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Calcium in PDB 1dva: Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia

Enzymatic activity of Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia

All present enzymatic activity of Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia, PDB code: 1dva was solved by C.Eigenbrot, M.H.Ultsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.490, 55.260, 111.730, 90.00, 99.48, 90.00
R / Rfree (%) 22.5 / 29.5

Other elements in 1dva:

The structure of Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia (pdb code 1dva). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia, PDB code: 1dva:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1dva

Go back to Calcium Binding Sites List in 1dva
Calcium binding site 1 out of 4 in the Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia


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 the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca300

b:32.9
occ:1.00
 O H:ASP72 2.4 35.3 1.0
O H:HOH400 2.5 33.5 1.0
O H:GLU75 2.6 59.3 1.0
OD1 H:ASP77 2.9 60.7 1.0
OE1 H:GLU70 3.0 37.9 1.0
OE2 H:GLU80 3.1 30.6 1.0
C H:ASP72 3.3 32.0 1.0
OE2 H:GLU70 3.3 34.6 1.0
CD H:GLU70 3.5 31.2 1.0
N H:ASP72 3.7 37.7 1.0
C H:GLU75 3.8 60.5 1.0
CA H:ASP72 3.9 33.2 1.0
CG H:ASP77 4.1 56.9 1.0
CB H:ASP72 4.1 36.0 1.0
CD H:GLU80 4.2 30.6 1.0
N H:LEU73 4.3 28.9 1.0
CA H:HIS76 4.4 52.5 1.0
N H:HIS71 4.4 39.2 1.0
CA H:LEU73 4.5 30.7 1.0
CG H:GLU75 4.5 72.0 1.0
CG H:GLU80 4.5 30.9 1.0
N H:HIS76 4.6 54.5 1.0
N H:GLU75 4.6 53.1 1.0
OD2 H:ASP77 4.6 56.2 1.0
C H:HIS71 4.7 39.1 1.0
N H:ASP77 4.7 50.9 1.0
CA H:GLU75 4.7 59.3 1.0
C H:HIS76 4.8 52.8 1.0
CG H:GLU70 4.9 30.7 1.0
CB H:HIS71 5.0 42.4 1.0
N H:SER74 5.0 36.2 1.0
CA H:HIS71 5.0 37.6 1.0

Calcium binding site 2 out of 4 in 1dva

Go back to Calcium Binding Sites List in 1dva
Calcium binding site 2 out of 4 in the Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia


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 the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca302

b:72.5
occ:1.00
 OD2 L:ASP63 2.5 69.6 1.0
O L:GLN64 2.5 67.7 1.0
O L:GLY47 2.6 75.9 1.0
OD1 L:ASP63 2.7 62.4 1.0
CG L:ASP63 2.9 65.4 1.0
OD2 L:ASP46 3.0 80.0 1.0
OE1 L:GLN49 3.1 74.8 1.0
OD1 L:ASP46 3.3 80.0 1.0
CG L:ASP46 3.3 80.0 1.0
C L:GLN64 3.5 63.2 1.0
C L:GLY47 3.8 75.8 1.0
N L:GLN64 3.8 57.5 1.0
CA L:GLN64 4.1 58.3 1.0
N L:GLN49 4.1 73.5 1.0
CD L:GLN49 4.2 77.2 1.0
CA L:ASP48 4.3 73.3 1.0
CB L:ASP63 4.3 63.7 1.0
C L:ASP63 4.4 57.5 1.0
N L:LEU65 4.5 64.8 1.0
N L:ASP48 4.5 74.3 1.0
CB L:ASP46 4.6 77.6 1.0
N L:GLY47 4.6 78.8 1.0
C L:ASP46 4.7 78.9 1.0
CA L:LEU65 4.8 63.3 1.0
C L:ASP48 4.8 73.1 1.0
CA L:ASP63 4.8 59.5 1.0
CA L:GLY47 4.8 76.9 1.0
CB L:GLN49 4.8 75.6 1.0
N L:GLN66 4.8 67.2 1.0
O L:SER67 4.8 68.1 1.0
NE2 L:GLN49 4.9 79.7 1.0
O L:ASP46 4.9 80.0 1.0

Calcium binding site 3 out of 4 in 1dva

Go back to Calcium Binding Sites List in 1dva
Calcium binding site 3 out of 4 in the Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia


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 the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca301

b:33.3
occ:1.00
 O I:ASP72 2.5 35.2 1.0
O I:GLU75 2.6 59.4 1.0
OD1 I:ASP77 2.9 57.8 1.0
OE1 I:GLU70 2.9 37.3 1.0
OE2 I:GLU80 3.0 30.1 1.0
OE2 I:GLU70 3.2 34.5 1.0
CD I:GLU70 3.4 30.8 1.0
C I:ASP72 3.4 32.0 1.0
C I:GLU75 3.7 60.7 1.0
N I:ASP72 3.8 38.5 1.0
CA I:ASP72 4.0 34.1 1.0
CD I:GLU80 4.0 28.7 1.0
CG I:ASP77 4.1 54.6 1.0
CB I:ASP72 4.2 36.9 1.0
CA I:HIS76 4.3 52.5 1.0
N I:LEU73 4.4 28.7 1.0
CG I:GLU80 4.4 30.6 1.0
N I:HIS76 4.5 54.9 1.0
N I:HIS71 4.5 38.6 1.0
CA I:LEU73 4.5 31.4 1.0
N I:ASP77 4.6 50.1 1.0
N I:GLU75 4.6 53.1 1.0
CG I:GLU75 4.6 73.0 1.0
OD2 I:ASP77 4.6 53.4 1.0
CA I:GLU75 4.7 59.6 1.0
C I:HIS76 4.7 52.1 1.0
C I:HIS71 4.8 39.1 1.0
CG I:GLU70 4.8 31.2 1.0
N I:SER74 5.0 36.7 1.0

Calcium binding site 4 out of 4 in 1dva

Go back to Calcium Binding Sites List in 1dva
Calcium binding site 4 out of 4 in the Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor Viia within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca303

b:74.7
occ:1.00
 O M:GLY47 2.5 75.5 0.0
OD2 M:ASP63 2.6 64.8 0.0
OD1 M:ASP63 2.6 63.0 0.0
O M:GLN64 2.7 68.6 1.0
CG M:ASP63 2.9 63.0 0.0
OD2 M:ASP46 3.0 80.0 1.0
OE1 M:GLN49 3.1 74.5 0.0
OD1 M:ASP46 3.4 80.0 1.0
CG M:ASP46 3.4 80.0 1.0
C M:GLN64 3.6 64.5 1.0
C M:GLY47 3.7 75.5 0.0
N M:GLN64 3.9 58.4 1.0
N M:GLN49 4.0 73.5 1.0
CD M:GLN49 4.2 75.5 0.0
CA M:ASP48 4.2 73.0 0.0
CA M:GLN64 4.2 59.2 1.0
CB M:ASP63 4.3 62.8 0.0
N M:ASP48 4.4 74.1 0.0
C M:ASP63 4.5 59.3 1.0
N M:GLY47 4.5 78.4 0.0
N M:LEU65 4.6 66.1 1.0
CB M:ASP46 4.6 77.7 1.0
C M:ASP48 4.6 73.2 0.0
C M:ASP46 4.7 79.8 1.0
CA M:GLY47 4.7 76.6 0.0
CB M:GLN49 4.8 75.6 1.0
CA M:ASP63 4.8 60.8 1.0
NE2 M:GLN49 4.9 76.6 0.0
O M:SER67 4.9 69.4 1.0
CA M:LEU65 4.9 64.2 1.0
O M:ASP46 4.9 80.0 1.0
N M:GLN66 4.9 67.5 1.0
OD1 M:ASP48 5.0 69.3 0.0

Reference:

M.S.Dennis, C.Eigenbrot, N.J.Skelton, M.H.Ultsch, L.Santell, M.A.Dwyer, M.P.O'connell, R.A.Lazarus. Peptide Exosite Inhibitors of Factor Viia As Anticoagulants. Nature V. 404 465 2000.
ISSN: ISSN 0028-0836
PubMed: 10761907
DOI: 10.1038/35006574
Page generated: Mon Jul 7 14:30:44 2025

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