Calcium in PDB 6n29: Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly

The structure of Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly, PDB code: 6n29 was solved by X.Dong, J.W.Arndt, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	174.690, 174.690, 104.620, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.2

The binding sites of Calcium atom in the Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly (pdb code 6n29). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly, PDB code: 6n29:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1304 b:80.0 occ:1.00 OD1 A:ASP1000 2.2 82.2 1.0 OD1 A:ASP1006 2.3 69.5 1.0 OD1 A:ASN998 2.3 93.5 1.0 OD1 A:ASN1005 2.3 0.9 1.0 O A:ILE1002 2.3 89.5 1.0 OD2 A:ASP879 2.4 77.5 1.0 CG A:ASP1006 3.3 77.1 1.0 CG A:ASP1000 3.3 79.0 1.0 CG A:ASN1005 3.4 94.6 1.0 C A:ILE1002 3.5 92.4 1.0 CG A:ASN998 3.5 84.8 1.0 CG A:ASP879 3.5 76.5 1.0 OD2 A:ASP1000 3.8 87.7 1.0 OD2 A:ASP1006 3.8 76.5 1.0 ND2 A:ASN1005 4.0 86.0 1.0 N A:ILE1002 4.0 98.1 1.0 ND2 A:ASN998 4.1 81.7 1.0 N A:ASP1000 4.1 60.8 1.0 CB A:ASP879 4.1 75.3 1.0 N A:ASP1006 4.1 80.9 1.0 CA A:ILE1002 4.2 94.4 1.0 O A:HOH1415 4.3 67.7 1.0 N A:PHE999 4.3 72.3 1.0 CA A:ASP1006 4.3 79.7 1.0 CB A:ILE1002 4.4 92.1 1.0 C A:ASN1005 4.4 90.8 1.0 CB A:ASP1006 4.4 75.3 1.0 N A:ASN998 4.4 79.3 1.0 CB A:ASP1000 4.4 80.6 1.0 N A:GLN1003 4.5 83.9 1.0 OD1 A:ASP879 4.6 73.7 1.0 CB A:ASN998 4.7 79.3 1.0 CA A:ASP1000 4.7 73.1 1.0 CA A:GLN1003 4.7 70.3 1.0 CB A:ASN1005 4.7 83.6 1.0 O A:ASN1005 4.7 91.8 1.0 N A:ASN1005 4.8 92.7 1.0 C A:ASN998 4.8 81.8 1.0 N A:GLY1001 4.8 77.6 1.0 CA A:ASN998 4.8 81.5 1.0 CA A:ASN1005 4.8 91.5 1.0 C A:ASP1000 4.9 78.2 1.0 C A:GLN1003 4.9 77.9 1.0 O A:GLN1003 4.9 70.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1305 b:0.4 occ:1.00 O A:HOH1408 2.5 88.6 1.0 OE2 A:GLU1161 2.5 0.9 1.0 O A:HOH1428 2.5 96.9 1.0 O A:HOH1438 2.6 99.6 1.0 O A:GLY1203 2.6 0.3 1.0 CD A:GLU1161 3.4 0.8 1.0 OE1 A:GLU1161 3.6 0.6 1.0 C A:GLY1203 3.8 89.3 1.0 CA A:GLY1203 4.6 95.7 1.0 O A:HOH1442 4.6 96.6 1.0 CG A:GLU1161 4.7 78.6 1.0 N A:ARG1204 4.8 76.0 1.0 CA A:ARG1204 4.9 81.6 1.0 O A:HOH1430 4.9 90.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Monomeric Von Willebrand Factor D`D3 Assembly within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1303 b:0.8 occ:1.00 OD1 B:ASN1005 2.2 94.6 1.0 O B:ILE1002 2.3 83.6 1.0 OD1 B:ASP1006 2.3 62.2 1.0 OD2 B:ASP879 2.3 73.5 1.0 OD1 B:ASN998 2.3 85.9 1.0 OD1 B:ASP1000 2.3 74.2 1.0 CG B:ASP1006 3.3 70.7 1.0 CG B:ASN1005 3.4 74.8 1.0 CG B:ASP1000 3.4 66.8 1.0 C B:ILE1002 3.4 76.1 1.0 CG B:ASP879 3.5 67.5 1.0 CG B:ASN998 3.5 77.1 1.0 OD2 B:ASP1000 3.9 70.5 1.0 ND2 B:ASN1005 3.9 74.9 1.0 OD2 B:ASP1006 3.9 74.2 1.0 CB B:ASP879 4.0 59.6 1.0 N B:ILE1002 4.1 73.0 1.0 N B:ASP1006 4.1 71.3 1.0 CA B:ILE1002 4.1 68.4 1.0 ND2 B:ASN998 4.1 76.3 1.0 N B:ASP1000 4.2 58.3 1.0 CB B:ILE1002 4.2 66.6 1.0 N B:PHE999 4.3 66.5 1.0 O B:HOH1422 4.3 56.9 1.0 N B:ASN998 4.3 66.7 1.0 CA B:ASP1006 4.3 64.0 1.0 C B:ASN1005 4.3 78.7 1.0 CB B:ASP1006 4.4 68.7 1.0 OD1 B:ASP879 4.5 72.7 1.0 N B:GLN1003 4.5 78.1 1.0 CB B:ASP1000 4.5 58.6 1.0 CB B:ASN1005 4.6 59.0 1.0 CB B:ASN998 4.6 59.5 1.0 O B:ASN1005 4.7 75.6 1.0 N B:ASN1005 4.7 68.8 1.0 C B:ASN998 4.7 71.5 1.0 CA B:GLN1003 4.7 73.7 1.0 CA B:ASN998 4.8 62.4 1.0 CA B:ASN1005 4.8 70.5 1.0 CA B:ASP1000 4.8 63.1 1.0 O B:GLN1003 4.9 77.6 1.0 C B:GLN1003 4.9 75.1 1.0 N B:GLY1001 4.9 64.6 1.0 CG2 B:ILE1002 5.0 56.8 1.0

X.Dong, N.C.Leksa, E.S.Chhabra, J.W.Arndt, Q.Lu, K.E.Knockenhauer, R.T.Peters, T.A.Springer. The Von Willebrand Factor D'D3 Assembly and Structural Principles For Factor VIII Binding and Concatemer Biogenesis. Blood V. 133 1523 2019.
ISSN: ESSN 1528-0020
PubMed: 30642920
DOI: 10.1182/BLOOD-2018-10-876300