Calcium in PDB 7wpp: Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit)
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit)
(pdb code 7wpp). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit), PDB code: 7wpp:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7wpp
Go back to
Calcium Binding Sites List in 7wpp
Calcium binding site 1 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca801
b:24.1
occ:1.00
|
OD1
|
E:ASN166
|
2.3
|
24.0
|
1.0
|
|
O
|
E:PHE168
|
2.4
|
27.0
|
1.0
|
|
OD1
|
E:ASP172
|
2.4
|
20.8
|
1.0
|
|
OD1
|
E:ASN164
|
2.4
|
19.4
|
1.0
|
|
OD1
|
E:ASP171
|
2.4
|
28.1
|
1.0
|
|
OD2
|
E:ASP47
|
3.1
|
19.3
|
1.0
|
|
CG
|
E:ASN164
|
3.3
|
19.4
|
1.0
|
|
CG
|
E:ASN166
|
3.3
|
24.0
|
1.0
|
|
CG
|
E:ASP171
|
3.4
|
28.1
|
1.0
|
|
CG
|
E:ASP172
|
3.4
|
20.8
|
1.0
|
|
O
|
E:ASP171
|
3.6
|
28.1
|
1.0
|
|
C
|
E:PHE168
|
3.6
|
27.0
|
1.0
|
|
ND2
|
E:ASN166
|
3.6
|
24.0
|
1.0
|
|
ND2
|
E:ASN164
|
3.6
|
19.4
|
1.0
|
|
C
|
E:ASP171
|
3.6
|
28.1
|
1.0
|
|
N
|
E:ASP172
|
3.8
|
20.8
|
1.0
|
|
CA
|
E:ASP172
|
3.9
|
20.8
|
1.0
|
|
OD2
|
E:ASP171
|
4.0
|
28.1
|
1.0
|
|
CG
|
E:ASP47
|
4.2
|
19.3
|
1.0
|
|
OD2
|
E:ASP172
|
4.2
|
20.8
|
1.0
|
|
O
|
E:ASN164
|
4.2
|
19.4
|
1.0
|
|
CB
|
E:ASP172
|
4.3
|
20.8
|
1.0
|
|
CA
|
E:ASP171
|
4.3
|
28.1
|
1.0
|
|
N
|
E:ASP171
|
4.4
|
28.1
|
1.0
|
|
CB
|
E:ASP171
|
4.4
|
28.1
|
1.0
|
|
N
|
E:ALA169
|
4.5
|
25.5
|
1.0
|
|
CA
|
E:PHE168
|
4.5
|
27.0
|
1.0
|
|
CA
|
E:ALA169
|
4.5
|
25.5
|
1.0
|
|
N
|
E:PHE168
|
4.5
|
27.0
|
1.0
|
|
CB
|
E:ASP47
|
4.6
|
19.3
|
1.0
|
|
C
|
E:ASN164
|
4.6
|
19.4
|
1.0
|
|
CB
|
E:ASN164
|
4.6
|
19.4
|
1.0
|
|
CB
|
E:ASN166
|
4.7
|
24.0
|
1.0
|
|
CB
|
E:PHE168
|
4.7
|
27.0
|
1.0
|
|
N
|
E:ASN166
|
4.7
|
24.0
|
1.0
|
|
C
|
E:ALA169
|
4.9
|
25.5
|
1.0
|
|
N
|
E:ASN164
|
4.9
|
19.4
|
1.0
|
|
CA
|
E:ASN164
|
5.0
|
19.4
|
1.0
|
|
C
|
E:ASN166
|
5.0
|
24.0
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7wpp
Go back to
Calcium Binding Sites List in 7wpp
Calcium binding site 2 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca802
b:23.6
occ:1.00
|
OD1
|
E:ASP533
|
2.4
|
16.9
|
1.0
|
|
OD2
|
E:ASP400
|
2.4
|
16.5
|
1.0
|
|
OD1
|
E:ASN528
|
2.5
|
12.3
|
1.0
|
|
O
|
E:ASN530
|
2.6
|
11.8
|
1.0
|
|
OD1
|
E:ASP534
|
2.6
|
20.8
|
1.0
|
|
CG
|
E:ASN528
|
3.3
|
12.3
|
1.0
|
|
CG
|
E:ASP533
|
3.3
|
16.9
|
1.0
|
|
CG
|
E:ASP400
|
3.6
|
16.5
|
1.0
|
|
ND2
|
E:ASN528
|
3.6
|
12.3
|
1.0
|
|
CG
|
E:ASP534
|
3.6
|
20.8
|
1.0
|
|
OD2
|
E:ASP533
|
3.7
|
16.9
|
1.0
|
|
C
|
E:ASN530
|
3.7
|
11.8
|
1.0
|
|
CB
|
E:ASN526
|
3.8
|
14.8
|
1.0
|
|
OD1
|
E:ASN526
|
4.0
|
14.8
|
1.0
|
|
N
|
E:ASN526
|
4.1
|
14.8
|
1.0
|
|
OD2
|
E:ASP534
|
4.2
|
20.8
|
1.0
|
|
C
|
E:ASP533
|
4.2
|
16.9
|
1.0
|
|
CB
|
E:ASP400
|
4.2
|
16.5
|
1.0
|
|
O
|
E:ASP533
|
4.2
|
16.9
|
1.0
|
|
N
|
E:ASN530
|
4.3
|
11.8
|
1.0
|
|
N
|
E:TYR527
|
4.3
|
14.3
|
1.0
|
|
N
|
E:ASN528
|
4.3
|
12.3
|
1.0
|
|
N
|
E:ASP534
|
4.4
|
20.8
|
1.0
|
|
CA
|
E:ASN530
|
4.4
|
11.8
|
1.0
|
|
CG
|
E:ASN526
|
4.4
|
14.8
|
1.0
|
|
CA
|
E:ASN526
|
4.4
|
14.8
|
1.0
|
|
CB
|
E:ASN528
|
4.5
|
12.3
|
1.0
|
|
CA
|
E:ASP534
|
4.5
|
20.8
|
1.0
|
|
CB
|
E:ASN530
|
4.5
|
11.8
|
1.0
|
|
OD1
|
E:ASP400
|
4.5
|
16.5
|
1.0
|
|
CB
|
E:ASP533
|
4.6
|
16.9
|
1.0
|
|
CB
|
E:ASP534
|
4.7
|
20.8
|
1.0
|
|
C
|
E:ASN526
|
4.7
|
14.8
|
1.0
|
|
CA
|
E:ASP533
|
4.7
|
16.9
|
1.0
|
|
N
|
E:ASP533
|
4.8
|
16.9
|
1.0
|
|
N
|
E:GLN531
|
4.8
|
15.8
|
1.0
|
|
CA
|
E:ASN528
|
4.9
|
12.3
|
1.0
|
|
N
|
E:GLY529
|
5.0
|
11.0
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7wpp
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Calcium Binding Sites List in 7wpp
Calcium binding site 3 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca1302
b:23.6
occ:1.00
|
OD1
|
F:ASN998
|
2.3
|
12.1
|
1.0
|
|
O
|
F:ILE1002
|
2.4
|
12.1
|
1.0
|
|
OD1
|
F:ASP1006
|
2.4
|
10.5
|
1.0
|
|
OD1
|
F:ASN1005
|
2.4
|
11.0
|
1.0
|
|
OD1
|
F:ASP1000
|
2.4
|
14.4
|
1.0
|
|
OD2
|
F:ASP879
|
2.4
|
10.9
|
1.0
|
|
CG
|
F:ASP1000
|
3.3
|
14.4
|
1.0
|
|
CG
|
F:ASP1006
|
3.3
|
10.5
|
1.0
|
|
CG
|
F:ASN998
|
3.4
|
12.1
|
1.0
|
|
CG
|
F:ASN1005
|
3.5
|
11.0
|
1.0
|
|
OD2
|
F:ASP1000
|
3.6
|
14.4
|
1.0
|
|
C
|
F:ILE1002
|
3.6
|
12.1
|
1.0
|
|
CG
|
F:ASP879
|
3.6
|
10.9
|
1.0
|
|
ND2
|
F:ASN998
|
3.8
|
12.1
|
1.0
|
|
OD2
|
F:ASP1006
|
3.9
|
10.5
|
1.0
|
|
ND2
|
F:ASN1005
|
4.1
|
11.0
|
1.0
|
|
N
|
F:ASP1006
|
4.1
|
10.5
|
1.0
|
|
C
|
F:ASN1005
|
4.1
|
11.0
|
1.0
|
|
CA
|
F:ASP1006
|
4.2
|
10.5
|
1.0
|
|
O
|
F:ASN1005
|
4.3
|
11.0
|
1.0
|
|
N
|
F:ASN998
|
4.3
|
12.1
|
1.0
|
|
CB
|
F:ASP1006
|
4.4
|
10.5
|
1.0
|
|
CB
|
F:ASP879
|
4.4
|
10.9
|
1.0
|
|
N
|
F:ASP1000
|
4.4
|
14.4
|
1.0
|
|
CA
|
F:ILE1002
|
4.4
|
12.1
|
1.0
|
|
N
|
F:ILE1002
|
4.4
|
12.1
|
1.0
|
|
N
|
F:PHE999
|
4.5
|
14.4
|
1.0
|
|
N
|
F:GLN1003
|
4.5
|
11.0
|
1.0
|
|
CB
|
F:ILE1002
|
4.6
|
12.1
|
1.0
|
|
OD1
|
F:ASP879
|
4.6
|
10.9
|
1.0
|
|
CB
|
F:ASP1000
|
4.6
|
14.4
|
1.0
|
|
CB
|
F:ASN998
|
4.6
|
12.1
|
1.0
|
|
CB
|
F:ASN1005
|
4.6
|
11.0
|
1.0
|
|
CA
|
F:ASN1005
|
4.7
|
11.0
|
1.0
|
|
CA
|
F:GLN1003
|
4.7
|
11.0
|
1.0
|
|
N
|
F:ASN1005
|
4.7
|
11.0
|
1.0
|
|
CA
|
F:ASN998
|
4.8
|
12.1
|
1.0
|
|
C
|
F:ASN998
|
4.9
|
12.1
|
1.0
|
|
CA
|
F:ASP1000
|
4.9
|
14.4
|
1.0
|
|
N
|
F:GLY1001
|
5.0
|
23.6
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7wpp
Go back to
Calcium Binding Sites List in 7wpp
Calcium binding site 4 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca801
b:14.5
occ:1.00
|
OD1
|
G:ASN166
|
2.3
|
22.4
|
1.0
|
|
O
|
G:PHE168
|
2.4
|
24.6
|
1.0
|
|
OD1
|
G:ASP172
|
2.4
|
18.1
|
1.0
|
|
OD1
|
G:ASN164
|
2.4
|
17.9
|
1.0
|
|
OD1
|
G:ASP171
|
2.4
|
23.8
|
1.0
|
|
OD2
|
G:ASP47
|
3.1
|
16.9
|
1.0
|
|
CG
|
G:ASN164
|
3.3
|
17.9
|
1.0
|
|
CG
|
G:ASN166
|
3.3
|
22.4
|
1.0
|
|
CG
|
G:ASP171
|
3.4
|
23.8
|
1.0
|
|
CG
|
G:ASP172
|
3.4
|
18.1
|
1.0
|
|
O
|
G:ASP171
|
3.5
|
23.8
|
1.0
|
|
C
|
G:PHE168
|
3.6
|
24.6
|
1.0
|
|
ND2
|
G:ASN166
|
3.6
|
22.4
|
1.0
|
|
ND2
|
G:ASN164
|
3.6
|
17.9
|
1.0
|
|
C
|
G:ASP171
|
3.6
|
23.8
|
1.0
|
|
N
|
G:ASP172
|
3.8
|
18.1
|
1.0
|
|
CA
|
G:ASP172
|
3.9
|
18.1
|
1.0
|
|
OD2
|
G:ASP171
|
4.0
|
23.8
|
1.0
|
|
CG
|
G:ASP47
|
4.2
|
16.9
|
1.0
|
|
OD2
|
G:ASP172
|
4.2
|
18.1
|
1.0
|
|
O
|
G:ASN164
|
4.2
|
17.9
|
1.0
|
|
CB
|
G:ASP172
|
4.3
|
18.1
|
1.0
|
|
CA
|
G:ASP171
|
4.3
|
23.8
|
1.0
|
|
N
|
G:ASP171
|
4.4
|
23.8
|
1.0
|
|
CB
|
G:ASP171
|
4.4
|
23.8
|
1.0
|
|
N
|
G:ALA169
|
4.5
|
22.7
|
1.0
|
|
CA
|
G:PHE168
|
4.5
|
24.6
|
1.0
|
|
CA
|
G:ALA169
|
4.5
|
22.7
|
1.0
|
|
N
|
G:PHE168
|
4.5
|
24.6
|
1.0
|
|
CB
|
G:ASP47
|
4.6
|
16.9
|
1.0
|
|
C
|
G:ASN164
|
4.6
|
17.9
|
1.0
|
|
CB
|
G:ASN164
|
4.6
|
17.9
|
1.0
|
|
CB
|
G:ASN166
|
4.7
|
22.4
|
1.0
|
|
CB
|
G:PHE168
|
4.7
|
24.6
|
1.0
|
|
N
|
G:ASN166
|
4.7
|
22.4
|
1.0
|
|
C
|
G:ALA169
|
4.9
|
22.7
|
1.0
|
|
N
|
G:ASN164
|
4.9
|
17.9
|
1.0
|
|
CA
|
G:ASN164
|
5.0
|
17.9
|
1.0
|
|
C
|
G:ASN166
|
5.0
|
22.4
|
1.0
|
|
Calcium binding site 5 out
of 6 in 7wpp
Go back to
Calcium Binding Sites List in 7wpp
Calcium binding site 5 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca802
b:23.6
occ:1.00
|
OD1
|
G:ASP533
|
2.4
|
15.3
|
1.0
|
|
OD2
|
G:ASP400
|
2.4
|
9.4
|
1.0
|
|
OD1
|
G:ASN528
|
2.5
|
10.2
|
1.0
|
|
O
|
G:ASN530
|
2.6
|
11.7
|
1.0
|
|
OD1
|
G:ASP534
|
2.6
|
13.7
|
1.0
|
|
CG
|
G:ASN528
|
3.3
|
10.2
|
1.0
|
|
CG
|
G:ASP533
|
3.3
|
15.3
|
1.0
|
|
CG
|
G:ASP400
|
3.6
|
9.4
|
1.0
|
|
ND2
|
G:ASN528
|
3.6
|
10.2
|
1.0
|
|
CG
|
G:ASP534
|
3.6
|
13.7
|
1.0
|
|
OD2
|
G:ASP533
|
3.7
|
15.3
|
1.0
|
|
C
|
G:ASN530
|
3.7
|
11.7
|
1.0
|
|
CB
|
G:ASN526
|
3.8
|
10.7
|
1.0
|
|
OD1
|
G:ASN526
|
4.0
|
10.7
|
1.0
|
|
N
|
G:ASN526
|
4.1
|
10.7
|
1.0
|
|
OD2
|
G:ASP534
|
4.2
|
13.7
|
1.0
|
|
C
|
G:ASP533
|
4.2
|
15.3
|
1.0
|
|
O
|
G:ASP533
|
4.2
|
15.3
|
1.0
|
|
CB
|
G:ASP400
|
4.2
|
9.4
|
1.0
|
|
N
|
G:ASN530
|
4.3
|
11.7
|
1.0
|
|
N
|
G:TYR527
|
4.3
|
10.1
|
1.0
|
|
N
|
G:ASN528
|
4.3
|
10.2
|
1.0
|
|
N
|
G:ASP534
|
4.4
|
13.7
|
1.0
|
|
CA
|
G:ASN530
|
4.4
|
11.7
|
1.0
|
|
CG
|
G:ASN526
|
4.4
|
10.7
|
1.0
|
|
CA
|
G:ASN526
|
4.4
|
10.7
|
1.0
|
|
CB
|
G:ASN528
|
4.5
|
10.2
|
1.0
|
|
CA
|
G:ASP534
|
4.5
|
13.7
|
1.0
|
|
CB
|
G:ASN530
|
4.5
|
11.7
|
1.0
|
|
OD1
|
G:ASP400
|
4.5
|
9.4
|
1.0
|
|
CB
|
G:ASP533
|
4.6
|
15.3
|
1.0
|
|
CB
|
G:ASP534
|
4.7
|
13.7
|
1.0
|
|
C
|
G:ASN526
|
4.7
|
10.7
|
1.0
|
|
CA
|
G:ASP533
|
4.7
|
15.3
|
1.0
|
|
N
|
G:ASP533
|
4.8
|
15.3
|
1.0
|
|
N
|
G:GLN531
|
4.8
|
12.2
|
1.0
|
|
CA
|
G:ASN528
|
4.9
|
10.2
|
1.0
|
|
N
|
G:GLY529
|
5.0
|
10.8
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7wpp
Go back to
Calcium Binding Sites List in 7wpp
Calcium binding site 6 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 2.85 Angstron Resolution (1 Unit) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca1302
b:23.6
occ:1.00
|
OD1
|
H:ASN998
|
2.3
|
13.1
|
1.0
|
|
OD1
|
H:ASP1006
|
2.4
|
11.6
|
1.0
|
|
O
|
H:ILE1002
|
2.4
|
12.6
|
1.0
|
|
OD1
|
H:ASN1005
|
2.4
|
12.4
|
1.0
|
|
OD1
|
H:ASP1000
|
2.4
|
15.4
|
1.0
|
|
OD2
|
H:ASP879
|
2.4
|
12.2
|
1.0
|
|
CG
|
H:ASP1000
|
3.3
|
15.4
|
1.0
|
|
CG
|
H:ASP1006
|
3.3
|
11.6
|
1.0
|
|
CG
|
H:ASN998
|
3.4
|
13.1
|
1.0
|
|
CG
|
H:ASN1005
|
3.5
|
12.4
|
1.0
|
|
OD2
|
H:ASP1000
|
3.6
|
15.4
|
1.0
|
|
C
|
H:ILE1002
|
3.6
|
12.6
|
1.0
|
|
CG
|
H:ASP879
|
3.6
|
12.2
|
1.0
|
|
ND2
|
H:ASN998
|
3.8
|
13.1
|
1.0
|
|
OD2
|
H:ASP1006
|
3.9
|
11.6
|
1.0
|
|
ND2
|
H:ASN1005
|
4.1
|
12.4
|
1.0
|
|
N
|
H:ASP1006
|
4.1
|
11.6
|
1.0
|
|
C
|
H:ASN1005
|
4.1
|
12.4
|
1.0
|
|
CA
|
H:ASP1006
|
4.2
|
11.6
|
1.0
|
|
O
|
H:ASN1005
|
4.3
|
12.4
|
1.0
|
|
N
|
H:ASN998
|
4.3
|
13.1
|
1.0
|
|
CB
|
H:ASP1006
|
4.4
|
11.6
|
1.0
|
|
CB
|
H:ASP879
|
4.4
|
12.2
|
1.0
|
|
N
|
H:ASP1000
|
4.4
|
15.4
|
1.0
|
|
CA
|
H:ILE1002
|
4.4
|
12.6
|
1.0
|
|
N
|
H:ILE1002
|
4.4
|
12.6
|
1.0
|
|
N
|
H:PHE999
|
4.5
|
14.2
|
1.0
|
|
N
|
H:GLN1003
|
4.5
|
11.6
|
1.0
|
|
CB
|
H:ILE1002
|
4.6
|
12.6
|
1.0
|
|
CB
|
H:ASP1000
|
4.6
|
15.4
|
1.0
|
|
OD1
|
H:ASP879
|
4.6
|
12.2
|
1.0
|
|
CB
|
H:ASN998
|
4.6
|
13.1
|
1.0
|
|
CB
|
H:ASN1005
|
4.6
|
12.4
|
1.0
|
|
CA
|
H:ASN1005
|
4.7
|
12.4
|
1.0
|
|
CA
|
H:GLN1003
|
4.7
|
11.6
|
1.0
|
|
N
|
H:ASN1005
|
4.7
|
12.4
|
1.0
|
|
CA
|
H:ASN998
|
4.8
|
13.1
|
1.0
|
|
C
|
H:ASN998
|
4.9
|
13.1
|
1.0
|
|
CA
|
H:ASP1000
|
4.9
|
15.4
|
1.0
|
|
N
|
H:GLY1001
|
5.0
|
23.6
|
1.0
|
|
Reference:
J.Zeng,
Z.Shu,
Q.Liang,
J.Zhang,
W.Wu,
X.Wang,
A.Zhou.
Structural Basis of Von Willebrand Factor Multimerization and Tubular Storage. Blood V. 139 3314 2022.
ISSN: ESSN 1528-0020
PubMed: 35148377
DOI: 10.1182/BLOOD.2021014729
Page generated: Tue Apr 4 19:12:53 2023
|
