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Sodium 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:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Thrombin-Thrombomodulin Complex (pdb code 1dx5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of the Thrombin-Thrombomodulin Complex, PDB code: 1dx5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1dx5

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Sodium binding site 1 out of 8 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na503

b:16.7
occ:1.00
 O1 I:FMT501 2.9 62.2 1.0
O2 I:FMT501 3.0 63.5 1.0
N I:ALA373 3.2 12.5 1.0
C I:FMT501 3.5 63.0 1.0
CB I:CYS372 3.6 8.2 1.0
CG I:TYR358 3.6 11.4 1.0
SG I:CYS386 3.7 9.8 1.0
CB I:CYS386 3.7 9.4 1.0
CD1 I:TYR358 3.7 12.8 1.0
CG I:PHE376 3.8 8.3 1.0
CB I:PHE376 3.8 8.1 1.0
CB I:ALA373 3.8 10.3 1.0
CB I:TYR358 3.9 8.9 1.0
CA I:CYS372 3.9 11.2 1.0
CD2 I:PHE376 4.1 9.6 1.0
C I:CYS372 4.1 11.8 1.0
CA I:ALA373 4.1 11.5 1.0
CD2 I:TYR358 4.1 9.2 1.0
CD1 I:PHE376 4.2 10.0 1.0
CE1 I:TYR358 4.4 16.7 1.0
SG I:CYS372 4.4 11.2 1.0
CE2 I:TYR358 4.7 14.0 1.0
CE2 I:PHE376 4.7 8.9 1.0
O I:ALA373 4.8 11.0 1.0
CZ I:TYR358 4.8 16.3 1.0
OE2 I:GLU357 4.8 23.3 1.0
CE1 I:PHE376 4.8 11.1 1.0
C I:ALA373 4.9 9.8 1.0

Sodium binding site 2 out of 8 in 1dx5

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Sodium binding site 2 out of 8 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na503

b:17.2
occ:1.00
 O2 J:FMT501 2.9 61.3 1.0
O1 J:FMT501 3.0 61.8 1.0
N J:ALA373 3.1 11.4 1.0
CB J:ALA373 3.4 8.6 1.0
C J:FMT501 3.5 62.0 1.0
CB J:CYS372 3.7 8.2 1.0
CG J:TYR358 3.7 12.0 1.0
CG J:PHE376 3.7 9.8 1.0
CB J:PHE376 3.7 8.4 1.0
SG J:CYS386 3.8 11.3 1.0
CB J:CYS386 3.8 11.0 1.0
CD1 J:TYR358 3.8 12.5 1.0
CA J:ALA373 3.8 10.2 1.0
CA J:CYS372 3.9 9.8 1.0
C J:CYS372 4.0 9.5 1.0
CB J:TYR358 4.0 9.7 1.0
CD2 J:PHE376 4.1 10.1 1.0
CD1 J:PHE376 4.1 10.4 1.0
CD2 J:TYR358 4.1 10.6 1.0
CE1 J:TYR358 4.3 14.7 1.0
SG J:CYS372 4.6 11.5 1.0
CE2 J:TYR358 4.6 8.7 1.0
O J:ALA373 4.6 12.2 1.0
C J:ALA373 4.7 11.7 1.0
CZ J:TYR358 4.7 13.2 1.0
OE2 J:GLU357 4.7 19.7 1.0
CE2 J:PHE376 4.7 10.5 1.0
CE1 J:PHE376 4.8 10.7 1.0

Sodium binding site 3 out of 8 in 1dx5

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Sodium binding site 3 out of 8 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na503

b:15.7
occ:1.00
 O2 K:FMT501 2.8 55.6 1.0
O1 K:FMT501 2.8 54.7 1.0
N K:ALA373 3.3 11.7 1.0
C K:FMT501 3.3 56.5 1.0
CB K:CYS372 3.6 8.6 1.0
CG K:TYR358 3.6 11.2 1.0
SG K:CYS386 3.7 13.1 1.0
CB K:ALA373 3.7 8.6 1.0
CG K:PHE376 3.7 6.6 1.0
CB K:CYS386 3.7 11.1 1.0
CD1 K:TYR358 3.7 12.8 1.0
CB K:PHE376 3.8 6.5 1.0
CB K:TYR358 3.9 9.5 1.0
CA K:CYS372 3.9 10.2 1.0
CD2 K:PHE376 4.1 11.8 1.0
CA K:ALA373 4.1 11.0 1.0
C K:CYS372 4.1 9.5 1.0
CD1 K:PHE376 4.1 10.2 1.0
CD2 K:TYR358 4.1 9.8 1.0
CE1 K:TYR358 4.3 15.1 1.0
SG K:CYS372 4.5 12.8 1.0
CE2 K:TYR358 4.6 8.6 1.0
CZ K:TYR358 4.7 14.0 1.0
CE2 K:PHE376 4.7 8.8 1.0
OE2 K:GLU357 4.8 21.6 1.0
O K:ALA373 4.8 12.7 1.0
CE1 K:PHE376 4.8 9.8 1.0
C K:ALA373 4.9 10.7 1.0

Sodium binding site 4 out of 8 in 1dx5

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Sodium binding site 4 out of 8 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na503

b:19.2
occ:1.00
 O1 L:FMT501 2.8 52.4 1.0
O2 L:FMT501 2.9 55.1 1.0
N L:ALA373 3.1 9.7 1.0
C L:FMT501 3.3 53.5 1.0
CB L:CYS372 3.6 6.8 1.0
CB L:ALA373 3.7 9.7 1.0
CG L:TYR358 3.7 11.2 1.0
CB L:PHE376 3.7 6.7 1.0
CD1 L:TYR358 3.7 12.4 1.0
CG L:PHE376 3.7 9.1 1.0
SG L:CYS386 3.7 11.7 1.0
CB L:CYS386 3.8 11.0 1.0
CA L:CYS372 3.9 8.8 1.0
CB L:TYR358 4.0 10.9 1.0
CA L:ALA373 4.0 10.3 1.0
C L:CYS372 4.0 8.4 1.0
CD2 L:PHE376 4.0 9.9 1.0
CD1 L:PHE376 4.1 8.8 1.0
CD2 L:TYR358 4.2 7.6 1.0
CE1 L:TYR358 4.2 16.5 1.0
SG L:CYS372 4.5 10.1 1.0
O L:ALA373 4.6 11.9 1.0
CE2 L:TYR358 4.7 8.4 1.0
CZ L:TYR358 4.7 11.9 1.0
CE2 L:PHE376 4.8 11.9 1.0
C L:ALA373 4.8 11.7 1.0
OE2 L:GLU357 4.8 23.7 1.0
CE1 L:PHE376 4.8 10.4 1.0

Sodium binding site 5 out of 8 in 1dx5

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Sodium binding site 5 out of 8 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na302

b:38.2
occ:1.00
 OD1 M:ASP221 2.7 19.5 1.0
O M:HOH446 2.8 21.9 1.0
O M:HOH444 3.1 12.1 1.0
O M:HOH505 3.3 18.2 1.0
O M:HOH463 3.4 12.1 1.0
O M:ARG221A 3.5 16.9 1.0
O M:HOH440 3.5 15.3 1.0
CG M:ASP221 3.6 14.2 1.0
O M:ASP221 3.7 15.8 1.0
NH2 M:ARG187 3.7 22.7 1.0
C M:ASP221 3.8 13.8 1.0
CA M:ASP221 4.0 13.5 1.0
CB M:ARG187 4.0 24.0 1.0
CZ M:ARG187 4.1 22.8 1.0
C M:ARG221A 4.2 16.5 1.0
O M:TYR184A 4.2 18.6 1.0
N M:ARG221A 4.4 11.3 1.0
O M:GLY188 4.4 16.0 1.0
OD2 M:ASP221 4.4 18.3 1.0
NE M:ARG187 4.4 21.3 1.0
CB M:ASP221 4.5 13.6 1.0
N M:GLY188 4.5 18.6 1.0
O M:HOH500 4.5 17.7 1.0
CA M:ARG187 4.6 23.7 1.0
O M:HOH452 4.6 14.4 1.0
O M:LYS224 4.7 13.7 1.0
NH1 M:ARG187 4.8 26.4 1.0
N M:ASP222 4.8 18.9 1.0
OD1 M:ASP222 4.8 26.8 1.0
CA M:ARG221A 4.9 13.6 1.0
CA M:ASP222 4.9 19.5 1.0

Sodium binding site 6 out of 8 in 1dx5

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Sodium binding site 6 out of 8 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na302

b:17.2
occ:1.00
 O N:ARG221A 2.3 16.6 1.0
O N:HOH500 2.4 19.7 1.0
O N:HOH404 2.5 15.3 1.0
O N:LYS224 2.6 16.4 1.0
O N:HOH493 2.7 15.8 1.0
C N:ARG221A 3.4 18.1 1.0
C N:LYS224 3.7 14.4 1.0
N N:ARG221A 3.8 12.3 1.0
C N:ASP221 3.9 15.1 1.0
O N:HOH490 3.9 14.6 1.0
N N:LYS224 4.1 17.5 1.0
O N:TYR184A 4.2 19.9 1.0
CA N:ASP221 4.2 14.9 1.0
O N:HOH425 4.2 12.2 1.0
CA N:ARG221A 4.2 16.2 1.0
N N:ASP222 4.3 20.9 1.0
O N:ASP221 4.3 14.8 1.0
OD1 N:ASP221 4.4 17.7 1.0
CA N:LYS224 4.4 16.1 1.0
CA N:ASP222 4.4 22.6 1.0
N N:GLY223 4.5 21.0 1.0
CB N:LYS224 4.6 15.5 1.0
O N:HOH469 4.6 12.0 1.0
C N:ASP222 4.7 21.2 1.0
N N:TYR225 4.8 13.6 1.0

Sodium binding site 7 out of 8 in 1dx5

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Sodium binding site 7 out of 8 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na302

b:22.1
occ:1.00
 O O:ARG221A 2.2 18.1 1.0
O O:HOH491 2.4 20.7 1.0
O O:HOH435 2.5 11.8 1.0
O O:HOH436 2.6 12.7 1.0
O O:LYS224 2.6 14.9 1.0
O O:HOH478 2.7 15.6 1.0
C O:ARG221A 3.3 18.5 1.0
C O:LYS224 3.6 15.0 1.0
O O:HOH487 3.8 23.8 1.0
N O:ARG221A 3.9 13.2 1.0
N O:LYS224 3.9 17.8 1.0
C O:ASP221 4.0 15.8 1.0
O O:HOH486 4.0 16.1 1.0
O O:TYR184A 4.1 18.8 1.0
O O:HOH432 4.2 14.0 1.0
N O:ASP222 4.2 21.7 1.0
CA O:ASP222 4.3 22.8 1.0
CA O:ARG221A 4.3 17.7 1.0
CA O:LYS224 4.3 15.4 1.0
CA O:ASP221 4.3 15.4 1.0
O O:ASP221 4.3 16.2 1.0
N O:GLY223 4.3 19.6 1.0
OD1 O:ASP221 4.5 22.4 1.0
CB O:LYS224 4.6 14.5 1.0
C O:ASP222 4.6 20.6 1.0
N O:TYR225 4.7 13.5 1.0
O O:HOH444 4.8 13.9 1.0
NH2 O:ARG187 4.9 14.9 1.0
CA O:TYR225 5.0 14.8 1.0
C O:GLY223 5.0 16.2 1.0

Sodium binding site 8 out of 8 in 1dx5

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Sodium binding site 8 out of 8 in the Crystal Structure of the Thrombin-Thrombomodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Thrombin-Thrombomodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na302

b:28.2
occ:1.00
 O P:ARG221A 2.3 19.5 1.0
O P:HOH509 2.4 15.8 1.0
O P:HOH427 2.6 15.2 1.0
O P:LYS224 2.7 14.9 1.0
O P:HOH455 2.7 14.7 1.0
C P:ARG221A 3.4 19.5 1.0
C P:LYS224 3.8 11.7 1.0
O P:HOH494 3.8 27.4 1.0
N P:ARG221A 3.9 13.4 1.0
C P:ASP221 3.9 15.2 1.0
O P:HOH500 4.0 17.6 1.0
O P:TYR184A 4.1 21.0 1.0
O P:HOH435 4.1 16.0 1.0
N P:LYS224 4.1 14.5 1.0
CA P:ASP221 4.3 14.7 1.0
CA P:ARG221A 4.3 17.2 1.0
N P:ASP222 4.3 20.3 1.0
O P:ASP221 4.3 14.3 1.0
CA P:ASP222 4.4 20.9 1.0
CA P:LYS224 4.4 13.4 1.0
OD1 P:ASP221 4.4 18.6 1.0
N P:GLY223 4.5 19.1 1.0
C P:ASP222 4.7 19.8 1.0
N P:TYR225 4.7 11.7 1.0
CB P:LYS224 4.8 11.4 1.0
O P:HOH487 4.8 17.0 1.0
CA P:TYR225 5.0 13.4 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: Sun Oct 6 18:19:20 2024

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