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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


Mono view


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

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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


Mono view


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


Mono view


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


Mono view


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

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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


Mono view


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


Mono view


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


Mono view


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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