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Sodium in PDB 3p6z: 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: 3p6z 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) 31.92 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.208, 62.259, 67.510, 99.38, 110.46, 92.26
R / Rfree (%) 20 / 23.9

Other elements in 3p6z:

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 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

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 3p6z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 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: 3p6z:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3p6z

Go back to Sodium Binding Sites List in 3p6z
Sodium binding site 1 out of 9 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
A:Na809

b:57.3
occ:1.00
 OE1 A:GLU348 2.5 46.5 1.0
O A:HOH993 2.8 26.4 1.0
CD A:GLU348 3.5 43.2 1.0
CB A:GLU348 3.6 29.2 1.0
O A:HOH1366 3.8 34.5 1.0
CB A:ARG353 3.8 25.4 1.0
CG A:GLU348 3.9 35.0 1.0
O A:ASP349 4.3 26.6 1.0
CD A:ARG353 4.3 31.0 0.6
O A:HOH1138 4.3 45.1 1.0
NE A:ARG353 4.3 30.6 0.4
CZ A:ARG353 4.4 27.6 0.4
N A:ARG353 4.5 22.1 1.0
OE2 A:GLU348 4.6 43.6 1.0
CG A:GLU352 4.6 21.7 1.0
CG A:ARG353 4.6 29.0 1.0
CA A:ARG353 4.6 22.9 1.0
CD A:ARG353 4.7 26.4 0.4
NH2 A:ARG353 4.7 31.2 0.4
NH1 A:ARG353 4.8 26.0 0.4

Sodium binding site 2 out of 9 in 3p6z

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Sodium binding site 2 out of 9 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:Na802

b:24.0
occ:1.00
 O B:HOH1011 2.1 23.5 1.0
O B:HOH1012 2.4 21.5 1.0
O B:ARG596 2.5 27.3 1.0
O B:LYS599 2.5 26.6 1.0
O B:HOH905 2.5 23.1 1.0
O B:HOH952 2.8 24.8 1.0
C B:ARG596 3.5 30.5 1.0
C B:LYS599 3.6 26.5 1.0
O B:HOH1014 3.9 34.5 1.0
O B:TYR553 3.9 26.5 1.0
N B:ARG596 3.9 28.0 1.0
C B:ASP595 4.0 27.8 1.0
N B:LYS599 4.0 28.1 1.0
O B:HOH949 4.1 22.5 1.0
O B:HOH970 4.1 21.8 1.0
N B:ASP597 4.3 31.4 1.0
N B:GLY598 4.3 32.0 1.0
CA B:LYS599 4.3 27.5 1.0
CA B:ASP597 4.3 33.0 1.0
CA B:ASP595 4.3 25.8 1.0
CA B:ARG596 4.4 29.9 1.0
O B:ASP595 4.4 29.7 1.0
OD1 B:ASP595 4.4 25.9 1.0
C B:ASP597 4.6 33.1 1.0
N B:TYR600 4.7 25.1 1.0
CB B:LYS599 4.8 27.6 1.0
O B:HOH1045 4.8 27.9 1.0
C B:GLY598 4.9 29.8 1.0
CA B:TYR600 5.0 23.9 1.0

Sodium binding site 3 out of 9 in 3p6z

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Sodium binding site 3 out of 9 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
B:Na805

b:52.9
occ:1.00
 O B:PHE417 2.4 38.2 1.0
OD1 B:ASN416 3.3 40.0 1.0
O B:LEU408 3.5 25.6 1.0
C B:PHE417 3.5 35.6 1.0
N B:PHE417 3.6 31.2 1.0
CD1 B:ILE449 3.8 29.6 1.0
CB B:LEU408 3.9 22.8 1.0
C B:LEU408 3.9 23.8 1.0
CA B:PHE417 4.1 33.5 1.0
C B:ASN416 4.1 32.8 1.0
CA B:LEU408 4.4 23.7 1.0
CA B:ASN416 4.5 32.5 1.0
CG B:ASN416 4.5 40.2 1.0
CG2 B:ILE447 4.5 25.1 1.0
CD1 B:ILE447 4.6 28.8 1.0
N B:THR418 4.6 37.8 1.0
CB B:LEU409 4.6 24.0 1.0
O B:HOH1309 4.6 49.8 1.0
N B:LEU409 4.6 21.7 1.0
CB B:PHE417 4.7 31.8 1.0
O B:ASN416 4.8 33.4 1.0
CA B:LEU409 4.9 22.8 1.0
CA B:THR418 4.9 38.8 1.0
CG1 B:ILE449 5.0 26.7 1.0

Sodium binding site 4 out of 9 in 3p6z

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Sodium binding site 4 out of 9 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
G:Na804

b:31.7
occ:1.00
 O G:HOH1117 2.3 36.1 1.0
O H:HOH944 2.3 20.0 1.0
O G:TYR359 2.4 23.0 1.0
OH H:TYR497 2.8 20.6 1.0
C G:TYR359 3.5 22.1 1.0
CZ H:TYR497 3.9 20.9 1.0
CA G:ILE360 3.9 23.6 1.0
O G:ILE360 4.0 26.7 1.0
N G:ILE360 4.2 22.3 1.0
C G:ILE360 4.2 25.5 1.0
O H:HOH1232 4.3 19.3 1.0
CE1 H:TYR497 4.3 23.3 1.0
O H:HOH1339 4.6 21.2 1.0
CA G:TYR359 4.7 20.6 1.0
CE2 H:TYR497 4.9 20.4 1.0

Sodium binding site 5 out of 9 in 3p6z

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Sodium binding site 5 out of 9 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
H:Na801

b:22.9
occ:1.00
 O H:HOH1002 2.3 21.4 1.0
O H:ARG596 2.4 25.5 1.0
O H:LYS599 2.4 22.9 1.0
O H:HOH1025 2.4 20.4 1.0
O H:HOH1003 2.6 22.1 1.0
O H:HOH934 2.7 21.6 1.0
C H:ARG596 3.4 28.1 1.0
C H:LYS599 3.5 21.9 1.0
O H:HOH1086 3.9 25.1 1.0
N H:LYS599 3.9 23.2 1.0
O H:HOH1072 4.0 30.1 1.0
O H:TYR553 4.0 21.8 1.0
N H:ARG596 4.0 26.3 1.0
C H:ASP595 4.1 26.5 1.0
O H:HOH926 4.2 20.9 1.0
CA H:LYS599 4.2 23.1 1.0
N H:ASP597 4.3 27.6 1.0
CA H:ASP597 4.3 28.3 1.0
CA H:ASP595 4.3 25.4 1.0
CA H:ARG596 4.3 28.1 1.0
N H:GLY598 4.4 25.9 1.0
OD1 H:ASP595 4.5 25.7 1.0
N H:TYR600 4.5 22.5 1.0
C H:ASP597 4.5 27.3 1.0
O H:ASP595 4.6 27.3 1.0
CB H:LYS599 4.7 24.5 1.0
O H:HOH906 4.7 28.4 1.0
CA H:TYR600 4.8 18.6 1.0
C H:GLY598 4.9 24.6 1.0
CD1 H:TYR600 4.9 18.3 1.0
CE1 H:TYR600 5.0 21.5 1.0

Sodium binding site 6 out of 9 in 3p6z

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Sodium binding site 6 out of 9 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
H:Na803

b:42.6
occ:1.00
 O H:LYS470 2.5 33.1 1.0
OG H:SER442 3.0 30.6 1.0
O H:HOH1029 3.1 32.7 1.0
C H:LYS470 3.3 33.5 1.0
CB H:SER442 3.5 28.9 1.0
CG1 H:VAL472 3.6 31.9 0.4
CG2 H:VAL472 3.6 33.0 0.6
CB H:LYS470 3.8 33.9 1.0
CA H:LYS470 3.9 33.8 1.0
N H:LYS470 3.9 32.5 1.0
C H:PRO471 3.9 32.9 1.0
O H:PRO471 3.9 33.9 1.0
N H:VAL472 4.0 32.1 1.0
CA H:VAL472 4.2 31.5 1.0
CD1 H:LEU468 4.2 26.1 1.0
CA H:SER442 4.2 29.6 1.0
N H:PRO471 4.3 33.8 1.0
CB H:LEU468 4.3 25.7 1.0
CB H:VAL472 4.5 32.0 1.0
CA H:PRO471 4.5 33.5 1.0
CG H:LYS470 4.8 37.7 1.0
CG H:LEU468 4.8 25.6 1.0
O H:HOH1290 4.9 52.2 1.0

Sodium binding site 7 out of 9 in 3p6z

Go back to Sodium Binding Sites List in 3p6z
Sodium binding site 7 out of 9 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:Na806

b:50.5
occ:1.00
 O H:PRO555 2.4 33.0 1.0
O H:HOH936 3.1 26.2 1.0
C H:PRO555 3.4 31.7 1.0
CA H:PRO555 3.6 30.2 1.0
CA H:GLY558 3.7 33.2 1.0
N H:GLY558 3.9 32.6 1.0
O H:GLY558 4.0 35.5 1.0
NH1 H:ARG560 4.1 32.1 1.0
C H:GLY558 4.2 33.9 1.0
OD1 H:ASP597 4.2 35.5 1.0
O H:HOH1072 4.4 30.1 1.0
CB H:PRO555 4.4 30.7 1.0
N H:ASP556 4.6 33.6 1.0
O H:LYS554 4.7 28.1 1.0
CG H:ASP597 4.8 32.7 1.0
OD2 H:ASP597 4.8 37.5 1.0
N H:PRO555 4.9 29.0 1.0

Sodium binding site 8 out of 9 in 3p6z

Go back to Sodium Binding Sites List in 3p6z
Sodium binding site 8 out of 9 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 8 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:Na807

b:53.7
occ:1.00
 OD1 H:ASP476 2.3 35.5 1.0
N H:ASP476 3.4 26.1 1.0
CG H:ASP476 3.4 31.6 1.0
C H:SER475 3.7 26.0 1.0
CA H:ASP476 3.8 26.2 1.0
CB G:PRO340 3.8 26.2 1.0
O H:SER475 4.1 25.7 1.0
O G:HOH985 4.1 41.8 1.0
O H:HOH1325 4.2 35.5 1.0
CB H:ASP476 4.2 27.7 1.0
CG G:PRO340 4.2 24.5 1.0
CA H:SER475 4.3 25.4 1.0
OD2 H:ASP476 4.4 35.0 1.0
O H:HOH1145 4.7 18.2 1.0
O G:HOH1123 4.7 31.4 1.0

Sodium binding site 9 out of 9 in 3p6z

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Sodium binding site 9 out of 9 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 9 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:Na808

b:60.5
occ:1.00
 O H:TRP455 2.4 29.0 1.0
OH H:TYR410 2.8 23.2 1.0
CE2 H:0G6707 3.5 29.4 1.0
CE1 H:TYR410 3.6 22.5 1.0
CZ H:TYR410 3.6 26.0 1.0
C H:TRP455 3.6 27.3 1.0
CZ H:0G6707 3.7 28.8 1.0
O H:ARG456 3.9 31.6 1.0
C H:ARG456 4.0 29.6 1.0
O H:GLU457 4.2 30.1 1.0
N H:GLU457 4.4 28.9 1.0
C H:GLU457 4.5 27.7 1.0
CA H:ARG456 4.5 30.0 1.0
N H:ARG456 4.5 27.8 1.0
CA H:TRP455 4.6 25.8 1.0
CD2 H:LEU459 4.6 25.6 1.0
CD2 H:0G6707 4.7 29.1 1.0
CA H:GLU457 4.8 28.3 1.0
CE2 H:TYR410 4.9 29.0 1.0
CD1 H:TYR410 4.9 19.4 1.0
CG H:PRO412 5.0 31.0 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: Mon Oct 7 12:11:25 2024

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