Calcium in PDB 7pnf: Vwf Tubules of D1D2D'D3 Domains

The binding sites of Calcium atom in the Vwf Tubules of D1D2D'D3 Domains (pdb code 7pnf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Vwf Tubules of D1D2D'D3 Domains, PDB code: 7pnf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Vwf Tubules of D1D2D'D3 Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Vwf Tubules of D1D2D'D3 Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1305 b:28.6 occ:1.00 OD1 B:ASP172 2.2 34.8 1.0 OD1 B:ASN166 2.2 32.2 1.0 OD2 B:ASP172 2.5 34.8 1.0 OD1 B:ASN164 2.5 27.6 1.0 OD2 B:ASP47 2.5 24.2 1.0 CG B:ASP172 2.7 34.8 1.0 O B:PHE168 2.8 40.3 1.0 H B:ASN166 2.9 32.2 1.0 O B:ASN166 3.1 32.2 1.0 CG B:ASN166 3.2 32.2 1.0 O B:ASN164 3.4 27.6 1.0 HA B:ALA169 3.7 36.8 1.0 CG B:ASN164 3.7 27.6 1.0 N B:ASN166 3.7 32.2 1.0 HD21 B:ASN166 3.7 32.2 1.0 CG B:ASP47 3.8 24.2 1.0 ND2 B:ASN166 3.9 32.2 1.0 C B:ASN166 3.9 32.2 1.0 OD1 B:ASP171 4.0 35.9 1.0 C B:PHE168 4.0 40.3 1.0 C B:ASN164 4.0 27.6 1.0 CB B:ASP172 4.2 34.8 1.0 CA B:ASN166 4.2 32.2 1.0 CB B:ASN166 4.3 32.2 1.0 HD21 B:ASN164 4.3 27.6 1.0 HB2 B:ASP47 4.3 24.2 1.0 ND2 B:ASN164 4.5 27.6 1.0 HA B:ASP172 4.5 34.8 1.0 CA B:ALA169 4.5 36.8 1.0 HA B:PHE165 4.5 29.1 1.0 HB3 B:ASP172 4.5 34.8 1.0 CB B:ASP47 4.6 24.2 1.0 OD1 B:ASP47 4.6 24.2 1.0 HB2 B:ASP172 4.7 34.8 1.0 N B:PHE165 4.7 29.1 1.0 HD22 B:ASN166 4.7 32.2 1.0 CB B:ASN164 4.7 27.6 1.0 N B:ALA169 4.7 36.8 1.0 H B:ASN164 4.7 27.6 1.0 C B:PHE165 4.7 29.1 1.0 CA B:ASN164 4.8 27.6 1.0 HB3 B:ASP47 4.8 24.2 1.0 CA B:ASP172 4.8 34.8 1.0 HB3 B:ASN166 4.9 32.2 1.0 HB3 B:PHE168 4.9 40.3 1.0 HB2 B:ASN164 4.9 27.6 1.0 CA B:PHE165 4.9 29.1 1.0 HB2 B:ASN166 4.9 32.2 1.0 N B:PHE168 4.9 40.3 1.0 H B:ASP171 4.9 35.9 1.0

Calcium binding site 2 out of 6 in the Vwf Tubules of D1D2D'D3 Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Vwf Tubules of D1D2D'D3 Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1306 b:35.6 occ:1.00 O B:ASN530 2.4 35.6 1.0 OD1 B:ASN528 2.6 35.6 1.0 OD2 B:ASP400 2.6 35.6 1.0 OD1 B:ASP533 2.7 29.7 1.0 OD1 B:ASN526 2.8 19.2 1.0 OD1 B:ASP534 3.1 20.3 1.0 C B:ASN530 3.6 35.6 1.0 CG B:ASN528 3.7 35.6 1.0 CG B:ASP533 3.8 29.7 1.0 O B:ASN526 3.8 19.2 1.0 CG B:ASP400 3.8 35.6 1.0 HD21 B:ASN528 3.9 35.6 1.0 H B:ASN528 3.9 35.6 1.0 HA B:GLN531 3.9 35.6 1.0 CG B:ASN526 4.0 19.2 1.0 H B:ASN530 4.0 35.6 1.0 HB3 B:ASN530 4.1 35.6 1.0 H B:ASP533 4.1 29.7 1.0 OD2 B:ASP533 4.2 29.7 1.0 CG B:ASP534 4.2 20.3 1.0 ND2 B:ASN528 4.2 35.6 1.0 O B:ASN528 4.2 35.6 1.0 HA B:ASP534 4.3 20.3 1.0 OD1 B:ASP400 4.3 35.6 1.0 HD21 B:ASN526 4.4 19.2 1.0 N B:ASN530 4.4 35.6 1.0 O B:ASP533 4.4 29.7 1.0 C B:ASN526 4.5 19.2 1.0 CA B:ASN530 4.5 35.6 1.0 N B:ASN528 4.5 35.6 1.0 C B:ASP533 4.6 29.7 1.0 N B:GLN531 4.6 35.6 1.0 ND2 B:ASN526 4.6 19.2 1.0 C B:ASN528 4.6 35.6 1.0 CA B:GLN531 4.7 35.6 1.0 CB B:ASN530 4.7 35.6 1.0 H B:ASN526 4.8 19.2 1.0 OD2 B:ASP534 4.8 20.3 1.0 N B:ASP534 4.8 20.3 1.0 HB2 B:ASP400 4.8 35.6 1.0 N B:ASP533 4.9 29.7 1.0 CB B:ASN528 4.9 35.6 1.0 CA B:ASP534 4.9 20.3 1.0 CA B:ASN528 4.9 35.6 1.0 CB B:ASP400 4.9 35.6 1.0 CB B:ASP533 5.0 29.7 1.0

Calcium binding site 3 out of 6 in the Vwf Tubules of D1D2D'D3 Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Vwf Tubules of D1D2D'D3 Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1307 b:20.2 occ:1.00 OD1 B:ASP1006 2.1 35.6 1.0 OD2 B:ASP1006 2.2 35.6 1.0 OD1 B:ASP1000 2.2 27.1 1.0 CG B:ASP1006 2.4 35.6 1.0 CG B:ASP1000 2.7 27.1 1.0 H B:ASP1000 2.7 27.1 1.0 OD1 B:ASN998 2.7 35.6 1.0 H B:ILE1002 2.8 35.6 1.0 O B:ILE1002 2.8 35.6 1.0 OD2 B:ASP1000 2.9 27.1 1.0 N B:ASP1000 3.4 27.1 1.0 HB B:ILE1002 3.4 35.6 1.0 H B:GLY1001 3.4 31.8 1.0 OD1 B:ASN1005 3.5 21.4 1.0 N B:ILE1002 3.6 35.6 1.0 OD2 B:ASP879 3.7 29.7 1.0 C B:ILE1002 3.8 35.6 1.0 CB B:ASP1000 3.8 27.1 1.0 N B:GLY1001 3.9 31.8 1.0 H B:PHE999 3.9 35.6 1.0 CG B:ASN998 3.9 35.6 1.0 CA B:ASP1000 4.0 27.1 1.0 CB B:ASP1006 4.0 35.6 1.0 CA B:ILE1002 4.1 35.6 1.0 H B:ASN998 4.1 35.6 1.0 N B:PHE999 4.1 35.6 1.0 HB3 B:ASP1000 4.1 27.1 1.0 C B:ASP1000 4.2 27.1 1.0 CB B:ILE1002 4.2 35.6 1.0 HD21 B:ASN998 4.3 35.6 1.0 HB3 B:ASP1006 4.4 35.6 1.0 HB2 B:ASP1006 4.4 35.6 1.0 HD21 B:ASN1005 4.4 21.4 1.0 C B:PHE999 4.4 35.6 1.0 HA B:PHE999 4.5 35.6 1.0 C B:ASN998 4.6 35.6 1.0 HB2 B:ASP1000 4.6 27.1 1.0 CG B:ASN1005 4.6 21.4 1.0 ND2 B:ASN998 4.6 35.6 1.0 HG22 B:ILE1002 4.6 35.6 1.0 HA B:ASP1006 4.6 35.6 1.0 CG B:ASP879 4.6 29.7 1.0 CA B:PHE999 4.6 35.6 1.0 C B:GLY1001 4.7 31.8 1.0 CA B:ASP1006 4.7 35.6 1.0 H B:ASP1006 4.8 35.6 1.0 CA B:GLY1001 4.8 31.8 1.0 N B:ASP1006 4.8 35.6 1.0 N B:ASN998 4.8 35.6 1.0 ND2 B:ASN1005 4.9 21.4 1.0 HA B:ASP1000 4.9 27.1 1.0 HB2 B:ASP879 4.9 29.7 1.0 HA B:GLN1003 4.9 35.6 1.0

Calcium binding site 4 out of 6 in the Vwf Tubules of D1D2D'D3 Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Vwf Tubules of D1D2D'D3 Domains within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1305 b:47.8 occ:1.00 HB3 D:ASP172 2.0 59.6 1.0 OD1 D:ASN166 2.3 54.5 1.0 OD1 D:ASN164 2.5 49.8 1.0 O D:PHE168 2.8 62.3 1.0 CB D:ASP172 2.9 59.6 1.0 HD21 D:ASN166 3.1 54.5 1.0 CG D:ASN166 3.2 54.5 1.0 HB2 D:ASP172 3.4 59.6 1.0 HA D:ALA169 3.5 62.7 1.0 ND2 D:ASN166 3.5 54.5 1.0 CG D:ASP172 3.6 59.6 1.0 O D:ASN164 3.6 49.8 1.0 OD1 D:ASP171 3.7 64.5 1.0 HB2 D:ASP47 3.7 47.1 1.0 HA D:ASP172 3.7 59.6 1.0 CG D:ASN164 3.7 49.8 1.0 CA D:ASP172 3.7 59.6 1.0 N D:ASP172 3.9 59.6 1.0 HD21 D:ASN164 4.0 49.8 1.0 HB3 D:ASP47 4.0 47.1 1.0 C D:PHE168 4.0 62.3 1.0 OD1 D:ASP172 4.0 59.6 1.0 OD2 D:ASP47 4.0 47.1 1.0 H D:ASN166 4.1 54.5 1.0 H D:ASP171 4.2 64.5 1.0 H D:ASP172 4.2 59.6 1.0 C D:ASP171 4.2 64.5 1.0 CB D:ASP47 4.2 47.1 1.0 ND2 D:ASN164 4.3 49.8 1.0 O D:ASP171 4.3 64.5 1.0 OD2 D:ASP172 4.3 59.6 1.0 CA D:ALA169 4.3 62.7 1.0 HD22 D:ASN166 4.4 54.5 1.0 O D:ASN166 4.4 54.5 1.0 C D:ASN164 4.5 49.8 1.0 CG D:ASP47 4.6 47.1 1.0 CB D:ASN166 4.6 54.5 1.0 N D:ALA169 4.6 62.7 1.0 H D:ASN164 4.7 49.8 1.0 N D:ASN166 4.7 54.5 1.0 C D:ALA169 4.7 62.7 1.0 N D:ASP171 4.7 64.5 1.0 CG D:ASP171 4.8 64.5 1.0 CB D:ASN164 4.9 49.8 1.0 C D:ASN166 4.9 54.5 1.0 N D:ASN164 4.9 49.8 1.0 CA D:ASN166 5.0 54.5 1.0

Calcium binding site 5 out of 6 in the Vwf Tubules of D1D2D'D3 Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Vwf Tubules of D1D2D'D3 Domains within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1306 b:28.2 occ:1.00 O D:ASN530 2.4 24.5 1.0 OD1 D:ASN526 2.4 23.4 1.0 OD1 D:ASN528 2.6 25.5 1.0 OD1 D:ASP533 2.7 27.9 1.0 OD1 D:ASP534 2.7 25.1 1.0 OD2 D:ASP400 3.4 25.3 1.0 O D:ASN526 3.5 23.4 1.0 CG D:ASN526 3.5 23.4 1.0 C D:ASN530 3.6 24.5 1.0 CG D:ASN528 3.7 25.5 1.0 CG D:ASP533 3.7 27.9 1.0 HD21 D:ASN528 3.8 25.5 1.0 CG D:ASP534 3.8 25.1 1.0 HA D:GLN531 3.9 24.7 1.0 HA D:ASP534 3.9 25.1 1.0 H D:ASN530 3.9 24.5 1.0 HB3 D:ASN530 4.1 24.5 1.0 HD21 D:ASN526 4.1 23.4 1.0 H D:ASN528 4.1 25.5 1.0 O D:ASP533 4.1 27.9 1.0 H D:ASP533 4.1 27.9 1.0 ND2 D:ASN528 4.1 25.5 1.0 OD2 D:ASP533 4.2 27.9 1.0 ND2 D:ASN526 4.2 23.4 1.0 C D:ASN526 4.3 23.4 1.0 C D:ASP533 4.3 27.9 1.0 O D:ASN528 4.3 25.5 1.0 CG D:ASP400 4.4 25.3 1.0 N D:ASN530 4.4 24.5 1.0 OD2 D:ASP534 4.5 25.1 1.0 CA D:ASN530 4.5 24.5 1.0 N D:ASP534 4.5 25.1 1.0 N D:GLN531 4.5 24.7 1.0 CA D:ASP534 4.5 25.1 1.0 H D:ASN526 4.6 23.4 1.0 CB D:ASN526 4.6 23.4 1.0 CA D:GLN531 4.6 24.7 1.0 N D:ASN528 4.6 25.5 1.0 CB D:ASN530 4.7 24.5 1.0 CB D:ASP534 4.7 25.1 1.0 HB2 D:ASN526 4.7 23.4 1.0 OD1 D:ASP400 4.7 25.3 1.0 C D:ASN528 4.8 25.5 1.0 CA D:ASN526 4.8 23.4 1.0 N D:ASN526 4.8 23.4 1.0 N D:ASP533 4.8 27.9 1.0 CB D:ASP533 4.9 27.9 1.0 CA D:ASP533 4.9 27.9 1.0 CB D:ASN528 4.9 25.5 1.0 H D:ASP534 4.9 25.1 1.0 HD22 D:ASN528 5.0 25.5 1.0

Calcium binding site 6 out of 6 in the Vwf Tubules of D1D2D'D3 Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Vwf Tubules of D1D2D'D3 Domains within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1307 b:24.0 occ:1.00 H D:ASP1000 2.3 30.3 1.0 OD2 D:ASP1006 2.3 24.9 1.0 OD1 D:ASP1006 2.3 24.9 1.0 OD1 D:ASP1000 2.3 30.3 1.0 O D:ILE1002 2.5 26.1 1.0 CG D:ASP1006 2.6 24.9 1.0 H D:ILE1002 2.9 26.1 1.0 OD2 D:ASP879 2.9 22.7 1.0 OD1 D:ASN998 2.9 27.7 1.0 CG D:ASP1000 3.0 30.3 1.0 N D:ASP1000 3.1 30.3 1.0 H D:PHE999 3.4 24.1 1.0 H D:GLY1001 3.4 26.4 1.0 OD2 D:ASP1000 3.4 30.3 1.0 N D:ILE1002 3.6 26.1 1.0 C D:ILE1002 3.6 26.1 1.0 N D:PHE999 3.7 24.1 1.0 OD1 D:ASN1005 3.8 26.1 1.0 N D:GLY1001 3.8 26.4 1.0 CA D:ASP1000 3.8 30.3 1.0 HA D:PHE999 3.8 24.1 1.0 CG D:ASP879 3.9 22.7 1.0 HB D:ILE1002 3.9 26.1 1.0 CB D:ASP1000 3.9 30.3 1.0 C D:ASP1000 4.1 30.3 1.0 C D:PHE999 4.1 24.1 1.0 CA D:ILE1002 4.1 26.1 1.0 CA D:PHE999 4.1 24.1 1.0 CB D:ASP1006 4.1 24.9 1.0 H D:ASN998 4.1 27.7 1.0 CG D:ASN998 4.1 27.7 1.0 HB3 D:ASP1000 4.3 30.3 1.0 HB2 D:ASP879 4.4 22.7 1.0 C D:ASN998 4.4 27.7 1.0 HB2 D:ASP1006 4.5 24.9 1.0 C D:GLY1001 4.5 26.4 1.0 OD1 D:ASP879 4.5 22.7 1.0 CB D:ILE1002 4.5 26.1 1.0 HB3 D:ASP1006 4.5 24.9 1.0 HA D:GLN1003 4.6 19.6 1.0 HD21 D:ASN998 4.7 27.7 1.0 CA D:GLY1001 4.7 26.4 1.0 CB D:ASP879 4.7 22.7 1.0 HB2 D:ASP1000 4.7 30.3 1.0 HD21 D:ASN1005 4.7 26.1 1.0 N D:ASN998 4.7 27.7 1.0 HA D:ASP1000 4.7 30.3 1.0 N D:GLN1003 4.8 19.6 1.0 HA D:ASP1006 4.8 24.9 1.0 CG D:ASN1005 4.8 26.1 1.0 H D:ASP1006 4.9 24.9 1.0 ND2 D:ASN998 4.9 27.7 1.0 CA D:ASP1006 4.9 24.9 1.0 HB3 D:ASP879 5.0 22.7 1.0 O D:ASP1000 5.0 30.3 1.0 N D:ASP1006 5.0 24.9 1.0 HA D:ILE1002 5.0 26.1 1.0 CA D:ASN998 5.0 27.7 1.0

G.Javitt, D.Fass. Helical Self-Assembly of A Mucin Segment Suggests An Evolutionary Origin For Von Willebrand Factor Tubules. Proc.Natl.Acad.Sci.Usa V. 119 90119 2022.
ISSN: ESSN 1091-6490
PubMed: 35377815
DOI: 10.1073/PNAS.2116790119