Atomistry » Calcium » PDB 1dva-1edh » 1dva
Atomistry »
  Calcium »
    PDB 1dva-1edh »
      1dva »

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: Thu Jul 11 07:41:22 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy