Sodium in PDB 1jou: Crystal Structure of Native S195A Thrombin with An Unoccupied Active Site

The structure of Crystal Structure of Native S195A Thrombin with An Unoccupied Active Site, PDB code: 1jou was solved by J.A.Huntington, C.T.Esmon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.69 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.230, 76.580, 97.320, 90.00, 106.64, 90.00
R / Rfree (%)	22.2 / 24.5

The binding sites of Sodium atom in the Crystal Structure of Native S195A Thrombin with An Unoccupied Active Site (pdb code 1jou). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Native S195A Thrombin with An Unoccupied Active Site, PDB code: 1jou:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Native S195A Thrombin with An Unoccupied Active Site


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 Native S195A Thrombin with An Unoccupied Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3001 b:27.4 occ:1.00 O B:HOH3053 2.3 28.7 1.0 O B:ARG221A 2.3 26.0 1.0 O B:LYS224 2.3 25.1 1.0 O B:HOH3027 2.5 26.7 1.0 O B:HOH3004 2.5 20.7 1.0 O B:HOH3057 2.8 33.2 1.0 C B:ARG221A 3.3 27.2 1.0 C B:LYS224 3.4 25.6 1.0 O B:HOH3016 3.7 25.6 1.0 N B:ARG221A 3.8 26.4 1.0 N B:LYS224 3.9 26.2 1.0 O B:HOH3047 4.0 34.4 1.0 C B:ASP221 4.1 26.6 1.0 O B:TYR184A 4.2 24.8 1.0 CA B:LYS224 4.2 26.4 1.0 CA B:ARG221A 4.2 27.7 1.0 N B:ASP222 4.2 27.2 1.0 CA B:ASP222 4.3 27.7 1.0 O B:HOH3018 4.3 19.6 1.0 N B:GLY223 4.3 26.5 1.0 N B:TYR225 4.4 25.0 1.0 CA B:ASP221 4.5 25.5 1.0 CB B:LYS224 4.5 24.9 1.0 C B:ASP222 4.6 27.4 1.0 CA B:TYR225 4.6 25.2 1.0 O B:ASP221 4.7 27.9 1.0 O B:HOH3038 4.7 33.2 1.0 OD1 B:ASP221 4.8 26.5 1.0 C B:GLY223 4.9 26.2 1.0 CD2 B:TYR225 5.0 26.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Native S195A Thrombin with An Unoccupied Active Site


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 Native S195A Thrombin with An Unoccupied Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Na3002 b:40.5 occ:1.00 O D:ARG221A 2.3 38.4 1.0 O D:HOH3049 2.3 38.8 1.0 O D:HOH3046 2.5 42.1 1.0 O D:HOH3016 2.5 28.9 1.0 O D:HOH3047 2.6 36.0 1.0 O D:LYS224 2.6 33.5 1.0 C D:ARG221A 3.3 41.6 1.0 C D:LYS224 3.8 33.6 1.0 N D:ARG221A 3.8 38.4 1.0 O D:HOH3020 4.0 38.3 1.0 C D:ASP221 4.0 37.4 1.0 N D:LYS224 4.0 34.9 1.0 O D:HOH3048 4.0 41.1 1.0 O D:TYR184A 4.0 38.7 1.0 O D:HOH3021 4.1 35.3 1.0 N D:ASP222 4.1 43.2 1.0 CA D:ARG221A 4.2 40.9 1.0 N D:GLY223 4.2 41.4 1.0 CA D:ASP222 4.2 44.4 1.0 CA D:ASP221 4.3 36.6 1.0 O D:ASP221 4.4 36.9 1.0 CA D:LYS224 4.4 35.0 1.0 OD1 D:ASP221 4.4 39.5 1.0 C D:ASP222 4.6 43.0 1.0 CB D:LYS224 4.8 36.0 1.0 N D:TYR225 4.8 32.3 1.0 C D:GLY223 5.0 36.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Native S195A Thrombin with An Unoccupied Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Native S195A Thrombin with An Unoccupied Active Site within 5.0Å range: probe atom residue distance (Å) B Occ F:Na3003 b:38.4 occ:1.00 O F:LYS224 2.2 31.5 1.0 O F:HOH3021 2.4 25.9 1.0 O F:HOH3057 2.4 32.2 1.0 O F:ARG221A 2.4 40.3 1.0 O F:HOH3019 2.5 32.8 1.0 O F:HOH3035 2.8 40.1 1.0 C F:LYS224 3.4 33.0 1.0 C F:ARG221A 3.5 41.9 1.0 O F:HOH3059 3.8 35.8 1.0 N F:ARG221A 3.9 41.9 1.0 N F:LYS224 3.9 35.2 1.0 O F:HOH3026 4.1 39.2 1.0 CA F:LYS224 4.1 33.6 1.0 C F:ASP221 4.1 41.6 1.0 O F:TYR184A 4.1 35.6 1.0 CA F:ARG221A 4.3 42.3 1.0 N F:ASP222 4.4 40.5 1.0 N F:TYR225 4.4 31.6 1.0 O F:HOH3049 4.4 36.8 1.0 CA F:ASP221 4.4 40.1 1.0 CB F:LYS224 4.4 36.2 1.0 N F:GLY223 4.5 36.1 1.0 CA F:ASP222 4.5 39.6 1.0 CA F:TYR225 4.5 32.2 1.0 O F:ASP221 4.6 42.0 1.0 OD1 F:ASP221 4.6 37.9 1.0 C F:ASP222 4.7 38.4 1.0 CD2 F:TYR225 4.9 30.8 1.0 C F:GLY223 4.9 35.5 1.0 O F:HOH3050 5.0 36.5 1.0

J.A.Huntington, C.T.Esmon. The Molecular Basis of Thrombin Allostery Revealed By A 1.8A Structure of the Slow Form Structure V. 11 469 2003.
ISSN: ISSN 0969-2126
PubMed: 12679024
DOI: 10.1016/S0969-2126(03)00049-2