Sodium in PDB 3p70: Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
Enzymatic activity of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
All present enzymatic activity of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction:
3.4.21.5;
Protein crystallography data
The structure of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction, PDB code: 3p70
was solved by
M.A.Corral-Rodriguez,
P.E.Bock,
E.Hernandez-Carvajal,
R.Gutierrez-Gallego,
P.Fuentes-Prior,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
61.28 /
2.55
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.243,
68.227,
98.972,
72.57,
84.05,
80.45
|
R / Rfree (%)
|
20.7 /
27.9
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
(pdb code 3p70). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction, PDB code: 3p70:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 3p70
Go back to
Sodium Binding Sites List in 3p70
Sodium binding site 1 out
of 7 in the Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
![](/pictures/NA/pdb/p7/3p70-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/p7/3p70-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1500
b:49.8
occ:1.00
|
O
|
B:HOH3517
|
2.5
|
6.6
|
1.0
|
O
|
B:ARG596
|
2.8
|
54.6
|
1.0
|
O
|
B:HOH3503
|
2.8
|
6.3
|
1.0
|
O
|
B:LYS599
|
3.2
|
42.8
|
1.0
|
C
|
B:ARG596
|
3.5
|
56.3
|
1.0
|
O
|
B:TYR553
|
3.8
|
48.1
|
1.0
|
C
|
B:ASP595
|
3.8
|
50.0
|
1.0
|
O
|
B:ASP595
|
3.8
|
51.6
|
1.0
|
N
|
B:ASP597
|
4.0
|
58.8
|
1.0
|
CA
|
B:ASP597
|
4.0
|
59.7
|
1.0
|
N
|
B:ARG596
|
4.0
|
50.5
|
1.0
|
OD1
|
B:ASP595
|
4.2
|
47.7
|
1.0
|
CA
|
B:ASP595
|
4.2
|
47.5
|
1.0
|
C
|
B:LYS599
|
4.3
|
43.8
|
1.0
|
CA
|
B:ARG596
|
4.4
|
55.4
|
1.0
|
NH2
|
B:ARG560
|
4.5
|
57.1
|
1.0
|
N
|
B:LYS599
|
4.5
|
50.6
|
1.0
|
N
|
B:GLY598
|
4.5
|
57.2
|
1.0
|
C
|
B:ASP597
|
4.5
|
59.1
|
1.0
|
OD1
|
B:ASP597
|
4.7
|
64.7
|
1.0
|
CG
|
B:ASP595
|
4.8
|
49.7
|
1.0
|
CA
|
B:LYS599
|
4.9
|
47.7
|
1.0
|
C
|
B:TYR553
|
5.0
|
47.9
|
1.0
|
|
Sodium binding site 2 out
of 7 in 3p70
Go back to
Sodium Binding Sites List in 3p70
Sodium binding site 2 out
of 7 in the Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
![](/pictures/NA/pdb/p7/3p70-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/p7/3p70-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1501
b:50.9
occ:1.00
|
O
|
B:GLY569
|
2.6
|
29.2
|
1.0
|
O
|
B:LEU402
|
2.9
|
30.9
|
1.0
|
NE2
|
B:GLN584
|
3.3
|
36.3
|
1.0
|
OG
|
B:SER394
|
3.4
|
33.6
|
1.0
|
C
|
B:GLY570
|
3.6
|
27.0
|
1.0
|
C
|
B:GLY569
|
3.6
|
27.7
|
1.0
|
N
|
B:SER394
|
3.6
|
30.8
|
1.0
|
O
|
B:GLY570
|
3.7
|
28.1
|
1.0
|
C
|
B:ALA393
|
3.7
|
31.3
|
1.0
|
CB
|
B:SER394
|
3.8
|
30.8
|
1.0
|
CA
|
B:ALA393
|
3.8
|
31.9
|
1.0
|
C
|
B:LEU402
|
3.8
|
32.1
|
1.0
|
CA
|
B:GLY570
|
3.9
|
25.4
|
1.0
|
N
|
B:PRO571
|
3.9
|
27.4
|
1.0
|
CD
|
B:GLN584
|
4.1
|
36.1
|
1.0
|
CA
|
B:PRO571
|
4.1
|
27.2
|
1.0
|
CG1
|
B:ILE587
|
4.1
|
28.1
|
1.0
|
CG2
|
B:ILE587
|
4.2
|
27.5
|
1.0
|
N
|
B:GLY570
|
4.2
|
25.9
|
1.0
|
CA
|
B:THR403
|
4.2
|
31.3
|
1.0
|
OE1
|
B:GLN584
|
4.3
|
35.2
|
1.0
|
CD
|
B:PRO571
|
4.3
|
27.1
|
1.0
|
CA
|
B:SER394
|
4.3
|
31.0
|
1.0
|
N
|
B:THR403
|
4.4
|
32.4
|
1.0
|
O
|
B:ALA393
|
4.4
|
30.9
|
1.0
|
CB
|
B:PRO571
|
4.4
|
28.1
|
1.0
|
CB
|
B:LEU402
|
4.4
|
29.9
|
1.0
|
N
|
B:ALA393
|
4.4
|
30.3
|
1.0
|
CB
|
B:ILE587
|
4.5
|
28.6
|
1.0
|
CG
|
B:LEU402
|
4.6
|
31.5
|
1.0
|
CA
|
B:LEU402
|
4.7
|
32.4
|
1.0
|
CA
|
B:ILE587
|
4.7
|
27.0
|
1.0
|
CA
|
B:GLY569
|
4.8
|
29.0
|
1.0
|
CD1
|
B:ILE587
|
4.8
|
30.7
|
1.0
|
CG
|
B:PRO571
|
5.0
|
26.5
|
1.0
|
C
|
B:THR403
|
5.0
|
31.3
|
1.0
|
CB
|
B:ALA393
|
5.0
|
33.5
|
1.0
|
|
Sodium binding site 3 out
of 7 in 3p70
Go back to
Sodium Binding Sites List in 3p70
Sodium binding site 3 out
of 7 in the Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
![](/pictures/NA/pdb/p7/3p70-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/p7/3p70-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3200
b:66.0
occ:1.00
|
O
|
C:TYR359
|
2.5
|
41.6
|
1.0
|
OH
|
D:TYR497
|
2.5
|
33.1
|
1.0
|
O
|
C:HOH3511
|
2.6
|
22.2
|
1.0
|
CZ
|
D:TYR497
|
3.7
|
35.6
|
1.0
|
C
|
C:TYR359
|
3.7
|
39.8
|
1.0
|
CA
|
C:ILE360
|
4.1
|
40.9
|
1.0
|
CE1
|
D:TYR497
|
4.3
|
36.1
|
1.0
|
N
|
C:ILE360
|
4.4
|
40.0
|
1.0
|
O
|
C:ILE360
|
4.5
|
44.8
|
1.0
|
C
|
C:ILE360
|
4.5
|
43.7
|
1.0
|
CE2
|
D:TYR497
|
4.6
|
33.6
|
1.0
|
CA
|
C:TYR359
|
4.8
|
37.9
|
1.0
|
|
Sodium binding site 4 out
of 7 in 3p70
Go back to
Sodium Binding Sites List in 3p70
Sodium binding site 4 out
of 7 in the Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
![](/pictures/NA/pdb/p7/3p70-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/p7/3p70-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na1500
b:28.5
occ:1.00
|
O
|
D:ARG596
|
2.7
|
58.8
|
1.0
|
O
|
D:LYS599
|
2.8
|
50.2
|
1.0
|
C
|
D:ARG596
|
3.6
|
62.5
|
1.0
|
C
|
D:ASP595
|
3.9
|
54.2
|
1.0
|
O
|
D:TYR553
|
3.9
|
51.4
|
1.0
|
C
|
D:LYS599
|
3.9
|
51.8
|
1.0
|
N
|
D:ARG596
|
4.0
|
56.0
|
1.0
|
OD1
|
D:ASP595
|
4.1
|
49.4
|
1.0
|
O
|
D:ASP595
|
4.2
|
56.6
|
1.0
|
N
|
D:LYS599
|
4.2
|
60.5
|
1.0
|
CA
|
D:ASP595
|
4.2
|
49.4
|
1.0
|
N
|
D:ASP597
|
4.3
|
66.6
|
1.0
|
CA
|
D:ARG596
|
4.4
|
61.7
|
1.0
|
CA
|
D:ASP597
|
4.4
|
68.3
|
1.0
|
CA
|
D:LYS599
|
4.5
|
57.6
|
1.0
|
NH2
|
D:ARG560
|
4.6
|
67.7
|
1.0
|
N
|
D:GLY598
|
4.7
|
68.3
|
1.0
|
CB
|
D:LYS599
|
4.8
|
57.5
|
1.0
|
C
|
D:ASP597
|
4.9
|
69.9
|
1.0
|
CG
|
D:ASP595
|
4.9
|
50.4
|
1.0
|
N
|
D:TYR600
|
5.0
|
49.3
|
1.0
|
|
Sodium binding site 5 out
of 7 in 3p70
Go back to
Sodium Binding Sites List in 3p70
Sodium binding site 5 out
of 7 in the Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
![](/pictures/NA/pdb/p7/3p70-NA-sphere_05.jpg) Mono view
![](/pictures/NA/pdb/p7/3p70-NA-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na1500
b:42.2
occ:1.00
|
O
|
F:ARG596
|
2.6
|
58.8
|
1.0
|
O
|
F:HOH3505
|
2.8
|
12.2
|
1.0
|
O
|
F:LYS599
|
3.1
|
49.0
|
1.0
|
O
|
F:HOH3510
|
3.3
|
18.8
|
1.0
|
OD1
|
F:ASP595
|
3.5
|
53.3
|
1.0
|
C
|
F:ARG596
|
3.5
|
60.7
|
1.0
|
C
|
F:ASP595
|
3.6
|
57.3
|
1.0
|
N
|
F:ARG596
|
3.8
|
57.2
|
1.0
|
CA
|
F:ASP595
|
3.9
|
55.0
|
1.0
|
O
|
F:ASP595
|
4.0
|
59.5
|
1.0
|
O
|
F:TYR553
|
4.1
|
50.8
|
1.0
|
N
|
F:ASP597
|
4.2
|
63.7
|
1.0
|
C
|
F:LYS599
|
4.2
|
50.9
|
1.0
|
CA
|
F:ASP597
|
4.2
|
64.0
|
1.0
|
CG
|
F:ASP595
|
4.3
|
57.1
|
1.0
|
CA
|
F:ARG596
|
4.3
|
60.5
|
1.0
|
NH2
|
F:ARG560
|
4.4
|
57.8
|
1.0
|
OD1
|
F:ASP597
|
4.5
|
67.8
|
1.0
|
CB
|
F:ASP595
|
4.7
|
55.1
|
1.0
|
N
|
F:LYS599
|
4.7
|
56.9
|
1.0
|
N
|
F:GLY598
|
4.9
|
61.3
|
1.0
|
N
|
F:ASP595
|
4.9
|
54.7
|
1.0
|
CA
|
F:LYS599
|
4.9
|
54.1
|
1.0
|
C
|
F:ASP597
|
5.0
|
64.0
|
1.0
|
O
|
F:GLY561
|
5.0
|
46.8
|
1.0
|
|
Sodium binding site 6 out
of 7 in 3p70
Go back to
Sodium Binding Sites List in 3p70
Sodium binding site 6 out
of 7 in the Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
![](/pictures/NA/pdb/p7/3p70-NA-sphere_06.jpg) Mono view
![](/pictures/NA/pdb/p7/3p70-NA-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na1501
b:50.2
occ:1.00
|
OH
|
H:TYR497
|
2.7
|
32.8
|
1.0
|
O
|
G:TYR359
|
2.9
|
37.0
|
1.0
|
CZ
|
H:TYR497
|
3.8
|
33.6
|
1.0
|
C
|
G:TYR359
|
4.1
|
37.8
|
1.0
|
CE1
|
H:TYR497
|
4.1
|
32.2
|
1.0
|
O
|
G:ILE360
|
4.4
|
48.2
|
1.0
|
C
|
G:ILE360
|
4.7
|
46.6
|
1.0
|
CA
|
G:ILE360
|
4.8
|
43.2
|
1.0
|
N
|
G:ILE360
|
4.9
|
40.8
|
1.0
|
CE2
|
H:TYR497
|
4.9
|
31.3
|
1.0
|
O
|
G:ASP361
|
5.0
|
50.2
|
1.0
|
|
Sodium binding site 7 out
of 7 in 3p70
Go back to
Sodium Binding Sites List in 3p70
Sodium binding site 7 out
of 7 in the Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction
![](/pictures/NA/pdb/p7/3p70-NA-sphere_07.jpg) Mono view
![](/pictures/NA/pdb/p7/3p70-NA-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structural Basis of Thrombin-Mediated Factor V Activation: Essential Role of the Hirudin-Like Sequence GLU666-GLU672 For Processing at the Heavy Chain-B Domain Junction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na1500
b:48.6
occ:1.00
|
O
|
H:ARG596
|
2.6
|
49.9
|
1.0
|
O
|
H:LYS599
|
2.7
|
40.5
|
1.0
|
O
|
H:HOH3501
|
2.8
|
15.2
|
1.0
|
O
|
H:HOH3502
|
3.2
|
13.2
|
1.0
|
C
|
H:ARG596
|
3.5
|
51.8
|
1.0
|
C
|
H:ASP595
|
3.8
|
46.9
|
1.0
|
C
|
H:LYS599
|
3.9
|
40.7
|
1.0
|
O
|
H:TYR553
|
4.0
|
45.5
|
1.0
|
OD1
|
H:ASP595
|
4.0
|
47.1
|
1.0
|
O
|
H:ASP595
|
4.0
|
48.5
|
1.0
|
N
|
H:ARG596
|
4.0
|
47.5
|
1.0
|
CA
|
H:ASP595
|
4.1
|
44.6
|
1.0
|
CA
|
H:ASP597
|
4.1
|
54.7
|
1.0
|
N
|
H:ASP597
|
4.2
|
54.5
|
1.0
|
N
|
H:LYS599
|
4.3
|
46.7
|
1.0
|
CA
|
H:ARG596
|
4.4
|
51.2
|
1.0
|
N
|
H:GLY598
|
4.5
|
52.8
|
1.0
|
CA
|
H:LYS599
|
4.5
|
43.8
|
1.0
|
C
|
H:ASP597
|
4.6
|
54.8
|
1.0
|
CB
|
H:LYS599
|
4.8
|
43.3
|
1.0
|
CG
|
H:ASP595
|
4.8
|
47.7
|
1.0
|
NH2
|
H:ARG560
|
4.9
|
47.0
|
1.0
|
OD1
|
H:ASP597
|
4.9
|
52.0
|
1.0
|
N
|
H:TYR600
|
4.9
|
38.7
|
1.0
|
|
Reference:
M.A.Corral-Rodriguez,
P.E.Bock,
E.Hernandez-Carvajal,
R.Gutierrez-Gallego,
P.Fuentes-Prior.
Structural Basis of Thrombin-Mediated Factor V Activation: the GLU666-GLU672 Sequence Is Critical For Processing at the Heavy Chain-B Domain Junction. Blood V. 117 7164 2011.
ISSN: ISSN 0006-4971
PubMed: 21555742
DOI: 10.1182/BLOOD-2010-10-315309
Page generated: Tue Dec 15 06:20:51 2020
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