4.6 76.2 1.0
C A:ASP729 4.7 60.3 1.0
N A:TYR730 4.7 61.5 1.0
CA A:ASP733 4.7 68.9 1.0
N A:ASP737 4.8 69.8 1.0
CA A:LEU736 4.8 40.8 1.0
CA A:ASP731 4.9 60.1 1.0
CA A:ALA748 4.9 63.2 1.0
C A:ASP733 4.9 67.8 1.0
C A:ALA748 5.0 72.7 1.0
N A:GLY734 5.0 62.4 1.0
C A:ASP731 5.0 72.7 1.0

Calcium binding site 8 out of 10 in 7c7r

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Calcium binding site 8 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:62.6
occ:1.00
OD2 A:ASP733 2.4 80.3 1.0
OD2 A:ASP731 2.4 67.3 1.0
O A:ASP747 2.4 74.9 1.0
O A:ASN750 2.5 80.3 1.0
OE1 A:GLU740 2.5 79.0 1.0
OE2 A:GLU740 2.5 85.0 1.0
OD2 A:ASP760 2.5 56.9 1.0
CD A:GLU740 2.8 72.0 1.0
CG A:ASP731 3.5 68.0 1.0
CG A:ASP760 3.5 57.1 1.0
CG A:ASP733 3.6 79.2 1.0
C A:ASN750 3.6 68.1 1.0
C A:ASP747 3.6 63.4 1.0
CB A:ASP760 3.9 43.8 1.0
OD1 A:ASP731 4.1 71.5 1.0
CA A:CA802 4.1 50.7 1.0
N A:ASN750 4.1 72.9 1.0
OD1 A:ASP733 4.2 79.7 1.0
CA A:ALA748 4.2 63.2 1.0
CG A:GLU740 4.3 56.8 1.0
C A:ALA748 4.4 72.7 1.0
N A:ALA748 4.4 64.1 1.0
CA A:ASN750 4.4 58.4 1.0
CG2 A:THR753 4.4 31.1 1.0
N A:GLU751 4.5 77.7 1.0
O A:ALA748 4.6 76.2 1.0
OD1 A:ASP760 4.6 53.1 1.0
CA A:GLU751 4.6 83.8 1.0
CB A:ASP733 4.6 73.0 1.0
N A:ASP747 4.7 65.8 1.0
CA A:ASP747 4.7 63.6 1.0
CB A:ASP731 4.7 54.7 1.0
OG A:SER746 4.7 65.1 1.0
CB A:SER746 4.8 62.6 1.0
O A:HOH901 4.8 89.7 1.0
N A:GLU749 4.8 72.1 1.0
C A:GLU751 4.9 87.5 1.0
CB A:ASN750 4.9 70.3 1.0

Calcium binding site 9 out of 10 in 7c7r

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Calcium binding site 9 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:63.3
occ:1.00
OD1 A:ASP752 2.3 81.1 1.0
OD2 A:ASP756 2.3 64.0 1.0
O A:LYS758 2.3 74.2 1.0
OE2 A:GLU763 2.4 73.0 1.0
OD1 A:ASP754 2.4 77.9 1.0
O A:HOH903 2.6 69.8 1.0
CG A:ASP754 3.1 69.5 1.0
OD2 A:ASP754 3.2 67.8 1.0
CG A:ASP756 3.3 66.9 1.0
CD A:GLU763 3.4 67.1 1.0
CG A:ASP752 3.5 81.7 1.0
C A:LYS758 3.5 64.1 1.0
OD1 A:ASP756 3.7 61.5 1.0
CG A:GLU763 3.9 53.8 1.0
CA A:CA805 4.0 52.1 1.0
N A:LYS758 4.1 62.7 1.0
OD2 A:ASP752 4.1 85.2 1.0
CA A:LYS758 4.2 58.3 1.0
OD1 A:ASP760 4.2 53.1 1.0
CB A:LYS758 4.2 63.8 1.0
N A:ASP756 4.3 56.8 1.0
CA A:ASP752 4.5 72.0 1.0
O A:PRO771 4.5 77.8 1.0
CB A:ASP752 4.5 78.0 1.0
OE1 A:GLU763 4.5 81.9 1.0
N A:ASP754 4.5 52.3 1.0
CB A:ASP756 4.5 72.4 1.0
CB A:ASP754 4.6 68.3 1.0
N A:ASN759 4.6 67.2 1.0
N A:GLY755 4.6 59.5 1.0
C A:ASN759 4.6 70.6 1.0
O A:ASN759 4.7 79.1 1.0
N A:THR753 4.7 54.7 1.0
CA A:PRO771 4.8 59.1 1.0
C A:ASP752 4.8 69.2 1.0
CA A:ASP756 4.8 66.2 1.0
CA A:ASN759 4.9 74.3 1.0
C A:PRO771 4.9 63.4 1.0
CA A:ASP754 4.9 65.0 1.0
N A:ASP760 5.0 64.3 1.0
C A:ASP756 5.0 70.3 1.0
N A:GLY757 5.0 65.6 1.0

Calcium binding site 10 out of 10 in 7c7r

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Calcium binding site 10 out of 10 in the Biofilm Associated Protein - B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Biofilm Associated Protein - B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca805

b:52.1
occ:1.00
O A:VAL773 2.4 79.0 1.0
OE2 A:GLU763 2.4 73.0 1.0
OD2 A:ASP754 2.5 67.8 1.0
O A:SER770 2.5 68.6 1.0
OE1 A:GLU763 2.6 81.9 1.0
OD1 A:ASP756 2.7 61.5 1.0
CD A:GLU763 2.9 67.1 1.0
C A:VAL773 3.5 77.6 1.0
CG A:ASP754 3.5 69.5 1.0
CG A:ASP756 3.6 66.9 1.0
C A:SER770 3.7 64.5 1.0
N A:VAL773 4.0 83.2 1.0
CA A:PRO771 4.0 59.1 1.0
OD1 A:ASP754 4.0 77.9 1.0
CA A:CA804 4.0 63.3 1.0
OD2 A:ASP756 4.0 64.0 1.0
NZ A:LYS758 4.1 81.6 1.0
C A:PRO771 4.2 63.4 1.0
N A:LEU772 4.3 70.7 1.0
N A:PRO771 4.3 67.7 1.0
CG A:GLU763 4.4 53.8 1.0
CA A:VAL773 4.4 76.5 1.0
OG1 A:THR769 4.4 76.4 1.0
N A:GLY774 4.4 86.8 1.0
CA A:GLY774 4.5 92.0 1.0
CB A:ASP754 4.7 68.3 1.0
CE A:LYS758 4.7 79.0 1.0
O A:PRO771 4.7 77.8 1.0
CB A:ASP756 4.8 72.4 1.0
CG2 A:VAL773 4.8 87.5 1.0
C A:LEU772 4.8 75.5 1.0
CA A:SER770 4.9 66.5 1.0
N A:SER770 4.9 73.0 1.0
O A:HOH903 5.0 69.8 1.0

Reference:

J.F.Ma, Z.H.Xu, Y.K.Zhang, X.Cheng, S.L.Fan, J.W.Wang, X.Y.Fang. Structural Mechanism For Modulation of Functional Amyloid and Biofilm Formation By Staphylococcal Bap Protein Switch. Embo J. 2021.
ISSN: ESSN 1460-2075
DOI: 10.15252/EMBJ.2020107500
Page generated: Wed Jul 9 21:09:39 2025

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