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Calcium in PDB 1dx5: Crystal Structure of the Thrombin-Thrombomodulin Complex

Enzymatic activity of Crystal Structure of the Thrombin-Thrombomodulin Complex

All present enzymatic activity of Crystal Structure of the Thrombin-Thrombomodulin Complex:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of the Thrombin-Thrombomodulin Complex, PDB code: 1dx5 was solved by P.Fuentes-Prior, Y.Iwanaga, R.Huber, R.Pagila, G.Rumennik, M.Seto, J.Morser, D.R.Light, W.Bode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 214.400, 214.400, 131.410, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 24.1

Other elements in 1dx5:

The structure of Crystal Structure of the Thrombin-Thrombomodulin Complex also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Thrombin-Thrombomodulin Complex (pdb code 1dx5). 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 Thrombin-Thrombomodulin Complex, PDB code: 1dx5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1dx5

Go back to Calcium Binding Sites List in 1dx5
Calcium binding site 1 out of 4 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


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 Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca502

b:8.5
occ:1.00
 O I:ILE424 2.4 11.1 1.0
OD1 I:ASP423 2.4 18.3 1.0
O I:LEU440 2.4 10.7 1.0
OD1 I:ASN439 2.4 9.8 1.0
O I:HOH609 2.4 14.5 1.0
OE1 I:GLU426 2.5 15.1 1.0
O I:THR443 2.8 13.4 1.0
OD2 I:ASP423 2.9 13.2 1.0
CG I:ASP423 3.0 13.6 1.0
CG I:ASN439 3.5 3.5 1.0
CD I:GLU426 3.5 10.6 1.0
C I:ILE424 3.5 9.5 1.0
C I:LEU440 3.6 11.1 1.0
OE2 I:GLU426 3.7 10.3 1.0
C I:THR443 3.8 11.7 1.0
N I:THR443 3.9 12.1 1.0
N I:LEU440 3.9 8.2 1.0
ND2 I:ASN439 3.9 4.0 1.0
N I:GLY442 4.0 11.5 1.0
N I:ILE424 4.2 8.8 1.0
CA I:THR443 4.3 12.2 1.0
CA I:ASP425 4.4 11.2 1.0
N I:ASP425 4.4 8.7 1.0
CA I:LEU440 4.4 10.2 1.0
C I:GLY442 4.5 10.1 1.0
N I:GLU426 4.5 14.2 1.0
CA I:ILE424 4.5 10.2 1.0
O I:GLY412 4.5 5.5 1.0
CB I:ASP423 4.6 7.6 1.0
N I:PRO441 4.6 10.1 1.0
CA I:PRO441 4.7 12.9 1.0
CA I:GLY442 4.7 12.8 1.0
C I:PRO441 4.7 11.9 1.0
CB I:ASN439 4.8 7.8 1.0
C I:ASP423 4.8 9.7 1.0
C I:ASN439 4.8 11.1 1.0
N I:PHE444 4.9 14.0 1.0
CA I:ASN439 4.9 9.8 1.0
CG I:GLU426 4.9 11.2 1.0
CB I:ILE424 5.0 8.0 1.0

Calcium binding site 2 out of 4 in 1dx5

Go back to Calcium Binding Sites List in 1dx5
Calcium binding site 2 out of 4 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


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 Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca502

b:7.0
occ:1.00
 O J:ILE424 2.3 10.4 1.0
O J:LEU440 2.4 12.2 1.0
OD1 J:ASP423 2.4 11.9 1.0
OD1 J:ASN439 2.4 6.4 1.0
O J:HOH609 2.5 16.8 1.0
OE1 J:GLU426 2.5 14.4 1.0
OD2 J:ASP423 2.7 12.9 1.0
O J:THR443 2.8 11.3 1.0
CG J:ASP423 2.9 10.4 1.0
CG J:ASN439 3.4 7.1 1.0
CD J:GLU426 3.4 12.0 1.0
C J:ILE424 3.5 8.6 1.0
C J:LEU440 3.6 10.2 1.0
OE2 J:GLU426 3.7 11.1 1.0
ND2 J:ASN439 3.8 6.1 1.0
C J:THR443 3.8 11.6 1.0
N J:THR443 3.9 12.3 1.0
N J:LEU440 4.0 7.8 1.0
N J:GLY442 4.0 9.3 1.0
N J:ILE424 4.2 7.9 1.0
CA J:ASP425 4.2 10.4 1.0
N J:ASP425 4.3 7.0 1.0
CA J:THR443 4.3 12.4 1.0
N J:GLU426 4.4 15.6 1.0
CA J:ILE424 4.4 7.3 1.0
CA J:LEU440 4.4 10.4 1.0
CB J:ASP423 4.5 6.8 1.0
CA J:PRO441 4.5 12.2 1.0
O J:GLY412 4.5 7.2 1.0
C J:GLY442 4.5 8.3 1.0
N J:PRO441 4.5 8.9 1.0
C J:PRO441 4.6 9.4 1.0
CA J:GLY442 4.7 7.6 1.0
C J:ASP423 4.8 8.2 1.0
CB J:ASN439 4.8 8.0 1.0
CG J:GLU426 4.9 12.9 1.0
C J:ASP425 4.9 11.3 1.0
CB J:ILE424 4.9 7.2 1.0
N J:PHE444 4.9 14.2 1.0
C J:ASN439 4.9 12.2 1.0

Calcium binding site 3 out of 4 in 1dx5

Go back to Calcium Binding Sites List in 1dx5
Calcium binding site 3 out of 4 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


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 Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca502

b:11.6
occ:1.00
 OD1 K:ASP423 2.3 13.2 1.0
O K:ILE424 2.4 11.5 1.0
OE1 K:GLU426 2.4 13.9 1.0
OD1 K:ASN439 2.4 6.7 1.0
O K:LEU440 2.5 12.0 1.0
O K:HOH604 2.6 17.2 1.0
O K:THR443 2.8 15.9 1.0
OD2 K:ASP423 2.8 13.7 1.0
CG K:ASP423 2.9 9.8 1.0
CD K:GLU426 3.4 13.1 1.0
CG K:ASN439 3.5 6.9 1.0
C K:ILE424 3.6 9.8 1.0
C K:LEU440 3.7 11.0 1.0
OE2 K:GLU426 3.7 12.9 1.0
C K:THR443 3.8 14.6 1.0
N K:THR443 3.9 15.2 1.0
ND2 K:ASN439 3.9 4.6 1.0
N K:LEU440 3.9 9.5 1.0
N K:GLY442 4.0 11.0 1.0
N K:ILE424 4.2 9.6 1.0
CA K:THR443 4.3 13.4 1.0
CA K:ASP425 4.3 11.2 1.0
N K:ASP425 4.4 9.3 1.0
N K:GLU426 4.4 13.8 1.0
CA K:LEU440 4.5 10.6 1.0
O K:GLY412 4.5 6.0 1.0
CB K:ASP423 4.5 7.2 1.0
C K:GLY442 4.5 11.5 1.0
CA K:ILE424 4.5 9.3 1.0
CA K:PRO441 4.6 13.3 1.0
N K:PRO441 4.6 11.4 1.0
C K:PRO441 4.7 12.3 1.0
CA K:GLY442 4.7 12.5 1.0
CB K:ASN439 4.8 8.8 1.0
CG K:GLU426 4.8 13.8 1.0
C K:ASP423 4.9 9.1 1.0
C K:ASN439 4.9 13.4 1.0
N K:PHE444 4.9 16.3 1.0
CA K:ASN439 4.9 12.3 1.0
CB K:ILE424 5.0 7.8 1.0
C K:ASP425 5.0 11.1 1.0

Calcium binding site 4 out of 4 in 1dx5

Go back to Calcium Binding Sites List in 1dx5
Calcium binding site 4 out of 4 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


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 Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca502

b:12.2
occ:1.00
 O L:ILE424 2.4 11.2 1.0
O L:LEU440 2.4 13.8 1.0
OD1 L:ASN439 2.4 6.0 1.0
OD1 L:ASP423 2.5 18.7 1.0
O L:HOH606 2.5 13.8 1.0
OE1 L:GLU426 2.5 15.6 1.0
O L:THR443 2.7 14.1 1.0
OD2 L:ASP423 2.8 14.6 1.0
CG L:ASP423 3.0 14.3 1.0
CD L:GLU426 3.4 14.3 1.0
CG L:ASN439 3.5 6.5 1.0
C L:ILE424 3.6 9.7 1.0
C L:LEU440 3.6 11.2 1.0
OE2 L:GLU426 3.7 13.4 1.0
C L:THR443 3.8 12.2 1.0
N L:THR443 3.8 12.9 1.0
ND2 L:ASN439 3.9 4.5 1.0
N L:LEU440 3.9 7.7 1.0
N L:GLY442 3.9 11.6 1.0
N L:ILE424 4.3 8.0 1.0
CA L:THR443 4.3 11.8 1.0
CA L:ASP425 4.4 12.0 1.0
C L:GLY442 4.4 11.6 1.0
CA L:LEU440 4.4 9.4 1.0
N L:ASP425 4.4 10.8 1.0
N L:GLU426 4.5 16.1 1.0
O L:GLY412 4.5 6.7 1.0
CB L:ASP423 4.5 11.3 1.0
CA L:ILE424 4.6 7.5 1.0
CA L:GLY442 4.6 12.1 1.0
N L:PRO441 4.6 11.4 1.0
CA L:PRO441 4.7 11.7 1.0
C L:PRO441 4.7 11.1 1.0
CB L:ASN439 4.8 5.1 1.0
N L:PHE444 4.8 13.3 1.0
C L:ASN439 4.9 10.4 1.0
C L:ASP423 4.9 9.5 1.0
CG L:GLU426 4.9 13.1 1.0
CA L:ASN439 4.9 9.6 1.0

Reference:

P.Fuentes-Prior, Y.Iwanaga, R.Huber, R.Pagila, G.Rumennik, M.Seto, J.Morser, D.R.Light, W.Bode. Structural Basis For the Anticoagulant Activity of the Thrombin-Thrombomodulin Complex Nature V. 404 518 2000.
ISSN: ISSN 0028-0836
PubMed: 10761923
DOI: 10.1038/35006683
Page generated: Mon Jul 7 14:30:46 2025

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