Atomistry » Calcium » PDB 7wa2-7wwn » 7wpq
Atomistry »
  Calcium »
    PDB 7wa2-7wwn »
      7wpq »

Calcium in PDB 7wpq: Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units) (pdb code 7wpq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units), PDB code: 7wpq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 1 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


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 3.27 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:28.3
occ:1.00
OD2 A:ASP47 2.4 27.8 1.0
OD1 A:ASN166 2.4 31.8 1.0
O A:PHE168 2.4 39.8 1.0
CB A:ASP172 3.0 30.5 1.0
CB A:ASP47 3.0 27.8 1.0
CG A:ASP47 3.1 27.8 1.0
OD1 A:ASN164 3.1 25.6 1.0
OD2 A:ASP172 3.1 30.5 1.0
CG A:ASP172 3.3 30.5 1.0
O A:ASN164 3.4 25.6 1.0
CG A:ASN166 3.5 31.8 1.0
C A:PHE168 3.5 39.8 1.0
CA A:ALA169 3.9 34.1 1.0
ND2 A:ASN166 4.0 31.8 1.0
OD1 A:ASP171 4.0 36.7 1.0
N A:ALA169 4.1 34.1 1.0
CA A:ASP172 4.2 30.5 1.0
CG A:ASN164 4.3 25.6 1.0
CA A:ASP47 4.3 27.8 1.0
OD1 A:ASP47 4.3 27.8 1.0
OD1 A:ASP172 4.4 30.5 1.0
N A:ASP172 4.4 30.5 1.0
C A:ASN164 4.5 25.6 1.0
N A:ASN166 4.5 31.8 1.0
N A:ASP47 4.5 27.8 1.0
O A:ASN166 4.6 31.8 1.0
C A:ALA169 4.6 34.1 1.0
O A:ASP47 4.6 27.8 1.0
CA A:PHE168 4.7 39.8 1.0
C A:ASN166 4.8 31.8 1.0
CB A:ASN166 4.8 31.8 1.0
N A:PHE168 4.9 39.8 1.0
N A:ASN164 4.9 25.6 1.0
O A:ALA169 4.9 34.1 1.0
CB A:ALA169 5.0 34.1 1.0
CA A:ASN166 5.0 31.8 1.0
C A:ASP47 5.0 27.8 1.0

Calcium binding site 2 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 2 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


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 3.27 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:29.9
occ:1.00
OD1 A:ASP533 2.4 23.9 1.0
OD2 A:ASP400 2.4 23.0 1.0
OD1 A:ASN528 2.4 22.1 1.0
OD1 A:ASP534 2.5 25.4 1.0
O A:ASN530 2.8 20.1 1.0
CG A:ASP533 3.2 23.9 1.0
CG A:ASN528 3.2 22.1 1.0
OD2 A:ASP533 3.3 23.9 1.0
ND2 A:ASN528 3.4 22.1 1.0
CB A:ASN526 3.6 25.6 1.0
CG A:ASP534 3.6 25.4 1.0
CG A:ASP400 3.6 23.0 1.0
N A:ASN526 3.7 25.6 1.0
ND2 A:ASN526 3.8 25.6 1.0
C A:ASN530 4.0 20.1 1.0
CG A:ASN526 4.1 25.6 1.0
CA A:ASN526 4.1 25.6 1.0
N A:TYR527 4.2 26.7 1.0
OD2 A:ASP534 4.3 25.4 1.0
N A:ASN528 4.4 22.1 1.0
N A:ASP534 4.4 25.4 1.0
OD1 A:ASP400 4.4 23.0 1.0
CB A:ASN528 4.5 22.1 1.0
CA A:ASP534 4.5 25.4 1.0
C A:ASN526 4.5 25.6 1.0
CB A:ASP533 4.5 23.9 1.0
CB A:ASP400 4.6 23.0 1.0
N A:ASN530 4.6 20.1 1.0
C A:ASP533 4.6 23.9 1.0
CB A:ASN530 4.6 20.1 1.0
CA A:ASN530 4.6 20.1 1.0
CB A:ASP534 4.7 25.4 1.0
C A:GLY525 4.8 24.4 1.0
CA A:ASN528 4.9 22.1 1.0
CA A:ASP533 5.0 23.9 1.0
O A:ASP533 5.0 23.9 1.0
CA A:GLY525 5.0 24.4 1.0

Calcium binding site 3 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 3 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


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 3.27 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:55.5
occ:1.00
OD2 B:ASP47 2.4 34.5 1.0
OD1 B:ASN166 2.4 37.7 1.0
O B:PHE168 2.4 42.5 1.0
CB B:ASP172 3.0 36.4 1.0
CB B:ASP47 3.0 34.5 1.0
CG B:ASP47 3.1 34.5 1.0
OD1 B:ASN164 3.1 31.8 1.0
OD2 B:ASP172 3.1 36.4 1.0
CG B:ASP172 3.3 36.4 1.0
O B:ASN164 3.4 31.8 1.0
CG B:ASN166 3.5 37.7 1.0
C B:PHE168 3.5 42.5 1.0
CA B:ALA169 3.9 36.4 1.0
ND2 B:ASN166 4.0 37.7 1.0
OD1 B:ASP171 4.0 41.4 1.0
N B:ALA169 4.1 36.4 1.0
CA B:ASP172 4.2 36.4 1.0
CG B:ASN164 4.3 31.8 1.0
CA B:ASP47 4.3 34.5 1.0
OD1 B:ASP47 4.3 34.5 1.0
OD1 B:ASP172 4.4 36.4 1.0
N B:ASP172 4.4 36.4 1.0
C B:ASN164 4.5 31.8 1.0
N B:ASN166 4.5 37.7 1.0
N B:ASP47 4.5 34.5 1.0
O B:ASN166 4.6 37.7 1.0
C B:ALA169 4.6 36.4 1.0
O B:ASP47 4.6 34.5 1.0
CA B:PHE168 4.7 42.5 1.0
C B:ASN166 4.8 37.7 1.0
CB B:ASN166 4.8 37.7 1.0
N B:PHE168 4.9 42.5 1.0
N B:ASN164 4.9 31.8 1.0
O B:ALA169 4.9 36.4 1.0
CB B:ALA169 5.0 36.4 1.0
CA B:ASN166 5.0 37.7 1.0
C B:ASP47 5.0 34.5 1.0

Calcium binding site 4 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 4 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


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 3.27 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:32.9
occ:1.00
OD1 B:ASP533 2.4 24.4 1.0
OD2 B:ASP400 2.4 32.9 1.0
OD1 B:ASN528 2.4 22.1 1.0
OD1 B:ASP534 2.5 25.9 1.0
O B:ASN530 2.8 23.4 1.0
CG B:ASP533 3.2 24.4 1.0
CG B:ASN528 3.2 22.1 1.0
OD2 B:ASP533 3.3 24.4 1.0
ND2 B:ASN528 3.4 22.1 1.0
CB B:ASN526 3.6 23.4 1.0
CG B:ASP534 3.6 25.9 1.0
CG B:ASP400 3.6 32.9 1.0
N B:ASN526 3.7 23.4 1.0
ND2 B:ASN526 3.8 23.4 1.0
C B:ASN530 4.0 23.4 1.0
CG B:ASN526 4.1 23.4 1.0
CA B:ASN526 4.1 23.4 1.0
N B:TYR527 4.2 24.9 1.0
OD2 B:ASP534 4.3 25.9 1.0
N B:ASN528 4.4 22.1 1.0
N B:ASP534 4.4 25.9 1.0
OD1 B:ASP400 4.4 32.9 1.0
CB B:ASN528 4.5 22.1 1.0
CA B:ASP534 4.5 25.9 1.0
C B:ASN526 4.5 23.4 1.0
CB B:ASP533 4.5 24.4 1.0
CB B:ASP400 4.6 32.9 1.0
N B:ASN530 4.6 23.4 1.0
C B:ASP533 4.6 24.4 1.0
CB B:ASN530 4.6 23.4 1.0
CA B:ASN530 4.6 23.4 1.0
CB B:ASP534 4.7 25.9 1.0
C B:GLY525 4.8 24.2 1.0
CA B:ASN528 4.9 22.1 1.0
CA B:ASP533 5.0 24.4 1.0
O B:ASP533 5.0 24.4 1.0
CA B:GLY525 5.0 24.2 1.0

Calcium binding site 5 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 5 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


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 3.27 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1304

b:16.4
occ:1.00
OD1 C:ASP1006 2.3 18.9 1.0
OD1 C:ASN1005 2.3 20.2 1.0
O C:ILE1002 2.4 19.4 1.0
OD1 C:ASN998 2.4 24.5 1.0
OD1 C:ASP1000 2.4 22.5 1.0
OD2 C:ASP879 2.4 18.2 1.0
CG C:ASP1006 3.2 18.9 1.0
CG C:ASP1000 3.2 22.5 1.0
CG C:ASN998 3.4 24.5 1.0
CG C:ASN1005 3.5 20.2 1.0
OD2 C:ASP1000 3.5 22.5 1.0
C C:ILE1002 3.6 19.4 1.0
CG C:ASP879 3.6 18.2 1.0
OD2 C:ASP1006 3.6 18.9 1.0
ND2 C:ASN998 3.8 24.5 1.0
C C:ASN1005 4.1 20.2 1.0
N C:ASP1006 4.1 18.9 1.0
ND2 C:ASN1005 4.2 20.2 1.0
O C:ASN1005 4.2 20.2 1.0
CB C:ASP879 4.3 18.2 1.0
N C:ASP1000 4.3 22.5 1.0
CB C:ASP1006 4.4 18.9 1.0
CA C:ASP1006 4.4 18.9 1.0
N C:ASN998 4.4 24.5 1.0
N C:PHE999 4.4 26.8 1.0
CA C:ILE1002 4.5 19.4 1.0
N C:GLN1003 4.5 18.1 1.0
CB C:ASP1000 4.5 22.5 1.0
N C:ILE1002 4.5 19.4 1.0
N C:ASN1005 4.6 20.2 1.0
OD1 C:ASP879 4.6 18.2 1.0
CB C:ILE1002 4.6 19.4 1.0
CB C:ASN1005 4.6 20.2 1.0
CA C:ASN1005 4.6 20.2 1.0
CB C:ASN998 4.7 24.5 1.0
CA C:GLN1003 4.7 18.1 1.0
N C:GLY1001 4.8 21.1 1.0
CA C:ASP1000 4.9 22.5 1.0
CA C:ASN998 4.9 24.5 1.0
C C:GLN1003 5.0 18.1 1.0
C C:ASN998 5.0 24.5 1.0

Calcium binding site 6 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 6 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


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 3.27 Angstron Resolution (2 Units) within 5.0Å range:

Calcium binding site 7 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 7 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1304

b:32.9
occ:1.00
OD1 D:ASP1006 2.3 16.5 1.0
OD1 D:ASN1005 2.3 20.7 1.0
O D:ILE1002 2.4 20.6 1.0
OD1 D:ASN998 2.4 23.7 1.0
OD1 D:ASP1000 2.4 23.1 1.0
OD2 D:ASP879 2.4 15.9 1.0
CG D:ASP1006 3.2 16.5 1.0
CG D:ASP1000 3.2 23.1 1.0
CG D:ASN998 3.4 23.7 1.0
CG D:ASN1005 3.5 20.7 1.0
OD2 D:ASP1000 3.5 23.1 1.0
C D:ILE1002 3.6 20.6 1.0
CG D:ASP879 3.6 15.9 1.0
OD2 D:ASP1006 3.6 16.5 1.0
ND2 D:ASN998 3.8 23.7 1.0
C D:ASN1005 4.1 20.7 1.0
N D:ASP1006 4.1 16.5 1.0
ND2 D:ASN1005 4.2 20.7 1.0
O D:ASN1005 4.2 20.7 1.0
CB D:ASP879 4.3 15.9 1.0
N D:ASP1000 4.3 23.1 1.0
CB D:ASP1006 4.4 16.5 1.0
CA D:ASP1006 4.4 16.5 1.0
N D:ASN998 4.4 23.7 1.0
N D:PHE999 4.4 25.0 1.0
CA D:ILE1002 4.5 20.6 1.0
N D:GLN1003 4.5 19.5 1.0
CB D:ASP1000 4.5 23.1 1.0
N D:ILE1002 4.5 20.6 1.0
N D:ASN1005 4.6 20.7 1.0
OD1 D:ASP879 4.6 15.9 1.0
CB D:ILE1002 4.6 20.6 1.0
CB D:ASN1005 4.6 20.7 1.0
CA D:ASN1005 4.6 20.7 1.0
CB D:ASN998 4.7 23.7 1.0
CA D:GLN1003 4.7 19.5 1.0
N D:GLY1001 4.8 22.2 1.0
CA D:ASP1000 4.9 23.1 1.0
CA D:ASN998 4.9 23.7 1.0
C D:GLN1003 5.0 19.5 1.0
C D:ASN998 5.0 23.7 1.0

Calcium binding site 8 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 8 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units) within 5.0Å range:

Calcium binding site 9 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 9 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca803

b:50.3
occ:1.00
OD2 E:ASP47 2.4 29.3 1.0
OD1 E:ASN166 2.4 31.4 1.0
O E:PHE168 2.4 33.4 1.0
CB E:ASP172 3.0 30.6 1.0
CB E:ASP47 3.0 29.3 1.0
CG E:ASP47 3.1 29.3 1.0
OD1 E:ASN164 3.1 28.1 1.0
OD2 E:ASP172 3.1 30.6 1.0
CG E:ASP172 3.3 30.6 1.0
O E:ASN164 3.4 28.1 1.0
CG E:ASN166 3.5 31.4 1.0
C E:PHE168 3.5 33.4 1.0
CA E:ALA169 3.9 30.6 1.0
ND2 E:ASN166 4.0 31.4 1.0
OD1 E:ASP171 4.0 33.8 1.0
N E:ALA169 4.1 30.6 1.0
CA E:ASP172 4.2 30.6 1.0
CG E:ASN164 4.3 28.1 1.0
CA E:ASP47 4.3 29.3 1.0
OD1 E:ASP47 4.3 29.3 1.0
OD1 E:ASP172 4.3 30.6 1.0
N E:ASP172 4.4 30.6 1.0
C E:ASN164 4.5 28.1 1.0
N E:ASN166 4.5 31.4 1.0
N E:ASP47 4.5 29.3 1.0
O E:ASN166 4.6 31.4 1.0
C E:ALA169 4.6 30.6 1.0
O E:ASP47 4.6 29.3 1.0
CA E:PHE168 4.7 33.4 1.0
C E:ASN166 4.8 31.4 1.0
CB E:ASN166 4.8 31.4 1.0
N E:PHE168 4.9 33.4 1.0
N E:ASN164 4.9 28.1 1.0
O E:ALA169 4.9 30.6 1.0
CB E:ALA169 5.0 30.6 1.0
CA E:ASN166 5.0 31.4 1.0
C E:ASP47 5.0 29.3 1.0

Calcium binding site 10 out of 16 in 7wpq

Go back to Calcium Binding Sites List in 7wpq
Calcium binding site 10 out of 16 in the Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of Vwf D'D3 Dimer Complexed with D1D2 at 3.27 Angstron Resolution (2 Units) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca804

b:32.9
occ:1.00
OD1 E:ASP533 2.4 25.6 1.0
OD2 E:ASP400 2.4 32.9 1.0
OD1 E:ASN528 2.4 21.5 1.0
OD1 E:ASP534 2.5 29.2 1.0
O E:ASN530 2.8 22.7 1.0
CG E:ASP533 3.2 25.6 1.0
CG E:ASN528 3.2 21.5 1.0
OD2 E:ASP533 3.3 25.6 1.0
ND2 E:ASN528 3.4 21.5 1.0
CB E:ASN526 3.6 23.4 1.0
CG E:ASP534 3.6 29.2 1.0
CG E:ASP400 3.6 32.9 1.0
N E:ASN526 3.7 23.4 1.0
ND2 E:ASN526 3.8 23.4 1.0
C E:ASN530 4.0 22.7 1.0
CG E:ASN526 4.1 23.4 1.0
CA E:ASN526 4.1 23.4 1.0
N E:TYR527 4.2 24.3 1.0
OD2 E:ASP534 4.3 29.2 1.0
N E:ASN528 4.4 21.5 1.0
N E:ASP534 4.4 29.2 1.0
OD1 E:ASP400 4.4 32.9 1.0
CB E:ASN528 4.5 21.5 1.0
CA E:ASP534 4.5 29.2 1.0
C E:ASN526 4.5 23.4 1.0
CB E:ASP533 4.5 25.6 1.0
CB E:ASP400 4.6 32.9 1.0
N E:ASN530 4.6 22.7 1.0
C E:ASP533 4.6 25.6 1.0
CB E:ASN530 4.6 22.7 1.0
CA E:ASN530 4.6 22.7 1.0
CB E:ASP534 4.7 29.2 1.0
C E:GLY525 4.8 22.0 1.0
CA E:ASN528 4.9 21.5 1.0
CA E:ASP533 5.0 25.6 1.0
O E:ASP533 5.0 25.6 1.0
CA E:GLY525 5.0 22.0 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: Fri Jul 19 05:48:09 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy