Sodium in PDB 5nhu: Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant

All present enzymatic activity of Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant:
3.4.21.5;

The structure of Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant, PDB code: 5nhu was solved by J.Ripoll-Rozada, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.18 / 1.45
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.710, 78.640, 136.109, 90.00, 101.84, 90.00
R / Rfree (%)	17.9 / 20.3

The binding sites of Sodium atom in the Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant (pdb code 5nhu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant, PDB code: 5nhu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant within 5.0Å range: probe atom residue distance (Å) B Occ H:Na602 b:20.5 occ:1.00 O H:ARG553 2.3 22.3 1.0 O H:HOH877 2.3 24.1 1.0 O H:LYS556 2.3 21.2 1.0 O H:HOH795 2.4 20.1 1.0 O H:HOH741 2.4 22.1 1.0 O H:HOH820 2.7 24.0 1.0 C H:ARG553 3.3 21.9 1.0 C H:LYS556 3.5 21.0 1.0 N H:LYS556 3.9 22.1 1.0 O H:HOH825 3.9 20.7 1.0 N H:ARG553 3.9 22.4 1.0 C H:ASP552 4.0 20.1 1.0 O H:HOH804 4.1 26.4 1.0 CA H:LYS556 4.2 22.1 1.0 O H:TYR510 4.2 25.8 1.0 O H:HOH775 4.2 20.7 1.0 N H:ASP554 4.2 26.5 1.0 CA H:ARG553 4.2 25.8 1.0 N H:GLY555 4.3 26.2 1.0 CA H:ASP554 4.4 26.5 1.0 CA H:ASP552 4.4 18.8 1.0 O H:ASP552 4.5 23.7 1.0 N H:TYR557 4.5 21.0 1.0 C H:ASP554 4.5 25.5 1.0 CB H:LYS556 4.5 22.8 1.0 OD1 H:ASP552 4.6 24.3 1.0 CA H:TYR557 4.7 18.8 1.0 O H:HOH748 4.7 23.0 1.0 C H:GLY555 4.8 27.7 1.0

Sodium binding site 2 out of 3 in the Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:17.9 occ:1.00 O A:ARG553 2.3 17.5 1.0 O A:LYS556 2.3 17.4 1.0 O A:HOH899 2.4 18.9 1.0 O A:HOH753 2.4 21.6 1.0 O A:HOH776 2.5 15.8 1.0 O A:HOH791 2.6 19.1 1.0 C A:ARG553 3.4 16.4 1.0 C A:LYS556 3.4 15.3 1.0 N A:LYS556 3.8 17.9 1.0 N A:ARG553 3.9 18.3 1.0 O A:HOH824 4.0 17.0 1.0 O A:HOH783 4.0 23.1 1.0 C A:ASP552 4.0 17.1 1.0 O A:TYR510 4.1 19.1 1.0 CA A:LYS556 4.2 15.6 1.0 N A:GLY555 4.2 20.3 1.0 N A:ASP554 4.2 20.3 1.0 O A:HOH814 4.3 17.6 1.0 CA A:ARG553 4.3 18.6 1.0 CA A:ASP554 4.3 19.4 1.0 CA A:ASP552 4.4 18.0 1.0 N A:TYR557 4.5 14.2 1.0 C A:ASP554 4.5 21.0 1.0 O A:ASP552 4.5 20.6 1.0 CB A:LYS556 4.5 16.2 1.0 OD1 A:ASP552 4.6 20.3 1.0 CA A:TYR557 4.7 14.7 1.0 O A:HOH750 4.8 24.6 1.0 C A:GLY555 4.9 19.4 1.0 O A:HOH853 5.0 21.4 1.0

Sodium binding site 3 out of 3 in the Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Alpha Thrombin Complexed with Anopheles Gambiae CE5 Anticoagulant within 5.0Å range: probe atom residue distance (Å) B Occ C:Na602 b:32.1 occ:1.00 O C:HOH768 2.2 32.5 1.0 O C:HOH799 2.3 36.8 1.0 O C:LYS556 2.3 42.4 1.0 O C:ARG553 2.4 46.3 1.0 O C:HOH738 2.5 38.7 1.0 O C:HOH719 2.5 34.4 1.0 C C:ARG553 3.3 40.0 1.0 C C:LYS556 3.5 46.0 1.0 N C:ARG553 3.8 41.3 1.0 N C:LYS556 3.9 38.9 1.0 O C:TYR510 4.0 42.5 1.0 O C:HOH788 4.0 39.7 1.0 C C:ASP552 4.0 36.9 1.0 N C:GLY555 4.1 44.7 1.0 O C:HOH755 4.1 38.3 1.0 CA C:ARG553 4.2 43.7 1.0 CA C:LYS556 4.2 37.4 1.0 N C:ASP554 4.2 42.4 1.0 O C:HOH759 4.3 30.8 1.0 CA C:ASP554 4.4 46.9 1.0 N C:TYR557 4.5 37.8 1.0 CA C:ASP552 4.5 45.7 1.0 C C:ASP554 4.5 49.3 1.0 O C:ASP552 4.5 41.9 1.0 OD1 C:ASP552 4.7 41.8 1.0 CB C:LYS556 4.7 43.8 1.0 C C:GLY555 4.8 42.2 1.0 O C:HOH740 4.8 51.6 1.0 O C:HOH725 4.9 39.1 1.0 CA C:TYR557 4.9 42.2 1.0 CA C:GLY555 4.9 45.6 1.0

L.Pirone, J.Ripoll-Rozada, M.Leone, R.Ronca, F.Lombardo, G.Fiorentino, J.F.Andersen, P.J.B.Pereira, B.Arca, E.Pedone. Functional Analyses Yield Detailed Insight Into the Mechanism of Thrombin Inhibition By the Antihemostatic Salivary Protein CE5 From Anopheles Gambiae. J. Biol. Chem. V. 292 12632 2017.
ISSN: ESSN 1083-351X
PubMed: 28592490
DOI: 10.1074/JBC.M117.788042