Sodium in PDB 7mj5: Complex of Human Thrombin with Xc-43
Enzymatic activity of Complex of Human Thrombin with Xc-43
All present enzymatic activity of Complex of Human Thrombin with Xc-43:
3.4.21.5;
Protein crystallography data
The structure of Complex of Human Thrombin with Xc-43, PDB code: 7mj5
was solved by
S.Lu,
L.Tirloni,
J.F.Andersen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.24 /
2.15
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.35,
136.32,
193.95,
90,
90,
90
|
R / Rfree (%)
|
16.5 /
19.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Complex of Human Thrombin with Xc-43
(pdb code 7mj5). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Complex of Human Thrombin with Xc-43, PDB code: 7mj5:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 7mj5
Go back to
Sodium Binding Sites List in 7mj5
Sodium binding site 1 out
of 6 in the Complex of Human Thrombin with Xc-43
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na302
b:31.6
occ:1.00
|
O
|
H:ARG221
|
2.3
|
27.1
|
1.0
|
O
|
H:HOH488
|
2.4
|
31.5
|
1.0
|
O
|
H:HOH462
|
2.4
|
27.7
|
1.0
|
O
|
H:LYS224
|
2.4
|
32.3
|
1.0
|
O
|
H:HOH532
|
2.4
|
33.1
|
1.0
|
O
|
H:HOH477
|
2.6
|
30.8
|
1.0
|
C
|
H:ARG221
|
3.3
|
29.8
|
1.0
|
C
|
H:LYS224
|
3.5
|
32.1
|
1.0
|
O
|
H:HOH521
|
3.7
|
30.5
|
1.0
|
N
|
H:ARG221
|
3.8
|
27.3
|
1.0
|
N
|
H:LYS224
|
3.9
|
32.3
|
1.0
|
O
|
H:TYR184A
|
4.0
|
33.1
|
1.0
|
C
|
H:ASP220
|
4.1
|
27.7
|
1.0
|
O
|
H:HOH441
|
4.1
|
29.1
|
1.0
|
CA
|
H:ARG221
|
4.2
|
28.2
|
1.0
|
N
|
H:ASP222
|
4.2
|
28.1
|
1.0
|
O
|
H:HOH483
|
4.2
|
27.3
|
1.0
|
CA
|
H:LYS224
|
4.2
|
31.5
|
1.0
|
CA
|
H:ASP220
|
4.3
|
26.1
|
1.0
|
N
|
H:GLY223
|
4.3
|
31.8
|
1.0
|
CA
|
H:ASP222
|
4.3
|
28.4
|
1.0
|
N
|
H:TYR225
|
4.5
|
27.5
|
1.0
|
C
|
H:ASP222
|
4.6
|
33.1
|
1.0
|
CB
|
H:LYS224
|
4.6
|
28.7
|
1.0
|
O
|
H:ASP220
|
4.7
|
26.8
|
1.0
|
OD1
|
H:ASP220
|
4.7
|
27.5
|
1.0
|
CA
|
H:TYR225
|
4.7
|
29.1
|
1.0
|
O
|
H:HOH487
|
4.9
|
31.3
|
1.0
|
C
|
H:GLY223
|
4.9
|
32.3
|
1.0
|
N
|
H:ASP220
|
5.0
|
30.2
|
1.0
|
|
Sodium binding site 2 out
of 6 in 7mj5
Go back to
Sodium Binding Sites List in 7mj5
Sodium binding site 2 out
of 6 in the Complex of Human Thrombin with Xc-43
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na302
b:33.6
occ:1.00
|
O
|
C:ARG222
|
2.3
|
32.1
|
1.0
|
O
|
C:HOH459
|
2.3
|
28.3
|
1.0
|
O
|
C:HOH558
|
2.4
|
30.9
|
1.0
|
O
|
C:HOH440
|
2.5
|
29.9
|
1.0
|
O
|
C:LYS225
|
2.5
|
33.0
|
1.0
|
O
|
C:HOH529
|
2.7
|
33.1
|
1.0
|
C
|
C:ARG222
|
3.3
|
31.2
|
1.0
|
C
|
C:LYS225
|
3.5
|
32.2
|
1.0
|
N
|
C:ARG222
|
3.7
|
31.8
|
1.0
|
O
|
C:HOH559
|
3.8
|
32.7
|
1.0
|
N
|
C:LYS225
|
3.9
|
31.5
|
1.0
|
O
|
C:HOH497
|
4.0
|
31.4
|
1.0
|
C
|
C:ASP221
|
4.0
|
30.9
|
1.0
|
O
|
C:TYR184A
|
4.0
|
33.0
|
1.0
|
CA
|
C:ARG222
|
4.1
|
31.9
|
1.0
|
CA
|
C:LYS225
|
4.2
|
28.9
|
1.0
|
CA
|
C:ASP221
|
4.2
|
30.8
|
1.0
|
N
|
C:ASP223
|
4.2
|
31.2
|
1.0
|
O
|
C:HOH489
|
4.3
|
29.3
|
1.0
|
N
|
C:GLY224
|
4.3
|
33.9
|
1.0
|
CA
|
C:ASP223
|
4.4
|
32.9
|
1.0
|
N
|
C:TYR226
|
4.5
|
31.8
|
1.0
|
O
|
C:ASP221
|
4.6
|
30.9
|
1.0
|
CB
|
C:LYS225
|
4.6
|
31.8
|
1.0
|
OD1
|
C:ASP221
|
4.6
|
29.8
|
1.0
|
C
|
C:ASP223
|
4.6
|
34.7
|
1.0
|
CA
|
C:TYR226
|
4.8
|
33.6
|
1.0
|
O
|
C:HOH490
|
4.8
|
33.3
|
1.0
|
N
|
C:ASP221
|
4.9
|
31.4
|
1.0
|
C
|
C:GLY224
|
4.9
|
35.8
|
1.0
|
|
Sodium binding site 3 out
of 6 in 7mj5
Go back to
Sodium Binding Sites List in 7mj5
Sodium binding site 3 out
of 6 in the Complex of Human Thrombin with Xc-43
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na302
b:31.8
occ:1.00
|
O
|
E:ARG222
|
2.3
|
30.5
|
1.0
|
O
|
E:HOH526
|
2.4
|
31.9
|
1.0
|
O
|
E:LYS225
|
2.4
|
32.1
|
1.0
|
O
|
E:HOH429
|
2.4
|
27.6
|
1.0
|
O
|
E:HOH430
|
2.5
|
29.3
|
1.0
|
O
|
E:HOH459
|
2.6
|
29.7
|
1.0
|
C
|
E:ARG222
|
3.3
|
31.6
|
1.0
|
C
|
E:LYS225
|
3.4
|
30.7
|
1.0
|
O
|
E:HOH509
|
3.7
|
33.6
|
1.0
|
N
|
E:ARG222
|
3.8
|
28.4
|
1.0
|
N
|
E:LYS225
|
3.8
|
31.9
|
1.0
|
O
|
E:TYR184A
|
4.0
|
30.8
|
1.0
|
C
|
E:ASP221
|
4.1
|
31.1
|
1.0
|
O
|
E:HOH444
|
4.1
|
30.4
|
1.0
|
CA
|
E:LYS225
|
4.1
|
31.4
|
1.0
|
CA
|
E:ARG222
|
4.2
|
29.8
|
1.0
|
O
|
E:HOH479
|
4.2
|
28.9
|
1.0
|
N
|
E:ASP223
|
4.2
|
29.3
|
1.0
|
N
|
E:GLY224
|
4.3
|
31.5
|
1.0
|
CA
|
E:ASP221
|
4.3
|
30.5
|
1.0
|
CA
|
E:ASP223
|
4.4
|
29.3
|
1.0
|
N
|
E:TYR226
|
4.4
|
33.9
|
1.0
|
C
|
E:ASP223
|
4.6
|
31.2
|
1.0
|
CB
|
E:LYS225
|
4.6
|
30.5
|
1.0
|
CA
|
E:TYR226
|
4.7
|
29.7
|
1.0
|
OD1
|
E:ASP221
|
4.7
|
32.2
|
1.0
|
O
|
E:ASP221
|
4.7
|
31.5
|
1.0
|
C
|
E:GLY224
|
4.9
|
32.2
|
1.0
|
O
|
E:HOH435
|
4.9
|
32.4
|
1.0
|
CD1
|
E:TYR226
|
5.0
|
30.0
|
1.0
|
|
Sodium binding site 4 out
of 6 in 7mj5
Go back to
Sodium Binding Sites List in 7mj5
Sodium binding site 4 out
of 6 in the Complex of Human Thrombin with Xc-43
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na302
b:38.1
occ:1.00
|
O
|
G:ARG222
|
2.4
|
35.0
|
1.0
|
O
|
G:LYS225
|
2.4
|
36.4
|
1.0
|
O
|
G:HOH493
|
2.4
|
35.9
|
1.0
|
O
|
G:HOH481
|
2.4
|
33.9
|
1.0
|
O
|
G:HOH511
|
2.5
|
36.5
|
1.0
|
O
|
G:HOH440
|
2.7
|
35.9
|
1.0
|
C
|
G:ARG222
|
3.4
|
37.1
|
1.0
|
C
|
G:LYS225
|
3.5
|
40.4
|
1.0
|
N
|
G:ARG222
|
3.8
|
35.3
|
1.0
|
O
|
G:TYR184A
|
3.9
|
38.1
|
1.0
|
N
|
G:LYS225
|
4.0
|
37.7
|
1.0
|
O
|
G:HOH455
|
4.1
|
33.9
|
1.0
|
O
|
G:HOH470
|
4.1
|
34.3
|
1.0
|
C
|
G:ASP221
|
4.1
|
33.3
|
1.0
|
CA
|
G:ARG222
|
4.2
|
33.4
|
1.0
|
CA
|
G:LYS225
|
4.2
|
37.3
|
1.0
|
N
|
G:ASP223
|
4.2
|
35.0
|
1.0
|
CA
|
G:ASP221
|
4.3
|
32.5
|
1.0
|
N
|
G:TYR226
|
4.4
|
36.6
|
1.0
|
CA
|
G:ASP223
|
4.4
|
36.6
|
1.0
|
N
|
G:GLY224
|
4.4
|
37.6
|
1.0
|
CA
|
G:TYR226
|
4.6
|
37.5
|
1.0
|
C
|
G:ASP223
|
4.7
|
39.6
|
1.0
|
CB
|
G:LYS225
|
4.7
|
38.3
|
1.0
|
O
|
G:HOH501
|
4.7
|
39.2
|
1.0
|
OD1
|
G:ASP221
|
4.7
|
32.9
|
1.0
|
O
|
G:ASP221
|
4.8
|
37.6
|
1.0
|
CD1
|
G:TYR226
|
4.9
|
40.8
|
1.0
|
N
|
G:ASP221
|
5.0
|
33.6
|
1.0
|
C
|
G:GLY224
|
5.0
|
39.3
|
1.0
|
|
Sodium binding site 5 out
of 6 in 7mj5
Go back to
Sodium Binding Sites List in 7mj5
Sodium binding site 5 out
of 6 in the Complex of Human Thrombin with Xc-43
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Na302
b:36.0
occ:1.00
|
O
|
J:ARG222
|
2.3
|
33.4
|
1.0
|
O
|
J:HOH475
|
2.4
|
31.4
|
1.0
|
O
|
J:LYS225
|
2.4
|
35.0
|
1.0
|
O
|
J:HOH534
|
2.5
|
31.1
|
1.0
|
O
|
J:HOH451
|
2.5
|
33.9
|
1.0
|
O
|
J:HOH460
|
2.5
|
33.6
|
1.0
|
C
|
J:ARG222
|
3.3
|
33.4
|
1.0
|
C
|
J:LYS225
|
3.5
|
34.5
|
1.0
|
N
|
J:ARG222
|
3.8
|
31.3
|
1.0
|
N
|
J:LYS225
|
3.9
|
34.1
|
1.0
|
O
|
J:HOH514
|
3.9
|
34.2
|
1.0
|
O
|
J:TYR184A
|
3.9
|
37.6
|
1.0
|
O
|
J:HOH462
|
4.0
|
33.0
|
1.0
|
C
|
J:ASP221
|
4.1
|
31.5
|
1.0
|
CA
|
J:ARG222
|
4.1
|
32.7
|
1.0
|
CA
|
J:LYS225
|
4.2
|
34.7
|
1.0
|
N
|
J:ASP223
|
4.2
|
30.7
|
1.0
|
O
|
J:HOH461
|
4.2
|
31.5
|
1.0
|
N
|
J:GLY224
|
4.3
|
32.6
|
1.0
|
CA
|
J:ASP223
|
4.3
|
32.8
|
1.0
|
CA
|
J:ASP221
|
4.4
|
31.2
|
1.0
|
N
|
J:TYR226
|
4.5
|
33.7
|
1.0
|
C
|
J:ASP223
|
4.6
|
33.4
|
1.0
|
CB
|
J:LYS225
|
4.6
|
33.0
|
1.0
|
O
|
J:ASP221
|
4.7
|
32.1
|
1.0
|
CA
|
J:TYR226
|
4.7
|
33.5
|
1.0
|
O
|
J:HOH532
|
4.7
|
31.1
|
1.0
|
OD1
|
J:ASP221
|
4.8
|
35.0
|
1.0
|
C
|
J:GLY224
|
4.9
|
34.1
|
1.0
|
|
Sodium binding site 6 out
of 6 in 7mj5
Go back to
Sodium Binding Sites List in 7mj5
Sodium binding site 6 out
of 6 in the Complex of Human Thrombin with Xc-43
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Na302
b:34.3
occ:1.00
|
O
|
M:ARG222
|
2.3
|
32.9
|
1.0
|
O
|
M:HOH470
|
2.4
|
30.1
|
1.0
|
O
|
M:LYS225
|
2.5
|
33.8
|
1.0
|
O
|
M:HOH469
|
2.5
|
33.2
|
1.0
|
O
|
M:HOH457
|
2.7
|
34.4
|
1.0
|
C
|
M:ARG222
|
3.3
|
33.7
|
1.0
|
C
|
M:LYS225
|
3.5
|
35.3
|
1.0
|
N
|
M:ARG222
|
3.7
|
31.8
|
1.0
|
O
|
M:HOH514
|
3.8
|
34.7
|
1.0
|
N
|
M:LYS225
|
3.9
|
34.0
|
1.0
|
C
|
M:ASP221
|
4.0
|
32.3
|
1.0
|
O
|
M:TYR184A
|
4.1
|
33.3
|
1.0
|
O
|
M:HOH441
|
4.1
|
32.1
|
1.0
|
CA
|
M:ARG222
|
4.1
|
34.6
|
1.0
|
O
|
M:HOH453
|
4.2
|
31.6
|
1.0
|
N
|
M:ASP223
|
4.2
|
30.4
|
1.0
|
CA
|
M:ASP221
|
4.2
|
30.8
|
1.0
|
CA
|
M:LYS225
|
4.2
|
34.9
|
1.0
|
N
|
M:GLY224
|
4.4
|
35.4
|
1.0
|
CA
|
M:ASP223
|
4.4
|
34.4
|
1.0
|
N
|
M:TYR226
|
4.5
|
34.2
|
1.0
|
O
|
M:HOH522
|
4.6
|
33.8
|
1.0
|
O
|
M:ASP221
|
4.6
|
31.9
|
1.0
|
OD1
|
M:ASP221
|
4.6
|
33.0
|
1.0
|
CB
|
M:LYS225
|
4.6
|
37.7
|
1.0
|
C
|
M:ASP223
|
4.7
|
35.0
|
1.0
|
CA
|
M:TYR226
|
4.7
|
35.4
|
1.0
|
N
|
M:ASP221
|
4.9
|
28.6
|
1.0
|
C
|
M:GLY224
|
5.0
|
35.9
|
1.0
|
|
Reference:
S.Lu,
L.Tirloni,
M.B.Oliveira,
C.F.Bosio,
G.A.Nardone,
Y.Zhang,
B.J.Hinnebusch,
J.M.Ribeiro,
J.F.Andersen.
Identification of A Substrate-Like Cleavage-Resistant Thrombin Inhibitor From the Saliva of the Flea Xenopsylla Cheopis. J.Biol.Chem. V. 297 01322 2021.
ISSN: ESSN 1083-351X
PubMed: 34688666
DOI: 10.1016/J.JBC.2021.101322
Page generated: Tue Oct 8 17:58:51 2024
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