Calcium in PDB 5mhm: Fxiiia in Complex with the Inhibitor ZED1630
Enzymatic activity of Fxiiia in Complex with the Inhibitor ZED1630
All present enzymatic activity of Fxiiia in Complex with the Inhibitor ZED1630:
2.3.2.13;
Protein crystallography data
The structure of Fxiiia in Complex with the Inhibitor ZED1630, PDB code: 5mhm
was solved by
M.Stieler,
A.Heine,
G.Klebe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
24.88 /
2.12
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.912,
80.715,
103.190,
88.44,
76.60,
81.79
|
|
R / Rfree (%)
|
17 /
21.3
|
Other elements in 5mhm:
The structure of Fxiiia in Complex with the Inhibitor ZED1630 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Fxiiia in Complex with the Inhibitor ZED1630
(pdb code 5mhm). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Fxiiia in Complex with the Inhibitor ZED1630, PDB code: 5mhm:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 5mhm
Go back to
Calcium Binding Sites List in 5mhm
Calcium binding site 1 out
of 6 in the Fxiiia in Complex with the Inhibitor ZED1630
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca801
b:17.8
occ:1.00
|
O
|
A:ALA264
|
2.3
|
14.2
|
1.0
|
|
OD1
|
A:ASN267
|
2.3
|
15.6
|
1.0
|
|
O
|
A:LYS269
|
2.3
|
19.1
|
1.0
|
|
O
|
A:ASN267
|
2.4
|
17.2
|
1.0
|
|
OD1
|
A:ASP271
|
2.5
|
29.5
|
1.0
|
|
O
|
A:HOH982
|
2.5
|
17.4
|
1.0
|
|
OD2
|
A:ASP271
|
2.5
|
23.3
|
1.0
|
|
CG
|
A:ASP271
|
2.8
|
27.4
|
1.0
|
|
CG
|
A:ASN267
|
3.2
|
16.7
|
1.0
|
|
C
|
A:ALA264
|
3.3
|
15.5
|
1.0
|
|
C
|
A:ASN267
|
3.3
|
15.9
|
1.0
|
|
C
|
A:LYS269
|
3.5
|
21.4
|
1.0
|
|
N
|
A:LYS269
|
3.7
|
20.1
|
1.0
|
|
C
|
A:ALA268
|
3.9
|
21.5
|
1.0
|
|
ND2
|
A:ASN267
|
3.9
|
18.3
|
1.0
|
|
CA
|
A:LYS269
|
4.1
|
23.7
|
1.0
|
|
CA
|
A:ALA264
|
4.1
|
15.1
|
1.0
|
|
CA
|
A:ASN267
|
4.1
|
14.3
|
1.0
|
|
N
|
A:ALA268
|
4.2
|
14.8
|
1.0
|
|
N
|
A:MET265
|
4.2
|
15.4
|
1.0
|
|
CB
|
A:ASP271
|
4.2
|
22.8
|
1.0
|
|
CB
|
A:ASN267
|
4.2
|
15.4
|
1.0
|
|
CA
|
A:MET265
|
4.3
|
15.4
|
1.0
|
|
N
|
A:ASP271
|
4.3
|
21.6
|
1.0
|
|
N
|
A:ASN267
|
4.3
|
17.4
|
1.0
|
|
O
|
A:ALA268
|
4.3
|
21.7
|
1.0
|
|
O
|
A:TYR407
|
4.4
|
17.5
|
1.0
|
|
CA
|
A:ALA268
|
4.4
|
18.8
|
1.0
|
|
CB
|
A:LYS269
|
4.5
|
33.1
|
1.0
|
|
CB
|
A:ALA264
|
4.5
|
11.8
|
1.0
|
|
OD2
|
A:ASP270
|
4.5
|
23.3
|
1.0
|
|
CB
|
A:ASP270
|
4.6
|
22.2
|
1.0
|
|
N
|
A:ASP270
|
4.6
|
16.3
|
1.0
|
|
C
|
A:MET265
|
4.6
|
12.5
|
1.0
|
|
N
|
A:GLY273
|
4.7
|
16.9
|
1.0
|
|
CA
|
A:GLY273
|
4.8
|
14.8
|
1.0
|
|
CA
|
A:ASP271
|
4.8
|
23.0
|
1.0
|
|
O
|
A:MET265
|
4.8
|
14.7
|
1.0
|
|
CA
|
A:ASP270
|
5.0
|
19.6
|
1.0
|
|
Calcium binding site 2 out
of 6 in 5mhm
Go back to
Calcium Binding Sites List in 5mhm
Calcium binding site 2 out
of 6 in the Fxiiia in Complex with the Inhibitor ZED1630
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca802
b:39.5
occ:1.00
|
OD2
|
A:ASP367
|
2.3
|
31.7
|
1.0
|
|
OD1
|
A:ASN347
|
2.3
|
43.3
|
1.0
|
|
O
|
A:GLN349
|
2.3
|
35.2
|
1.0
|
|
OD1
|
A:ASP345
|
2.3
|
34.8
|
1.0
|
|
OD1
|
A:ASP343
|
2.4
|
28.1
|
1.0
|
|
OD2
|
A:ASP351
|
2.4
|
37.2
|
1.0
|
|
CG
|
A:ASP367
|
3.2
|
36.6
|
1.0
|
|
CG
|
A:ASN347
|
3.2
|
39.9
|
1.0
|
|
CG
|
A:ASP345
|
3.4
|
40.3
|
1.0
|
|
OD1
|
A:ASP367
|
3.4
|
40.2
|
1.0
|
|
CG
|
A:ASP343
|
3.4
|
35.5
|
1.0
|
|
C
|
A:GLN349
|
3.5
|
31.6
|
1.0
|
|
ND2
|
A:ASN347
|
3.6
|
43.4
|
1.0
|
|
CG
|
A:ASP351
|
3.7
|
46.6
|
1.0
|
|
OD2
|
A:ASP345
|
3.8
|
47.7
|
1.0
|
|
N
|
A:ASP351
|
4.0
|
44.0
|
1.0
|
|
OD2
|
A:ASP343
|
4.0
|
32.4
|
1.0
|
|
N
|
A:GLN349
|
4.2
|
36.5
|
1.0
|
|
CA
|
A:MET350
|
4.4
|
36.8
|
1.0
|
|
N
|
A:MET350
|
4.4
|
31.3
|
1.0
|
|
CB
|
A:ASP351
|
4.4
|
45.3
|
1.0
|
|
N
|
A:ASP345
|
4.4
|
36.6
|
1.0
|
|
CA
|
A:GLN349
|
4.5
|
31.0
|
1.0
|
|
O
|
A:HOH1214
|
4.5
|
44.7
|
1.0
|
|
CB
|
A:ASP343
|
4.5
|
35.5
|
1.0
|
|
CB
|
A:ASP367
|
4.5
|
37.5
|
1.0
|
|
CG
|
A:GLN349
|
4.6
|
40.5
|
1.0
|
|
N
|
A:ASN344
|
4.6
|
40.1
|
1.0
|
|
CB
|
A:ASN347
|
4.6
|
35.9
|
1.0
|
|
C
|
A:MET350
|
4.6
|
41.3
|
1.0
|
|
N
|
A:ASN347
|
4.6
|
35.5
|
1.0
|
|
OD1
|
A:ASP351
|
4.6
|
53.2
|
1.0
|
|
CA
|
A:ASP343
|
4.6
|
35.6
|
1.0
|
|
CB
|
A:ASP345
|
4.7
|
37.2
|
1.0
|
|
CE
|
A:MET350
|
4.8
|
33.6
|
1.0
|
|
CA
|
A:ASP351
|
4.8
|
45.2
|
1.0
|
|
N
|
A:LEU348
|
4.9
|
35.2
|
1.0
|
|
CA
|
A:ASP345
|
4.9
|
38.7
|
1.0
|
|
CA
|
A:ASN347
|
5.0
|
35.7
|
1.0
|
|
N
|
A:ALA346
|
5.0
|
40.9
|
1.0
|
|
C
|
A:ASP345
|
5.0
|
41.0
|
1.0
|
|
Calcium binding site 3 out
of 6 in 5mhm
Go back to
Calcium Binding Sites List in 5mhm
Calcium binding site 3 out
of 6 in the Fxiiia in Complex with the Inhibitor ZED1630
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca803
b:27.8
occ:1.00
|
O
|
A:HOH933
|
2.2
|
18.9
|
1.0
|
|
OE2
|
A:GLU485
|
2.3
|
28.6
|
1.0
|
|
OE2
|
A:GLU490
|
2.3
|
39.8
|
1.0
|
|
O
|
A:ALA457
|
2.4
|
31.8
|
1.0
|
|
O
|
A:HOH1094
|
2.4
|
30.7
|
1.0
|
|
OD1
|
A:ASN436
|
2.5
|
31.7
|
1.0
|
|
OE1
|
A:GLU485
|
2.5
|
35.4
|
1.0
|
|
CD
|
A:GLU485
|
2.8
|
31.8
|
1.0
|
|
CG
|
A:ASN436
|
3.4
|
38.7
|
1.0
|
|
CD
|
A:GLU490
|
3.5
|
38.5
|
1.0
|
|
C
|
A:ALA457
|
3.5
|
35.4
|
1.0
|
|
ND2
|
A:ASN436
|
3.8
|
26.9
|
1.0
|
|
O
|
A:HOH934
|
4.1
|
38.4
|
1.0
|
|
CA
|
A:THR458
|
4.1
|
32.2
|
1.0
|
|
OE1
|
A:GLU490
|
4.2
|
40.3
|
1.0
|
|
N
|
A:THR458
|
4.2
|
32.9
|
1.0
|
|
NZ
|
A:LYS482
|
4.3
|
33.1
|
1.0
|
|
CG
|
A:GLU485
|
4.3
|
35.3
|
1.0
|
|
NH2
|
A:ARG491
|
4.3
|
42.7
|
1.0
|
|
OD1
|
A:ASP438
|
4.4
|
35.4
|
1.0
|
|
O
|
A:ASN436
|
4.5
|
28.9
|
1.0
|
|
CG
|
A:GLU490
|
4.5
|
32.6
|
1.0
|
|
O
|
A:HOH993
|
4.5
|
28.0
|
1.0
|
|
CA
|
A:ALA457
|
4.6
|
37.6
|
1.0
|
|
CB
|
A:ASN436
|
4.7
|
27.6
|
1.0
|
|
O
|
A:ILE460
|
4.7
|
26.5
|
1.0
|
|
C
|
A:THR458
|
4.7
|
39.9
|
1.0
|
|
CA
|
A:ASN436
|
4.8
|
26.6
|
1.0
|
|
C
|
A:ASN436
|
4.9
|
30.8
|
1.0
|
|
O
|
A:HOH1005
|
4.9
|
33.8
|
1.0
|
|
CB
|
A:ALA457
|
5.0
|
34.9
|
1.0
|
|
Calcium binding site 4 out
of 6 in 5mhm
Go back to
Calcium Binding Sites List in 5mhm
Calcium binding site 4 out
of 6 in the Fxiiia in Complex with the Inhibitor ZED1630
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca801
b:18.3
occ:1.00
|
O
|
B:LYS269
|
2.3
|
17.7
|
1.0
|
|
OD1
|
B:ASN267
|
2.3
|
16.8
|
1.0
|
|
O
|
B:ASN267
|
2.4
|
15.6
|
1.0
|
|
O
|
B:ALA264
|
2.4
|
18.1
|
1.0
|
|
OD1
|
B:ASP271
|
2.4
|
23.4
|
1.0
|
|
O
|
B:HOH1061
|
2.4
|
10.6
|
1.0
|
|
OD2
|
B:ASP271
|
2.5
|
15.6
|
1.0
|
|
CG
|
B:ASP271
|
2.8
|
21.6
|
1.0
|
|
CG
|
B:ASN267
|
3.3
|
18.7
|
1.0
|
|
C
|
B:ASN267
|
3.3
|
23.4
|
1.0
|
|
C
|
B:ALA264
|
3.4
|
20.1
|
1.0
|
|
C
|
B:LYS269
|
3.4
|
21.7
|
1.0
|
|
N
|
B:LYS269
|
3.7
|
17.2
|
1.0
|
|
C
|
B:ALA268
|
3.8
|
23.5
|
1.0
|
|
ND2
|
B:ASN267
|
4.0
|
17.5
|
1.0
|
|
CA
|
B:LYS269
|
4.0
|
24.7
|
1.0
|
|
CA
|
B:ASN267
|
4.1
|
17.0
|
1.0
|
|
N
|
B:ALA268
|
4.1
|
17.2
|
1.0
|
|
CA
|
B:ALA264
|
4.2
|
22.2
|
1.0
|
|
O
|
B:ALA268
|
4.2
|
20.6
|
1.0
|
|
CB
|
B:ASP271
|
4.2
|
17.5
|
1.0
|
|
N
|
B:MET265
|
4.2
|
18.5
|
1.0
|
|
CB
|
B:ASN267
|
4.2
|
18.7
|
1.0
|
|
N
|
B:ASN267
|
4.3
|
16.6
|
1.0
|
|
CA
|
B:MET265
|
4.3
|
20.6
|
1.0
|
|
N
|
B:ASP271
|
4.3
|
17.2
|
1.0
|
|
CA
|
B:ALA268
|
4.4
|
18.0
|
1.0
|
|
O
|
B:TYR407
|
4.4
|
16.5
|
1.0
|
|
CB
|
B:LYS269
|
4.5
|
24.2
|
1.0
|
|
OD2
|
B:ASP270
|
4.6
|
18.7
|
1.0
|
|
N
|
B:ASP270
|
4.6
|
18.9
|
1.0
|
|
CB
|
B:ALA264
|
4.6
|
14.2
|
1.0
|
|
CB
|
B:ASP270
|
4.6
|
18.3
|
1.0
|
|
C
|
B:MET265
|
4.6
|
21.0
|
1.0
|
|
CA
|
B:ASP271
|
4.8
|
22.3
|
1.0
|
|
N
|
B:GLY273
|
4.8
|
17.9
|
1.0
|
|
O
|
B:MET265
|
4.9
|
14.5
|
1.0
|
|
CA
|
B:GLY273
|
4.9
|
15.7
|
1.0
|
|
CA
|
B:ASP270
|
5.0
|
21.6
|
1.0
|
|
Calcium binding site 5 out
of 6 in 5mhm
Go back to
Calcium Binding Sites List in 5mhm
Calcium binding site 5 out
of 6 in the Fxiiia in Complex with the Inhibitor ZED1630
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca802
b:29.9
occ:1.00
|
OD1
|
B:ASP345
|
2.3
|
35.1
|
1.0
|
|
OD2
|
B:ASP367
|
2.3
|
35.5
|
1.0
|
|
OD1
|
B:ASN347
|
2.3
|
34.4
|
1.0
|
|
O
|
B:GLN349
|
2.4
|
27.6
|
1.0
|
|
OD1
|
B:ASP343
|
2.4
|
22.8
|
1.0
|
|
OD2
|
B:ASP351
|
2.4
|
36.1
|
1.0
|
|
CG
|
B:ASP367
|
3.2
|
37.1
|
1.0
|
|
CG
|
B:ASP345
|
3.3
|
37.9
|
1.0
|
|
CG
|
B:ASN347
|
3.3
|
31.2
|
1.0
|
|
OD1
|
B:ASP367
|
3.4
|
37.5
|
1.0
|
|
C
|
B:GLN349
|
3.6
|
29.2
|
1.0
|
|
CG
|
B:ASP343
|
3.6
|
26.1
|
1.0
|
|
CG
|
B:ASP351
|
3.6
|
39.2
|
1.0
|
|
OD2
|
B:ASP345
|
3.7
|
40.4
|
1.0
|
|
ND2
|
B:ASN347
|
3.8
|
37.2
|
1.0
|
|
N
|
B:ASP351
|
4.0
|
33.5
|
1.0
|
|
OD2
|
B:ASP343
|
4.2
|
27.9
|
1.0
|
|
N
|
B:GLN349
|
4.3
|
33.5
|
1.0
|
|
CB
|
B:ASP351
|
4.4
|
35.2
|
1.0
|
|
CG
|
B:GLN349
|
4.4
|
33.0
|
1.0
|
|
CA
|
B:MET350
|
4.4
|
29.9
|
1.0
|
|
N
|
B:MET350
|
4.4
|
28.3
|
1.0
|
|
N
|
B:ASP345
|
4.4
|
32.7
|
1.0
|
|
CA
|
B:GLN349
|
4.5
|
32.1
|
1.0
|
|
O
|
B:HOH1152
|
4.5
|
36.7
|
1.0
|
|
CB
|
B:ASP367
|
4.6
|
32.8
|
1.0
|
|
OD1
|
B:ASP351
|
4.6
|
41.0
|
1.0
|
|
N
|
B:ASN347
|
4.6
|
30.8
|
1.0
|
|
N
|
B:ASN344
|
4.6
|
32.8
|
1.0
|
|
C
|
B:MET350
|
4.6
|
33.5
|
1.0
|
|
CE
|
B:MET350
|
4.6
|
23.1
|
1.0
|
|
CB
|
B:ASP345
|
4.7
|
24.9
|
1.0
|
|
CB
|
B:ASP343
|
4.7
|
22.0
|
1.0
|
|
CB
|
B:ASN347
|
4.7
|
32.0
|
1.0
|
|
CA
|
B:ASP343
|
4.7
|
25.3
|
1.0
|
|
O
|
B:HOH919
|
4.7
|
48.9
|
1.0
|
|
CA
|
B:ASP351
|
4.9
|
34.4
|
1.0
|
|
N
|
B:LEU348
|
4.9
|
22.6
|
1.0
|
|
CA
|
B:ASP345
|
4.9
|
30.6
|
1.0
|
|
CA
|
B:ASN347
|
5.0
|
30.2
|
1.0
|
|
Calcium binding site 6 out
of 6 in 5mhm
Go back to
Calcium Binding Sites List in 5mhm
Calcium binding site 6 out
of 6 in the Fxiiia in Complex with the Inhibitor ZED1630
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca805
b:22.4
occ:1.00
|
O
|
B:HOH1015
|
2.3
|
23.3
|
1.0
|
|
OE2
|
B:GLU490
|
2.3
|
35.2
|
1.0
|
|
O
|
B:ALA457
|
2.3
|
27.7
|
1.0
|
|
OE1
|
B:GLU485
|
2.4
|
30.6
|
1.0
|
|
OE2
|
B:GLU485
|
2.4
|
26.0
|
1.0
|
|
OD1
|
B:ASN436
|
2.4
|
26.3
|
1.0
|
|
O
|
B:HOH996
|
2.4
|
25.8
|
1.0
|
|
CD
|
B:GLU485
|
2.7
|
30.7
|
1.0
|
|
CG
|
B:ASN436
|
3.4
|
27.1
|
1.0
|
|
CD
|
B:GLU490
|
3.5
|
33.2
|
1.0
|
|
C
|
B:ALA457
|
3.5
|
28.6
|
1.0
|
|
ND2
|
B:ASN436
|
3.7
|
23.4
|
1.0
|
|
OE1
|
B:GLU490
|
4.1
|
27.2
|
1.0
|
|
CA
|
B:THR458
|
4.1
|
29.9
|
1.0
|
|
O
|
B:HOH982
|
4.2
|
26.4
|
1.0
|
|
NZ
|
B:LYS482
|
4.2
|
23.4
|
1.0
|
|
CG
|
B:GLU485
|
4.2
|
29.6
|
1.0
|
|
NH1
|
B:ARG491
|
4.3
|
27.6
|
1.0
|
|
N
|
B:THR458
|
4.3
|
30.8
|
1.0
|
|
O
|
B:ASN436
|
4.4
|
23.2
|
1.0
|
|
O
|
B:HOH1168
|
4.4
|
24.9
|
1.0
|
|
CG
|
B:GLU490
|
4.5
|
30.9
|
1.0
|
|
OD1
|
B:ASP438
|
4.5
|
33.2
|
1.0
|
|
CA
|
B:ALA457
|
4.6
|
34.5
|
1.0
|
|
CB
|
B:ASN436
|
4.6
|
30.9
|
1.0
|
|
O
|
B:ILE460
|
4.7
|
27.5
|
1.0
|
|
CA
|
B:ASN436
|
4.8
|
22.1
|
1.0
|
|
C
|
B:THR458
|
4.8
|
31.2
|
1.0
|
|
C
|
B:ASN436
|
4.9
|
24.5
|
1.0
|
|
CB
|
B:ALA457
|
5.0
|
33.6
|
1.0
|
|
Reference:
M.Stieler,
A.Heine,
G.Klebe.
Fxiiia in Complex with the Inhibitor MI0621 To Be Published.
Page generated: Mon Jul 15 08:14:12 2024
|
