Calcium in PDB 7wn4: Cryo-Em Structure of Vwf D'D3 Dimer (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit)
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Vwf D'D3 Dimer (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit)
(pdb code 7wn4). 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 (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit), PDB code: 7wn4:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7wn4
Go back to
Calcium Binding Sites List in 7wn4
Calcium binding site 1 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer (Wild Type) Complexed with D1D2 at 3.4 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 (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca801
b:56.2
occ:1.00
|
OD1
|
E:ASN166
|
2.2
|
47.6
|
1.0
|
OD1
|
E:ASP172
|
2.2
|
47.9
|
1.0
|
OD1
|
E:ASP171
|
2.3
|
52.7
|
1.0
|
O
|
E:PHE168
|
2.5
|
54.1
|
1.0
|
OD1
|
E:ASN164
|
2.6
|
41.4
|
1.0
|
CG
|
E:ASN166
|
2.9
|
47.6
|
1.0
|
ND2
|
E:ASN166
|
2.9
|
47.6
|
1.0
|
CG
|
E:ASP172
|
3.2
|
47.9
|
1.0
|
CG
|
E:ASP171
|
3.3
|
52.7
|
1.0
|
OD2
|
E:ASP47
|
3.3
|
43.0
|
1.0
|
O
|
E:ASP171
|
3.5
|
52.7
|
1.0
|
C
|
E:ASP171
|
3.5
|
52.7
|
1.0
|
C
|
E:PHE168
|
3.7
|
54.1
|
1.0
|
CG
|
E:ASN164
|
3.7
|
41.4
|
1.0
|
N
|
E:ASP172
|
3.7
|
47.9
|
1.0
|
OD2
|
E:ASP171
|
3.9
|
52.7
|
1.0
|
CA
|
E:ASP172
|
4.0
|
47.9
|
1.0
|
OD2
|
E:ASP172
|
4.0
|
47.9
|
1.0
|
N
|
E:ASP171
|
4.1
|
52.7
|
1.0
|
CB
|
E:ASP172
|
4.1
|
47.9
|
1.0
|
ND2
|
E:ASN164
|
4.2
|
41.4
|
1.0
|
CA
|
E:ASP171
|
4.2
|
52.7
|
1.0
|
CB
|
E:ASP171
|
4.3
|
52.7
|
1.0
|
CB
|
E:ASN166
|
4.4
|
47.6
|
1.0
|
O
|
E:ASN164
|
4.5
|
41.4
|
1.0
|
CG
|
E:ASP47
|
4.5
|
43.0
|
1.0
|
N
|
E:ALA169
|
4.5
|
54.7
|
1.0
|
CA
|
E:PHE168
|
4.6
|
54.1
|
1.0
|
CA
|
E:ALA169
|
4.6
|
54.7
|
1.0
|
CB
|
E:PHE168
|
4.7
|
54.1
|
1.0
|
N
|
E:ASN166
|
4.7
|
47.6
|
1.0
|
N
|
E:PHE168
|
4.7
|
54.1
|
1.0
|
C
|
E:ASN164
|
4.9
|
41.4
|
1.0
|
N
|
E:GLU170
|
4.9
|
61.3
|
1.0
|
CB
|
E:ASN164
|
4.9
|
41.4
|
1.0
|
C
|
E:ALA169
|
4.9
|
54.7
|
1.0
|
CA
|
E:ASN166
|
4.9
|
47.6
|
1.0
|
N
|
E:ASN164
|
5.0
|
41.4
|
1.0
|
C
|
E:ASN166
|
5.0
|
47.6
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7wn4
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Calcium Binding Sites List in 7wn4
Calcium binding site 2 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer (Wild Type) Complexed with D1D2 at 3.4 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 (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca802
b:37.9
occ:1.00
|
OD1
|
E:ASP533
|
2.3
|
37.8
|
1.0
|
OD2
|
E:ASP400
|
2.4
|
42.6
|
1.0
|
OD1
|
E:ASN528
|
2.4
|
36.2
|
1.0
|
OD1
|
E:ASP534
|
2.5
|
39.4
|
1.0
|
O
|
E:ASN530
|
2.5
|
33.8
|
1.0
|
CG
|
E:ASN528
|
3.5
|
36.2
|
1.0
|
CG
|
E:ASP533
|
3.5
|
37.8
|
1.0
|
CG
|
E:ASP400
|
3.6
|
42.6
|
1.0
|
CG
|
E:ASP534
|
3.7
|
39.4
|
1.0
|
C
|
E:ASN530
|
3.7
|
33.8
|
1.0
|
CB
|
E:ASN526
|
3.9
|
37.8
|
1.0
|
ND2
|
E:ASN528
|
3.9
|
36.2
|
1.0
|
OD2
|
E:ASP533
|
4.0
|
37.8
|
1.0
|
N
|
E:ASN526
|
4.0
|
37.8
|
1.0
|
ND2
|
E:ASN526
|
4.2
|
37.8
|
1.0
|
C
|
E:ASP533
|
4.3
|
37.8
|
1.0
|
N
|
E:TYR527
|
4.3
|
36.3
|
1.0
|
N
|
E:ASN528
|
4.3
|
36.2
|
1.0
|
N
|
E:ASP534
|
4.3
|
39.4
|
1.0
|
O
|
E:ASP533
|
4.4
|
37.8
|
1.0
|
OD2
|
E:ASP534
|
4.4
|
39.4
|
1.0
|
CA
|
E:ASN526
|
4.4
|
37.8
|
1.0
|
N
|
E:ASN530
|
4.4
|
33.8
|
1.0
|
CA
|
E:ASP534
|
4.5
|
39.4
|
1.0
|
CA
|
E:ASN530
|
4.5
|
33.8
|
1.0
|
OD1
|
E:ASP400
|
4.5
|
42.6
|
1.0
|
CB
|
E:ASP400
|
4.5
|
42.6
|
1.0
|
CG
|
E:ASN526
|
4.5
|
37.8
|
1.0
|
CB
|
E:ASN530
|
4.6
|
33.8
|
1.0
|
CB
|
E:ASP534
|
4.6
|
39.4
|
1.0
|
N
|
E:ASP533
|
4.6
|
37.8
|
1.0
|
CB
|
E:ASP533
|
4.7
|
37.8
|
1.0
|
CB
|
E:ASN528
|
4.7
|
36.2
|
1.0
|
N
|
E:GLN531
|
4.7
|
34.5
|
1.0
|
C
|
E:ASN526
|
4.7
|
37.8
|
1.0
|
CA
|
E:ASP533
|
4.8
|
37.8
|
1.0
|
CA
|
E:GLN531
|
4.9
|
34.5
|
1.0
|
CA
|
E:ASN528
|
4.9
|
36.2
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7wn4
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Calcium Binding Sites List in 7wn4
Calcium binding site 3 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer (Wild Type) Complexed with D1D2 at 3.4 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 (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca1301
b:33.7
occ:1.00
|
OD1
|
F:ASP1006
|
2.3
|
31.0
|
1.0
|
OD1
|
F:ASP1000
|
2.3
|
34.0
|
1.0
|
O
|
F:ILE1002
|
2.4
|
31.4
|
1.0
|
OD1
|
F:ASN1005
|
2.4
|
30.5
|
1.0
|
OD1
|
F:ASN998
|
2.5
|
32.8
|
1.0
|
OD2
|
F:ASP879
|
2.6
|
30.7
|
1.0
|
CG
|
F:ASP1000
|
3.2
|
34.0
|
1.0
|
CG
|
F:ASP1006
|
3.3
|
31.0
|
1.0
|
OD2
|
F:ASP1000
|
3.4
|
34.0
|
1.0
|
CG
|
F:ASN1005
|
3.5
|
30.5
|
1.0
|
CG
|
F:ASN998
|
3.6
|
32.8
|
1.0
|
C
|
F:ILE1002
|
3.6
|
31.4
|
1.0
|
CG
|
F:ASP879
|
3.8
|
30.7
|
1.0
|
OD2
|
F:ASP1006
|
4.0
|
31.0
|
1.0
|
ND2
|
F:ASN1005
|
4.0
|
30.5
|
1.0
|
ND2
|
F:ASN998
|
4.1
|
32.8
|
1.0
|
N
|
F:ASP1006
|
4.2
|
31.0
|
1.0
|
C
|
F:ASN1005
|
4.2
|
30.5
|
1.0
|
CA
|
F:ASP1006
|
4.3
|
31.0
|
1.0
|
CA
|
F:ILE1002
|
4.3
|
31.4
|
1.0
|
N
|
F:ILE1002
|
4.4
|
31.4
|
1.0
|
CB
|
F:ASP1006
|
4.4
|
31.0
|
1.0
|
N
|
F:ASP1000
|
4.4
|
34.0
|
1.0
|
N
|
F:ASN998
|
4.4
|
32.8
|
1.0
|
CB
|
F:ILE1002
|
4.4
|
31.4
|
1.0
|
O
|
F:ASN1005
|
4.4
|
30.5
|
1.0
|
OD1
|
F:ASP879
|
4.5
|
30.7
|
1.0
|
N
|
F:PHE999
|
4.5
|
33.0
|
1.0
|
N
|
F:GLN1003
|
4.6
|
31.7
|
1.0
|
CB
|
F:ASP1000
|
4.6
|
34.0
|
1.0
|
CB
|
F:ASN1005
|
4.7
|
30.5
|
1.0
|
CA
|
F:GLN1003
|
4.7
|
31.7
|
1.0
|
N
|
F:ASN1005
|
4.7
|
30.5
|
1.0
|
CB
|
F:ASP879
|
4.8
|
30.7
|
1.0
|
CA
|
F:ASN1005
|
4.8
|
30.5
|
1.0
|
CB
|
F:ASN998
|
4.8
|
32.8
|
1.0
|
C
|
F:ASN998
|
4.8
|
32.8
|
1.0
|
CA
|
F:ASN998
|
4.9
|
32.8
|
1.0
|
N
|
F:GLY1001
|
5.0
|
32.7
|
1.0
|
CA
|
F:ASP1000
|
5.0
|
34.0
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7wn4
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Calcium Binding Sites List in 7wn4
Calcium binding site 4 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer (Wild Type) Complexed with D1D2 at 3.4 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 (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca801
b:55.6
occ:1.00
|
OD1
|
G:ASP172
|
2.3
|
48.4
|
1.0
|
OD1
|
G:ASN166
|
2.3
|
48.4
|
1.0
|
O
|
G:PHE168
|
2.4
|
54.4
|
1.0
|
OD1
|
G:ASP171
|
2.4
|
52.4
|
1.0
|
OD2
|
G:ASP47
|
2.9
|
45.4
|
1.0
|
CG
|
G:ASP172
|
3.1
|
48.4
|
1.0
|
CG
|
G:ASN166
|
3.2
|
48.4
|
1.0
|
OD1
|
G:ASN164
|
3.2
|
42.1
|
1.0
|
C
|
G:PHE168
|
3.3
|
54.4
|
1.0
|
ND2
|
G:ASN166
|
3.5
|
48.4
|
1.0
|
CG
|
G:ASP171
|
3.5
|
52.4
|
1.0
|
OD2
|
G:ASP172
|
3.6
|
48.4
|
1.0
|
O
|
G:ASN166
|
3.7
|
48.4
|
1.0
|
O
|
G:ASN164
|
3.8
|
42.1
|
1.0
|
C
|
G:ASP171
|
3.9
|
52.4
|
1.0
|
O
|
G:ASP171
|
4.0
|
52.4
|
1.0
|
N
|
G:ASP172
|
4.0
|
48.4
|
1.0
|
CG
|
G:ASP47
|
4.1
|
45.4
|
1.0
|
CB
|
G:PHE168
|
4.1
|
54.4
|
1.0
|
N
|
G:ALA169
|
4.1
|
52.5
|
1.0
|
CA
|
G:PHE168
|
4.2
|
54.4
|
1.0
|
CB
|
G:ASP172
|
4.2
|
48.4
|
1.0
|
N
|
G:ASP171
|
4.2
|
52.4
|
1.0
|
OD2
|
G:ASP171
|
4.2
|
52.4
|
1.0
|
CA
|
G:ASP172
|
4.2
|
48.4
|
1.0
|
CG
|
G:ASN164
|
4.2
|
42.1
|
1.0
|
CA
|
G:ALA169
|
4.3
|
52.5
|
1.0
|
CA
|
G:ASP171
|
4.4
|
52.4
|
1.0
|
N
|
G:PHE168
|
4.5
|
54.4
|
1.0
|
C
|
G:ASN166
|
4.5
|
48.4
|
1.0
|
CB
|
G:ASN166
|
4.5
|
48.4
|
1.0
|
N
|
G:GLU170
|
4.6
|
56.8
|
1.0
|
CB
|
G:ASP171
|
4.6
|
52.4
|
1.0
|
C
|
G:ALA169
|
4.6
|
52.5
|
1.0
|
N
|
G:ASN166
|
4.6
|
48.4
|
1.0
|
ND2
|
G:ASN164
|
4.7
|
42.1
|
1.0
|
CB
|
G:ASP47
|
4.7
|
45.4
|
1.0
|
CA
|
G:ASN166
|
4.8
|
48.4
|
1.0
|
C
|
G:ASN164
|
4.9
|
42.1
|
1.0
|
OD1
|
G:ASP47
|
5.0
|
45.4
|
1.0
|
|
Calcium binding site 5 out
of 6 in 7wn4
Go back to
Calcium Binding Sites List in 7wn4
Calcium binding site 5 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer (Wild Type) Complexed with D1D2 at 3.4 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 (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca802
b:37.9
occ:1.00
|
OD1
|
G:ASN526
|
2.3
|
32.7
|
1.0
|
O
|
G:ASN530
|
2.4
|
33.5
|
1.0
|
OD1
|
G:ASP534
|
2.4
|
39.6
|
1.0
|
OD2
|
G:ASP400
|
2.4
|
32.3
|
1.0
|
OD1
|
G:ASN528
|
2.4
|
33.9
|
1.0
|
OD1
|
G:ASP533
|
2.8
|
40.8
|
1.0
|
O
|
G:ASP533
|
3.2
|
40.8
|
1.0
|
CG
|
G:ASN526
|
3.3
|
32.7
|
1.0
|
CG
|
G:ASN528
|
3.5
|
33.9
|
1.0
|
CG
|
G:ASP400
|
3.5
|
32.3
|
1.0
|
CG
|
G:ASP534
|
3.5
|
39.6
|
1.0
|
C
|
G:ASN530
|
3.5
|
33.5
|
1.0
|
ND2
|
G:ASN526
|
3.7
|
32.7
|
1.0
|
C
|
G:ASP533
|
3.8
|
40.8
|
1.0
|
CG
|
G:ASP533
|
3.8
|
40.8
|
1.0
|
ND2
|
G:ASN528
|
3.9
|
33.9
|
1.0
|
OD2
|
G:ASP534
|
4.1
|
39.6
|
1.0
|
CB
|
G:ASN530
|
4.1
|
33.5
|
1.0
|
CA
|
G:ASN530
|
4.2
|
33.5
|
1.0
|
N
|
G:ASN530
|
4.2
|
33.5
|
1.0
|
OD1
|
G:ASP400
|
4.2
|
32.3
|
1.0
|
CB
|
G:ASP400
|
4.3
|
32.3
|
1.0
|
N
|
G:ASN528
|
4.4
|
33.9
|
1.0
|
N
|
G:ASP534
|
4.4
|
39.6
|
1.0
|
N
|
G:ASN526
|
4.4
|
32.7
|
1.0
|
N
|
G:ASP533
|
4.4
|
40.8
|
1.0
|
OD2
|
G:ASP533
|
4.4
|
40.8
|
1.0
|
CA
|
G:ASP533
|
4.5
|
40.8
|
1.0
|
N
|
G:TYR527
|
4.6
|
34.4
|
1.0
|
CA
|
G:ASP534
|
4.6
|
39.6
|
1.0
|
CB
|
G:ASP534
|
4.6
|
39.6
|
1.0
|
N
|
G:GLN531
|
4.6
|
34.4
|
1.0
|
CB
|
G:ASN526
|
4.7
|
32.7
|
1.0
|
CG
|
G:ASN530
|
4.7
|
33.5
|
1.0
|
CB
|
G:ASP533
|
4.7
|
40.8
|
1.0
|
CB
|
G:ASN528
|
4.8
|
33.9
|
1.0
|
C
|
G:GLN531
|
4.9
|
34.4
|
1.0
|
CA
|
G:GLN531
|
4.9
|
34.4
|
1.0
|
CA
|
G:ASN526
|
4.9
|
32.7
|
1.0
|
CA
|
G:ASN528
|
5.0
|
33.9
|
1.0
|
C
|
G:ASN526
|
5.0
|
32.7
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7wn4
Go back to
Calcium Binding Sites List in 7wn4
Calcium binding site 6 out
of 6 in the Cryo-Em Structure of Vwf D'D3 Dimer (Wild Type) Complexed with D1D2 at 3.4 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 (Wild Type) Complexed with D1D2 at 3.4 Angstron Resolution (1 Unit) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca1301
b:32.1
occ:1.00
|
OD1
|
H:ASP1006
|
2.3
|
30.1
|
1.0
|
OD1
|
H:ASP1000
|
2.3
|
32.8
|
1.0
|
OD1
|
H:ASN998
|
2.4
|
30.8
|
1.0
|
O
|
H:ILE1002
|
2.4
|
32.1
|
1.0
|
OD1
|
H:ASN1005
|
2.4
|
30.4
|
1.0
|
OD2
|
H:ASP879
|
2.5
|
30.2
|
1.0
|
CG
|
H:ASP1000
|
3.3
|
32.8
|
1.0
|
CG
|
H:ASP1006
|
3.5
|
30.1
|
1.0
|
CG
|
H:ASN998
|
3.5
|
30.8
|
1.0
|
C
|
H:ILE1002
|
3.6
|
32.1
|
1.0
|
CG
|
H:ASN1005
|
3.6
|
30.4
|
1.0
|
OD2
|
H:ASP1000
|
3.7
|
32.8
|
1.0
|
CG
|
H:ASP879
|
3.7
|
30.2
|
1.0
|
ND2
|
H:ASN998
|
4.1
|
30.8
|
1.0
|
N
|
H:ASP1006
|
4.1
|
30.1
|
1.0
|
C
|
H:ASN1005
|
4.2
|
30.4
|
1.0
|
CA
|
H:ASP1006
|
4.2
|
30.1
|
1.0
|
N
|
H:ASN998
|
4.2
|
30.8
|
1.0
|
N
|
H:ASP1000
|
4.2
|
32.8
|
1.0
|
OD2
|
H:ASP1006
|
4.3
|
30.1
|
1.0
|
O
|
H:ASN1005
|
4.3
|
30.4
|
1.0
|
ND2
|
H:ASN1005
|
4.3
|
30.4
|
1.0
|
CB
|
H:ASP1006
|
4.4
|
30.1
|
1.0
|
N
|
H:PHE999
|
4.4
|
31.5
|
1.0
|
CA
|
H:ILE1002
|
4.5
|
32.1
|
1.0
|
N
|
H:ILE1002
|
4.5
|
32.1
|
1.0
|
OD1
|
H:ASP879
|
4.5
|
30.2
|
1.0
|
N
|
H:GLN1003
|
4.6
|
30.6
|
1.0
|
CB
|
H:ASP879
|
4.6
|
30.2
|
1.0
|
CB
|
H:ILE1002
|
4.6
|
32.1
|
1.0
|
CB
|
H:ASP1000
|
4.6
|
32.8
|
1.0
|
N
|
H:ASN1005
|
4.7
|
30.4
|
1.0
|
CA
|
H:GLN1003
|
4.7
|
30.6
|
1.0
|
CA
|
H:ASN1005
|
4.8
|
30.4
|
1.0
|
CB
|
H:ASN998
|
4.8
|
30.8
|
1.0
|
CB
|
H:ASN1005
|
4.8
|
30.4
|
1.0
|
CA
|
H:ASN998
|
4.8
|
30.8
|
1.0
|
CA
|
H:ASP1000
|
4.8
|
32.8
|
1.0
|
C
|
H:ASN998
|
4.9
|
30.8
|
1.0
|
CG2
|
H:ILE1002
|
4.9
|
32.1
|
1.0
|
C
|
H:GLN1003
|
5.0
|
30.6
|
1.0
|
|
Reference:
Z.Shu,
J.Zeng,
L.Xia,
H.Cai,
A.Zhou.
Structural Mechanism of Vwf D'D3 Dimer Formation. Cell Discov V. 8 14 2022.
ISSN: ESSN 2056-5968
PubMed: 35169124
DOI: 10.1038/S41421-022-00378-2
Page generated: Fri Jul 19 05:45:22 2024
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