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

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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 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 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 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 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 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 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 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 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 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 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

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