Calcium in PDB 5mhl: Fxiiia in Complex with the Inhibitor MI0621
Enzymatic activity of Fxiiia in Complex with the Inhibitor MI0621
All present enzymatic activity of Fxiiia in Complex with the Inhibitor MI0621:
2.3.2.13;
Protein crystallography data
The structure of Fxiiia in Complex with the Inhibitor MI0621, PDB code: 5mhl
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)
|
48.83 /
2.40
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.213,
80.993,
103.329,
88.12,
76.87,
81.47
|
|
R / Rfree (%)
|
17.2 /
23.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Fxiiia in Complex with the Inhibitor MI0621
(pdb code 5mhl). 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 MI0621, PDB code: 5mhl:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 5mhl
Go back to
Calcium Binding Sites List in 5mhl
Calcium binding site 1 out
of 6 in the Fxiiia in Complex with the Inhibitor MI0621
 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 MI0621 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca801
b:37.6
occ:1.00
|
O
|
A:HOH982
|
2.3
|
22.5
|
1.0
|
|
OE1
|
A:GLU485
|
2.3
|
54.8
|
1.0
|
|
OE2
|
A:GLU490
|
2.3
|
63.6
|
1.0
|
|
O
|
A:ALA457
|
2.4
|
46.1
|
1.0
|
|
OD1
|
A:ASN436
|
2.4
|
39.5
|
1.0
|
|
OE2
|
A:GLU485
|
2.4
|
46.7
|
1.0
|
|
O
|
A:HOH959
|
2.5
|
26.9
|
1.0
|
|
CD
|
A:GLU485
|
2.7
|
45.0
|
1.0
|
|
CD
|
A:GLU490
|
3.4
|
67.2
|
1.0
|
|
CG
|
A:ASN436
|
3.5
|
46.7
|
1.0
|
|
C
|
A:ALA457
|
3.6
|
43.7
|
1.0
|
|
ND2
|
A:ASN436
|
4.0
|
48.6
|
1.0
|
|
OE1
|
A:GLU490
|
4.0
|
77.2
|
1.0
|
|
NZ
|
A:LYS482
|
4.1
|
43.3
|
1.0
|
|
CA
|
A:THR458
|
4.2
|
48.5
|
1.0
|
|
CG
|
A:GLU485
|
4.2
|
48.2
|
1.0
|
|
CG
|
A:GLU490
|
4.3
|
62.2
|
1.0
|
|
N
|
A:THR458
|
4.4
|
42.0
|
1.0
|
|
O
|
A:HOH1004
|
4.4
|
36.9
|
1.0
|
|
NH1
|
A:ARG491
|
4.4
|
53.2
|
1.0
|
|
O
|
A:ASN436
|
4.5
|
43.1
|
1.0
|
|
CE
|
A:LYS482
|
4.6
|
40.6
|
1.0
|
|
CA
|
A:ALA457
|
4.6
|
48.4
|
1.0
|
|
CB
|
A:ASN436
|
4.7
|
33.4
|
1.0
|
|
O
|
A:ILE460
|
4.8
|
45.4
|
1.0
|
|
OD1
|
A:ASP438
|
4.8
|
43.5
|
1.0
|
|
CA
|
A:ASN436
|
4.8
|
38.6
|
1.0
|
|
C
|
A:THR458
|
4.9
|
51.1
|
1.0
|
|
CB
|
A:ALA457
|
4.9
|
44.1
|
1.0
|
|
C
|
A:ASN436
|
5.0
|
41.3
|
1.0
|
|
CB
|
A:GLU485
|
5.0
|
41.4
|
1.0
|
|
Calcium binding site 2 out
of 6 in 5mhl
Go back to
Calcium Binding Sites List in 5mhl
Calcium binding site 2 out
of 6 in the Fxiiia in Complex with the Inhibitor MI0621
 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 MI0621 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca802
b:38.9
occ:1.00
|
O
|
A:ALA264
|
2.2
|
30.7
|
1.0
|
|
O
|
A:ASN267
|
2.4
|
22.5
|
1.0
|
|
O
|
A:LYS269
|
2.4
|
32.4
|
1.0
|
|
OD1
|
A:ASP271
|
2.4
|
50.9
|
1.0
|
|
OD1
|
A:ASN267
|
2.4
|
23.1
|
1.0
|
|
O
|
A:HOH943
|
2.5
|
33.0
|
1.0
|
|
OD2
|
A:ASP271
|
2.8
|
49.2
|
1.0
|
|
CG
|
A:ASP271
|
2.9
|
52.2
|
1.0
|
|
C
|
A:ALA264
|
3.3
|
24.8
|
1.0
|
|
C
|
A:ASN267
|
3.4
|
27.1
|
1.0
|
|
CG
|
A:ASN267
|
3.4
|
33.4
|
1.0
|
|
C
|
A:LYS269
|
3.5
|
32.6
|
1.0
|
|
N
|
A:LYS269
|
3.7
|
32.5
|
1.0
|
|
C
|
A:ALA268
|
3.9
|
34.3
|
1.0
|
|
CA
|
A:LYS269
|
4.1
|
32.1
|
1.0
|
|
CA
|
A:ALA264
|
4.2
|
22.3
|
1.0
|
|
ND2
|
A:ASN267
|
4.2
|
22.6
|
1.0
|
|
N
|
A:MET265
|
4.2
|
32.8
|
1.0
|
|
N
|
A:ALA268
|
4.2
|
30.4
|
1.0
|
|
CA
|
A:ASN267
|
4.2
|
28.4
|
1.0
|
|
CA
|
A:MET265
|
4.3
|
32.8
|
1.0
|
|
CB
|
A:ASP271
|
4.3
|
41.2
|
1.0
|
|
N
|
A:ASP271
|
4.3
|
33.3
|
1.0
|
|
N
|
A:ASN267
|
4.3
|
21.4
|
1.0
|
|
O
|
A:ALA268
|
4.3
|
36.8
|
1.0
|
|
CB
|
A:ASN267
|
4.4
|
22.3
|
1.0
|
|
CA
|
A:ALA268
|
4.4
|
32.7
|
1.0
|
|
O
|
A:TYR407
|
4.5
|
30.6
|
1.0
|
|
CB
|
A:ALA264
|
4.5
|
22.9
|
1.0
|
|
CB
|
A:LYS269
|
4.6
|
36.1
|
1.0
|
|
N
|
A:ASP270
|
4.6
|
32.9
|
1.0
|
|
CB
|
A:ASP270
|
4.6
|
40.6
|
1.0
|
|
C
|
A:MET265
|
4.7
|
33.3
|
1.0
|
|
N
|
A:GLY273
|
4.7
|
30.8
|
1.0
|
|
OD2
|
A:ASP270
|
4.8
|
44.1
|
1.0
|
|
CA
|
A:GLY273
|
4.8
|
22.4
|
1.0
|
|
CA
|
A:ASP271
|
4.8
|
36.8
|
1.0
|
|
O
|
A:MET265
|
5.0
|
31.7
|
1.0
|
|
Calcium binding site 3 out
of 6 in 5mhl
Go back to
Calcium Binding Sites List in 5mhl
Calcium binding site 3 out
of 6 in the Fxiiia in Complex with the Inhibitor MI0621
 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 MI0621 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca803
b:46.9
occ:1.00
|
OD1
|
A:ASP345
|
2.2
|
60.1
|
1.0
|
|
OD1
|
A:ASP343
|
2.2
|
49.7
|
1.0
|
|
O
|
A:GLN349
|
2.3
|
44.4
|
1.0
|
|
OD2
|
A:ASP367
|
2.4
|
48.3
|
1.0
|
|
OD2
|
A:ASP351
|
2.4
|
66.5
|
1.0
|
|
OD1
|
A:ASN347
|
2.5
|
41.7
|
1.0
|
|
CG
|
A:ASP345
|
3.3
|
62.5
|
1.0
|
|
CG
|
A:ASP367
|
3.3
|
42.8
|
1.0
|
|
CG
|
A:ASP343
|
3.4
|
46.6
|
1.0
|
|
CG
|
A:ASN347
|
3.5
|
53.3
|
1.0
|
|
OD1
|
A:ASP367
|
3.5
|
43.4
|
1.0
|
|
C
|
A:GLN349
|
3.6
|
51.0
|
1.0
|
|
CG
|
A:ASP351
|
3.6
|
69.2
|
1.0
|
|
OD2
|
A:ASP345
|
3.6
|
67.3
|
1.0
|
|
ND2
|
A:ASN347
|
3.9
|
62.9
|
1.0
|
|
OD2
|
A:ASP343
|
4.0
|
42.6
|
1.0
|
|
N
|
A:ASP351
|
4.1
|
52.8
|
1.0
|
|
N
|
A:GLN349
|
4.1
|
49.4
|
1.0
|
|
N
|
A:ASP345
|
4.3
|
44.5
|
1.0
|
|
CB
|
A:ASP351
|
4.4
|
62.8
|
1.0
|
|
CA
|
A:GLN349
|
4.5
|
54.0
|
1.0
|
|
N
|
A:MET350
|
4.5
|
55.7
|
1.0
|
|
N
|
A:ASN344
|
4.5
|
46.7
|
1.0
|
|
OD1
|
A:ASP351
|
4.5
|
68.5
|
1.0
|
|
CA
|
A:MET350
|
4.5
|
58.1
|
1.0
|
|
CB
|
A:ASP345
|
4.6
|
55.0
|
1.0
|
|
N
|
A:ASN347
|
4.6
|
50.9
|
1.0
|
|
CB
|
A:ASP343
|
4.6
|
45.5
|
1.0
|
|
CG
|
A:GLN349
|
4.7
|
55.8
|
1.0
|
|
CB
|
A:ASP367
|
4.7
|
42.9
|
1.0
|
|
CA
|
A:ASP343
|
4.7
|
49.7
|
1.0
|
|
N
|
A:LEU348
|
4.7
|
48.2
|
1.0
|
|
C
|
A:MET350
|
4.7
|
58.7
|
1.0
|
|
CB
|
A:ASN347
|
4.8
|
54.7
|
1.0
|
|
CA
|
A:ASP345
|
4.8
|
44.0
|
1.0
|
|
N
|
A:ALA346
|
4.8
|
38.5
|
1.0
|
|
CE
|
A:MET350
|
4.8
|
54.2
|
1.0
|
|
C
|
A:ASP345
|
4.9
|
42.3
|
1.0
|
|
CA
|
A:ASP351
|
4.9
|
57.3
|
1.0
|
|
Calcium binding site 4 out
of 6 in 5mhl
Go back to
Calcium Binding Sites List in 5mhl
Calcium binding site 4 out
of 6 in the Fxiiia in Complex with the Inhibitor MI0621
 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 MI0621 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca801
b:36.9
occ:1.00
|
OD1
|
B:ASP343
|
2.2
|
33.6
|
1.0
|
|
OD2
|
B:ASP367
|
2.3
|
33.4
|
1.0
|
|
OD1
|
B:ASP345
|
2.3
|
63.8
|
1.0
|
|
O
|
B:GLN349
|
2.4
|
28.8
|
1.0
|
|
OD2
|
B:ASP351
|
2.4
|
45.4
|
1.0
|
|
OD1
|
B:ASN347
|
2.5
|
33.5
|
1.0
|
|
CG
|
B:ASP367
|
3.2
|
36.4
|
1.0
|
|
CG
|
B:ASP343
|
3.4
|
33.8
|
1.0
|
|
OD1
|
B:ASP367
|
3.4
|
36.2
|
1.0
|
|
CG
|
B:ASP345
|
3.4
|
56.5
|
1.0
|
|
CG
|
B:ASN347
|
3.4
|
30.6
|
1.0
|
|
C
|
B:GLN349
|
3.6
|
38.6
|
1.0
|
|
CG
|
B:ASP351
|
3.6
|
47.6
|
1.0
|
|
OD2
|
B:ASP345
|
3.8
|
54.4
|
1.0
|
|
ND2
|
B:ASN347
|
3.9
|
35.8
|
1.0
|
|
OD2
|
B:ASP343
|
3.9
|
32.5
|
1.0
|
|
N
|
B:GLN349
|
4.1
|
44.8
|
1.0
|
|
N
|
B:ASP351
|
4.2
|
34.2
|
1.0
|
|
N
|
B:ASP345
|
4.4
|
29.8
|
1.0
|
|
CB
|
B:ASP351
|
4.5
|
45.1
|
1.0
|
|
N
|
B:ASN347
|
4.5
|
36.6
|
1.0
|
|
CA
|
B:GLN349
|
4.5
|
40.6
|
1.0
|
|
OD1
|
B:ASP351
|
4.5
|
49.7
|
1.0
|
|
CB
|
B:ASP343
|
4.5
|
28.2
|
1.0
|
|
N
|
B:MET350
|
4.5
|
36.1
|
1.0
|
|
CG
|
B:GLN349
|
4.6
|
43.8
|
1.0
|
|
N
|
B:ASN344
|
4.6
|
34.6
|
1.0
|
|
CB
|
B:ASP367
|
4.6
|
36.7
|
1.0
|
|
CA
|
B:MET350
|
4.6
|
38.7
|
1.0
|
|
N
|
B:LEU348
|
4.6
|
32.6
|
1.0
|
|
CA
|
B:ASP343
|
4.6
|
28.7
|
1.0
|
|
CB
|
B:ASN347
|
4.7
|
34.5
|
1.0
|
|
CE
|
B:MET350
|
4.7
|
50.4
|
1.0
|
|
CB
|
B:ASP345
|
4.7
|
41.4
|
1.0
|
|
C
|
B:MET350
|
4.9
|
38.5
|
1.0
|
|
N
|
B:ALA346
|
4.9
|
36.6
|
1.0
|
|
CA
|
B:ASP345
|
4.9
|
33.7
|
1.0
|
|
CA
|
B:ASN347
|
4.9
|
36.4
|
1.0
|
|
C
|
B:ASP345
|
4.9
|
36.1
|
1.0
|
|
C
|
B:ASN347
|
5.0
|
33.9
|
1.0
|
|
CA
|
B:ASP351
|
5.0
|
37.7
|
1.0
|
|
Calcium binding site 5 out
of 6 in 5mhl
Go back to
Calcium Binding Sites List in 5mhl
Calcium binding site 5 out
of 6 in the Fxiiia in Complex with the Inhibitor MI0621
 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 MI0621 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca802
b:32.7
occ:1.00
|
O
|
B:ALA457
|
2.3
|
34.5
|
1.0
|
|
OD1
|
B:ASN436
|
2.3
|
40.0
|
1.0
|
|
OE2
|
B:GLU490
|
2.4
|
42.9
|
1.0
|
|
OE1
|
B:GLU485
|
2.4
|
50.0
|
1.0
|
|
OE2
|
B:GLU485
|
2.4
|
37.3
|
1.0
|
|
O
|
B:HOH993
|
2.4
|
27.1
|
1.0
|
|
O
|
B:HOH941
|
2.6
|
25.5
|
1.0
|
|
CD
|
B:GLU485
|
2.8
|
35.4
|
1.0
|
|
CG
|
B:ASN436
|
3.3
|
32.9
|
1.0
|
|
CD
|
B:GLU490
|
3.4
|
44.7
|
1.0
|
|
C
|
B:ALA457
|
3.5
|
30.9
|
1.0
|
|
ND2
|
B:ASN436
|
3.7
|
33.2
|
1.0
|
|
NH1
|
B:ARG491
|
4.0
|
32.5
|
1.0
|
|
O
|
B:HOH933
|
4.1
|
29.1
|
1.0
|
|
OE1
|
B:GLU490
|
4.1
|
37.3
|
1.0
|
|
CG
|
B:GLU485
|
4.3
|
34.0
|
1.0
|
|
CA
|
B:THR458
|
4.3
|
36.8
|
1.0
|
|
NZ
|
B:LYS482
|
4.3
|
31.0
|
1.0
|
|
N
|
B:THR458
|
4.3
|
38.9
|
1.0
|
|
O
|
B:HOH1031
|
4.4
|
41.3
|
1.0
|
|
CG
|
B:GLU490
|
4.4
|
43.4
|
1.0
|
|
O
|
B:ASN436
|
4.5
|
30.4
|
1.0
|
|
CA
|
B:ALA457
|
4.5
|
33.5
|
1.0
|
|
CB
|
B:ASN436
|
4.6
|
30.1
|
1.0
|
|
OD1
|
B:ASP438
|
4.7
|
40.6
|
1.0
|
|
CB
|
B:ALA457
|
4.7
|
40.1
|
1.0
|
|
CA
|
B:ASN436
|
4.8
|
26.7
|
1.0
|
|
O
|
B:ILE460
|
4.9
|
41.6
|
1.0
|
|
C
|
B:ASN436
|
4.9
|
29.1
|
1.0
|
|
C
|
B:THR458
|
4.9
|
38.9
|
1.0
|
|
Calcium binding site 6 out
of 6 in 5mhl
Go back to
Calcium Binding Sites List in 5mhl
Calcium binding site 6 out
of 6 in the Fxiiia in Complex with the Inhibitor MI0621
 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 MI0621 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca807
b:26.8
occ:1.00
|
O
|
B:LYS269
|
2.2
|
25.3
|
1.0
|
|
O
|
B:ASN267
|
2.4
|
28.4
|
1.0
|
|
OD1
|
B:ASN267
|
2.4
|
22.1
|
1.0
|
|
O
|
B:ALA264
|
2.4
|
32.2
|
1.0
|
|
OD1
|
B:ASP271
|
2.4
|
32.1
|
1.0
|
|
O
|
B:HOH991
|
2.4
|
25.6
|
1.0
|
|
OD2
|
B:ASP271
|
2.5
|
28.2
|
1.0
|
|
CG
|
B:ASP271
|
2.8
|
26.7
|
1.0
|
|
C
|
B:ASN267
|
3.3
|
29.9
|
1.0
|
|
C
|
B:LYS269
|
3.4
|
24.5
|
1.0
|
|
CG
|
B:ASN267
|
3.4
|
33.0
|
1.0
|
|
C
|
B:ALA264
|
3.5
|
28.8
|
1.0
|
|
N
|
B:LYS269
|
3.6
|
27.3
|
1.0
|
|
C
|
B:ALA268
|
3.7
|
26.0
|
1.0
|
|
CA
|
B:LYS269
|
3.9
|
28.5
|
1.0
|
|
N
|
B:ALA268
|
4.1
|
22.4
|
1.0
|
|
O
|
B:ALA268
|
4.1
|
32.2
|
1.0
|
|
CA
|
B:ASN267
|
4.2
|
34.0
|
1.0
|
|
ND2
|
B:ASN267
|
4.2
|
21.7
|
1.0
|
|
CB
|
B:ASP271
|
4.2
|
22.6
|
1.0
|
|
CA
|
B:ALA268
|
4.2
|
25.6
|
1.0
|
|
CA
|
B:ALA264
|
4.3
|
28.2
|
1.0
|
|
N
|
B:ASP271
|
4.3
|
24.0
|
1.0
|
|
CB
|
B:ASN267
|
4.3
|
21.9
|
1.0
|
|
N
|
B:ASN267
|
4.4
|
21.4
|
1.0
|
|
N
|
B:MET265
|
4.4
|
23.8
|
1.0
|
|
CB
|
B:LYS269
|
4.4
|
31.8
|
1.0
|
|
CA
|
B:MET265
|
4.4
|
31.5
|
1.0
|
|
OD2
|
B:ASP270
|
4.5
|
37.8
|
1.0
|
|
N
|
B:ASP270
|
4.5
|
26.6
|
1.0
|
|
CB
|
B:ASP270
|
4.6
|
23.7
|
1.0
|
|
CB
|
B:ALA264
|
4.7
|
21.3
|
1.0
|
|
O
|
B:TYR407
|
4.7
|
28.4
|
1.0
|
|
N
|
B:GLY273
|
4.7
|
30.4
|
1.0
|
|
C
|
B:MET265
|
4.8
|
32.2
|
1.0
|
|
CA
|
B:ASP271
|
4.8
|
27.2
|
1.0
|
|
CE
|
B:MET406
|
4.9
|
48.6
|
1.0
|
|
CA
|
B:GLY273
|
4.9
|
21.9
|
1.0
|
|
CA
|
B:ASP270
|
5.0
|
29.9
|
1.0
|
|
CG
|
B:ASP270
|
5.0
|
31.1
|
1.0
|
|
Reference:
M.Stieler,
A.Heine,
G.Klebe.
Fxiiia in Complex with the Inhibitor MI0621 To Be Published.
Page generated: Mon Jul 15 08:13:46 2024
|
