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

Protein crystallography data

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

Calcium Binding Sites:

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 6n29

Go back to Calcium Binding Sites List in 6n29
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 6n29

Go back to Calcium Binding Sites List in 6n29
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 6n29

Go back to Calcium Binding Sites List in 6n29
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

Reference:

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
Page generated: Sat Dec 12 07:22:18 2020

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