Sodium in PDB 1ypl: X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008

All present enzymatic activity of X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008:
3.4.21.5;

The structure of X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008, PDB code: 1ypl was solved by J.Fokkens, G.Radau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.131, 71.630, 72.198, 90.00, 100.45, 90.00
R / Rfree (%)	19.5 / 26.3

The binding sites of Sodium atom in the X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008 (pdb code 1ypl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008, PDB code: 1ypl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na7777 b:22.3 occ:1.00 O H:ARG221A 2.2 25.8 1.0 O H:HOH9100 2.2 19.7 1.0 O H:HOH9053 2.3 25.1 1.0 O H:LYS224 2.4 24.9 1.0 O H:HOH9096 2.7 32.2 1.0 O H:HOH9048 2.8 25.2 1.0 C H:ARG221A 3.3 30.2 1.0 C H:LYS224 3.5 19.8 1.0 O H:HOH9027 3.8 19.9 1.0 N H:LYS224 3.9 21.1 1.0 N H:ARG221A 3.9 25.0 1.0 O H:HOH9011 4.0 20.8 1.0 C H:ASP221 4.1 32.3 1.0 O H:TYR184A 4.1 29.3 1.0 N H:ASP222 4.1 32.2 1.0 CA H:LYS224 4.1 16.9 1.0 CA H:ASP222 4.2 26.9 1.0 CA H:ARG221A 4.2 30.6 1.0 O H:HOH9018 4.2 19.9 1.0 N H:GLY223 4.3 30.1 1.0 CA H:ASP221 4.4 29.5 1.0 OD1 H:ASP221 4.4 23.6 1.0 C H:ASP222 4.5 30.4 1.0 N H:TYR225 4.5 19.3 1.0 O H:ASP221 4.5 25.3 1.0 CB H:LYS224 4.6 19.3 1.0 O H:HOH9087 4.7 26.2 1.0 C H:GLY223 4.8 31.5 1.0 CA H:TYR225 4.9 23.2 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Thrombin Inhibited By Synthetic Cyanopeptide Analogue Ra-1008 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na7778 b:22.7 occ:1.00 O H:THR172 2.3 21.2 1.0 O H:LYS169 2.3 19.7 1.0 O H:HOH9095 2.6 28.1 1.0 O H:HOH9067 2.9 29.2 1.0 C H:LYS169 3.4 23.5 1.0 C H:THR172 3.5 15.8 1.0 CA H:ASP170 4.0 10.9 1.0 N H:ASP170 4.0 20.1 1.0 N H:THR172 4.2 20.2 1.0 CA H:ARG173 4.3 26.1 1.0 N H:ARG173 4.3 18.8 1.0 C H:ASP170 4.4 17.5 1.0 CA H:THR172 4.5 16.3 1.0 CA H:LYS169 4.5 18.3 1.0 O H:HOH9140 4.6 43.6 1.0 CG H:LYS169 4.6 32.7 1.0 OD1 H:ASP170 4.6 22.4 1.0 O H:ASP170 4.7 21.1 1.0 CG2 H:THR172 4.9 23.6 1.0 N H:SER171 4.9 17.4 1.0 C H:ARG173 4.9 29.5 1.0 CB H:LYS169 5.0 27.5 1.0

G.Radau, J.Fokkens. Design and X-Ray Crystal Structures of Human Thrombin with Synthetic Cyanopeptide-Analogues. Pharmazie V. 62 83 2007.
ISSN: ISSN 0031-7144
PubMed: 17341023