Sodium in PDB 6v64: Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan

All present enzymatic activity of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan:
3.4.21.5;

The structure of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan, PDB code: 6v64 was solved by E.A.Ruben, Z.Chen, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.16 / 2.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.869, 86.599, 50.516, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 27.7

The structure of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan (pdb code 6v64). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan, PDB code: 6v64:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:30.6 occ:0.50 O A:TYR14J 2.3 32.4 1.0 O A:HOH203 2.4 34.8 1.0 OH B:TYR134 2.6 29.2 1.0 C A:TYR14J 3.5 32.9 1.0 CZ B:TYR134 3.6 27.9 1.0 CE1 B:TYR134 4.0 28.2 1.0 O B:HOH426 4.0 12.3 0.5 CA A:ILE14K 4.2 38.2 1.0 O A:ILE14K 4.3 41.1 1.0 N A:ILE14K 4.3 34.9 1.0 C A:ILE14K 4.4 40.4 1.0 CA A:TYR14J 4.5 31.4 1.0 O A:ASP14L 4.5 60.7 1.0 CE2 B:TYR134 4.7 27.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:37.0 occ:1.00 O B:ARG221A 2.3 40.4 1.0 O B:LYS224 2.3 34.7 1.0 O B:HOH462 2.4 28.6 1.0 O B:HOH434 2.5 34.8 1.0 O B:HOH427 2.6 45.5 1.0 O B:HOH406 2.7 32.7 1.0 C B:ARG221A 3.3 43.8 1.0 O B:HOH487 3.3 40.4 1.0 C B:LYS224 3.5 34.8 1.0 N B:ARG221A 3.7 41.0 1.0 C B:ASP221 3.9 41.8 1.0 N B:LYS224 4.0 39.1 1.0 O B:HOH411 4.0 31.4 1.0 N B:ASP222 4.1 45.4 1.0 CA B:ARG221A 4.1 44.3 1.0 CA B:ASP221 4.2 41.3 1.0 O B:TYR184A 4.2 39.2 1.0 O B:HOH433 4.2 45.2 1.0 CA B:LYS224 4.2 37.1 1.0 O B:HOH422 4.4 32.1 1.0 N B:GLY223 4.4 41.8 1.0 CA B:ASP222 4.4 45.8 1.0 OD1 B:ASP221 4.4 42.7 1.0 O B:ASP221 4.5 45.3 1.0 N B:TYR225 4.5 32.1 1.0 CB B:LYS224 4.6 37.3 1.0 C B:ASP222 4.6 44.1 1.0 CA B:TYR225 4.8 31.8 1.0 O B:HOH450 4.9 38.5 1.0 N B:ASP221 5.0 39.5 1.0 CD1 B:TYR225 5.0 35.4 1.0

E.A.Ruben, P.S.Gandhi, Z.Chen, S.K.Koester, G.T.Dekoster, C.Frieden, E.Di Cera. 19F uc(Nmr) Reveals the Conformational Properties of Free Thrombin and Its Zymogen Precursor Prethrombin-2. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32358061
DOI: 10.1074/JBC.RA120.013419