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
|