Atomistry » Calcium » PDB 3gif-3gy5 » 3gis
Atomistry »
  Calcium »
    PDB 3gif-3gy5 »
      3gis »

Calcium in PDB 3gis: Crystal Structure of Na-Free Thrombin in Complex with Thrombomodulin

Enzymatic activity of Crystal Structure of Na-Free Thrombin in Complex with Thrombomodulin

All present enzymatic activity of Crystal Structure of Na-Free Thrombin in Complex with Thrombomodulin:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Na-Free Thrombin in Complex with Thrombomodulin, PDB code: 3gis was solved by T.E.Adams, J.A.Huntington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.250, 100.340, 229.280, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.9

Calcium Binding Sites:

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

Calcium binding site 1 out of 3 in 3gis

Go back to Calcium Binding Sites List in 3gis
Calcium binding site 1 out of 3 in the Crystal Structure of Na-Free Thrombin in Complex with Thrombomodulin


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 Na-Free Thrombin in Complex with Thrombomodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca1001

b:15.3
occ:1.00
O X:HOH148 2.2 11.8 1.0
OD1 X:ASN439 2.2 20.0 1.0
O X:LEU440 2.3 24.9 1.0
O X:ILE424 2.4 20.6 1.0
OD1 X:ASP423 2.4 16.6 1.0
O X:THR443 2.6 23.3 1.0
OE1 X:GLU426 2.7 26.0 1.0
OD2 X:ASP423 2.8 15.1 1.0
CG X:ASP423 3.0 14.0 1.0
CG X:ASN439 3.3 23.5 1.0
C X:LEU440 3.5 24.8 1.0
CD X:GLU426 3.5 26.3 1.0
C X:ILE424 3.5 19.5 1.0
OE2 X:GLU426 3.6 28.0 1.0
C X:THR443 3.7 23.2 1.0
N X:THR443 3.7 22.9 1.0
ND2 X:ASN439 3.8 22.0 1.0
N X:LEU440 3.9 24.2 1.0
N X:GLY442 4.0 25.2 1.0
CA X:THR443 4.2 22.9 1.0
N X:ILE424 4.2 15.9 1.0
CA X:LEU440 4.3 24.3 1.0
CA X:ASP425 4.3 23.2 1.0
N X:ASP425 4.4 21.5 1.0
N X:PRO441 4.4 25.9 1.0
C X:GLY442 4.4 24.0 1.0
CB X:ASP423 4.5 14.5 1.0
CA X:ILE424 4.5 18.4 1.0
N X:GLU426 4.5 22.3 1.0
CA X:PRO441 4.5 25.8 1.0
C X:PRO441 4.6 26.5 1.0
CB X:ASN439 4.6 22.1 1.0
O X:GLY412 4.6 24.0 1.0
CA X:GLY442 4.7 24.2 1.0
C X:ASN439 4.7 23.9 1.0
C X:ASP423 4.8 16.2 1.0
N X:PHE444 4.8 22.1 1.0
CA X:ASN439 4.9 23.5 1.0
CG X:GLU426 4.9 24.5 1.0
CB X:ILE424 4.9 17.3 1.0

Calcium binding site 2 out of 3 in 3gis

Go back to Calcium Binding Sites List in 3gis
Calcium binding site 2 out of 3 in the Crystal Structure of Na-Free Thrombin in Complex with Thrombomodulin


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 Na-Free Thrombin in Complex with Thrombomodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Ca1002

b:27.1
occ:1.00
OD1 Y:ASN439 2.4 32.8 1.0
OD1 Y:ASP423 2.4 24.5 1.0
O Y:LEU440 2.4 33.0 1.0
O Y:ILE424 2.4 22.8 1.0
OE1 Y:GLU426 2.6 25.2 1.0
OD2 Y:ASP423 2.6 20.6 1.0
O Y:THR443 2.8 25.5 1.0
CG Y:ASP423 2.9 24.5 1.0
CG Y:ASN439 3.4 33.5 1.0
CD Y:GLU426 3.4 26.1 1.0
C Y:ILE424 3.5 23.8 1.0
OE2 Y:GLU426 3.6 28.8 1.0
C Y:LEU440 3.6 33.8 1.0
ND2 Y:ASN439 3.8 33.0 1.0
C Y:THR443 3.9 26.7 1.0
N Y:THR443 4.0 25.7 1.0
N Y:LEU440 4.0 33.2 1.0
N Y:GLY442 4.0 30.5 1.0
CA Y:ASP425 4.2 26.7 1.0
N Y:ILE424 4.3 23.5 1.0
N Y:ASP425 4.3 25.2 1.0
CB Y:ASP423 4.4 23.6 1.0
CA Y:THR443 4.4 26.7 1.0
N Y:GLU426 4.4 25.7 1.0
CA Y:LEU440 4.5 32.8 1.0
CA Y:ILE424 4.5 23.3 1.0
C Y:GLY442 4.5 26.4 1.0
O Y:GLY412 4.5 20.8 1.0
N Y:PRO441 4.6 33.7 1.0
CA Y:PRO441 4.6 32.9 1.0
C Y:ASP423 4.7 24.0 1.0
CB Y:ASN439 4.7 32.3 1.0
C Y:PRO441 4.8 31.9 1.0
CA Y:GLY442 4.8 27.4 1.0
C Y:ASN439 4.8 34.2 1.0
CG Y:GLU426 4.8 25.6 1.0
C Y:ASP425 4.9 27.1 1.0
CA Y:ASN439 4.9 34.5 1.0

Calcium binding site 3 out of 3 in 3gis

Go back to Calcium Binding Sites List in 3gis
Calcium binding site 3 out of 3 in the Crystal Structure of Na-Free Thrombin in Complex with Thrombomodulin


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 Na-Free Thrombin in Complex with Thrombomodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca1003

b:32.5
occ:1.00
O Z:ILE424 2.4 25.4 1.0
OD1 Z:ASP423 2.4 29.8 1.0
O Z:LEU440 2.4 35.5 1.0
OD1 Z:ASN439 2.4 28.3 1.0
OE1 Z:GLU426 2.5 28.4 1.0
O Z:HOH256 2.5 20.7 1.0
O Z:THR443 2.7 35.3 1.0
OD2 Z:ASP423 3.0 28.6 1.0
CG Z:ASP423 3.0 29.2 1.0
CD Z:GLU426 3.4 29.7 1.0
CG Z:ASN439 3.5 28.2 1.0
C Z:ILE424 3.6 24.9 1.0
OE2 Z:GLU426 3.6 29.4 1.0
C Z:LEU440 3.6 37.1 1.0
N Z:THR443 3.6 35.0 1.0
C Z:THR443 3.7 34.3 1.0
N Z:GLY442 3.9 38.0 1.0
N Z:LEU440 4.0 35.8 1.0
ND2 Z:ASN439 4.0 28.8 1.0
CA Z:THR443 4.1 34.4 1.0
N Z:ILE424 4.2 23.8 1.0
C Z:GLY442 4.3 36.1 1.0
CA Z:LEU440 4.4 36.0 1.0
CA Z:ILE424 4.4 24.2 1.0
N Z:ASP425 4.5 26.0 1.0
CB Z:ASP423 4.5 28.8 1.0
CA Z:GLY442 4.5 36.9 1.0
N Z:GLU426 4.5 27.8 1.0
O Z:GLY412 4.5 30.0 1.0
CA Z:ASP425 4.6 27.9 1.0
N Z:PRO441 4.6 38.2 1.0
C Z:PRO441 4.6 38.9 1.0
C Z:ASP423 4.6 25.5 1.0
CA Z:PRO441 4.6 38.6 1.0
CB Z:ASN439 4.8 30.1 1.0
N Z:PHE444 4.8 34.4 1.0
CG Z:GLU426 4.8 28.5 1.0
CB Z:ILE424 4.8 23.9 1.0
C Z:ASN439 4.9 34.3 1.0
CA Z:ASN439 5.0 32.3 1.0

Reference:

T.E.Adams, W.Li, J.A.Huntington. Molecular Basis of Thrombomodulin Activation of Slow Thrombin J.Thromb.Haemost. V. 7 1688 2009.
ISSN: ISSN 1538-7933
PubMed: 19656282
DOI: 10.1111/J.1538-7836.2009.03563.X
Page generated: Sat Jul 13 10:41:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy