Calcium in PDB 3zqk: Von Willebrand Factor A2 Domain with Calcium

The structure of Von Willebrand Factor A2 Domain with Calcium, PDB code: 3zqk was solved by A.J.Jakobi, E.G.Huizinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.306 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.020, 35.540, 88.460, 90.00, 96.34, 90.00
R / Rfree (%)	15.49 / 19.96

The binding sites of Calcium atom in the Von Willebrand Factor A2 Domain with Calcium (pdb code 3zqk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Von Willebrand Factor A2 Domain with Calcium, PDB code: 3zqk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Von Willebrand Factor A2 Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Von Willebrand Factor A2 Domain with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4675 b:8.4 occ:0.63 O A:ALA1600 2.3 15.2 1.0 OD2 A:ASP1498 2.4 10.7 1.0 O A:ARG1597 2.4 14.1 1.0 OD1 A:ASP1596 2.4 14.9 1.0 OD1 A:ASN1602 2.4 10.2 1.0 O A:HOH2116 2.5 19.6 1.0 CG A:ASP1596 3.1 18.1 1.0 OD2 A:ASP1596 3.2 18.9 1.0 CG A:ASN1602 3.4 13.7 1.0 C A:ARG1597 3.4 13.3 1.0 CG A:ASP1498 3.4 12.8 1.0 C A:ALA1600 3.5 14.7 1.0 N A:ARG1597 3.8 9.1 1.0 ND2 A:ASN1602 3.9 10.5 1.0 CB A:ASP1498 3.9 7.0 1.0 N A:ALA1600 4.0 10.7 1.0 CA A:ALA1600 4.1 12.1 1.0 CB A:ALA1600 4.1 13.5 1.0 CA A:ARG1597 4.2 11.3 1.0 O A:GLU1598 4.3 22.4 1.0 N A:GLU1598 4.3 11.9 1.0 C A:PRO1601 4.4 9.7 1.0 N A:ASN1602 4.4 5.4 1.0 C A:GLU1598 4.4 20.6 1.0 CB A:ASP1596 4.4 10.1 1.0 OD1 A:ASP1498 4.5 8.7 1.0 CA A:GLU1598 4.5 18.8 1.0 O A:PRO1601 4.5 12.1 1.0 N A:PRO1601 4.6 10.8 1.0 C A:ASP1596 4.6 13.4 1.0 CB A:ASN1602 4.6 7.5 1.0 CA A:ASN1602 4.7 6.2 1.0 CB A:ARG1597 4.7 12.1 1.0 CA A:PRO1601 4.8 6.0 1.0 CA A:ASP1596 4.8 12.4 1.0 O2 A:GOL2676 4.9 21.3 1.0

Calcium binding site 2 out of 3 in the Von Willebrand Factor A2 Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Von Willebrand Factor A2 Domain with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4675 b:9.3 occ:0.65 OD1 B:ASP1596 2.4 23.2 1.0 O B:ALA1600 2.4 11.5 1.0 O B:ARG1597 2.4 11.6 1.0 OD2 B:ASP1498 2.4 12.1 1.0 OD1 B:ASN1602 2.4 10.1 1.0 O B:HOH2082 2.5 27.5 1.0 CG B:ASP1596 3.2 16.1 1.0 OD2 B:ASP1596 3.4 25.9 1.0 CG B:ASN1602 3.4 11.3 1.0 CG B:ASP1498 3.4 8.9 1.0 C B:ALA1600 3.5 12.2 1.0 C B:ARG1597 3.5 8.4 1.0 N B:ARG1597 3.8 12.5 1.0 ND2 B:ASN1602 3.8 21.6 1.0 CB B:ASP1498 3.9 5.1 1.0 CB B:ALA1600 4.0 9.1 1.0 CA B:ALA1600 4.1 12.6 1.0 O B:PRO1601 4.1 9.9 1.0 N B:ALA1600 4.1 14.7 1.0 CA B:ARG1597 4.2 9.3 1.0 C B:PRO1601 4.3 13.6 1.0 N B:GLU1598 4.5 18.6 1.0 N B:PRO1601 4.5 8.7 1.0 OD1 B:ASP1498 4.5 9.1 1.0 CB B:ASP1596 4.6 9.3 1.0 C B:ASP1596 4.7 13.9 1.0 CB B:ARG1597 4.7 7.7 1.0 N B:ASN1602 4.7 8.9 1.0 CB B:ASN1602 4.7 13.2 1.0 CA B:GLU1598 4.7 18.6 1.0 CA B:PRO1601 4.8 8.4 1.0 C B:GLU1598 4.8 17.1 1.0 CA B:ASP1596 4.9 10.9 1.0 CD2 B:PHE1590 4.9 5.8 1.0 O B:GLU1598 5.0 25.6 1.0 CA B:ASN1602 5.0 6.7 1.0

Calcium binding site 3 out of 3 in the Von Willebrand Factor A2 Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Von Willebrand Factor A2 Domain with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca4675 b:10.6 occ:0.61 OD2 C:ASP1498 2.3 15.0 1.0 OD1 C:ASP1596 2.4 19.8 1.0 O C:ARG1597 2.4 12.3 1.0 O C:ALA1600 2.4 15.4 1.0 OD1 C:ASN1602 2.4 22.5 1.0 O C:HOH2064 2.5 25.8 1.0 CG C:ASP1498 3.3 12.5 1.0 CG C:ASP1596 3.4 21.4 1.0 CG C:ASN1602 3.4 17.1 1.0 C C:ALA1600 3.5 14.4 1.0 C C:ARG1597 3.5 10.8 1.0 CB C:ASP1498 3.8 8.9 1.0 OD2 C:ASP1596 3.8 67.1 1.0 N C:ARG1597 3.8 15.7 1.0 ND2 C:ASN1602 3.8 15.2 1.0 CB C:ALA1600 4.1 15.9 1.0 CA C:ALA1600 4.1 10.4 1.0 O C:PRO1601 4.2 12.2 1.0 CA C:ARG1597 4.2 16.8 1.0 N C:ALA1600 4.2 16.3 1.0 C C:PRO1601 4.3 17.1 1.0 OD1 C:ASP1498 4.4 12.9 1.0 N C:GLU1598 4.5 20.5 1.0 N C:PRO1601 4.5 11.8 1.0 O C:GLU1598 4.5 21.6 1.0 N C:ASN1602 4.6 10.6 1.0 C C:GLU1598 4.6 28.1 1.0 CB C:ASP1596 4.6 14.6 1.0 CA C:GLU1598 4.6 22.0 1.0 CB C:ARG1597 4.7 16.3 1.0 CB C:ASN1602 4.7 8.8 1.0 C C:ASP1596 4.7 17.1 1.0 CA C:PRO1601 4.8 11.7 1.0 CA C:ASN1602 4.8 9.3 1.0 CA C:ASP1596 4.9 13.6 1.0

A.J.Jakobi, A.Mashaghi, S.J.Tans, E.G.Huizinga. Calcium Modulates Force Sensing By the Von Willebrand Factor A2 Domain. Nat.Commun. V. 2 385 2011.
ISSN: ISSN 2041-1723
PubMed: 21750539
DOI: 10.1038/NCOMMS1385