Sodium in PDB 1b5g: Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen

All present enzymatic activity of Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen:
3.4.21.5;

The structure of Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen, PDB code: 1b5g was solved by R.St Charles, A.Tulinsky, M.Kahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.840, 72.080, 73.000, 90.00, 100.90, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Sodium atom in the Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen (pdb code 1b5g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen, PDB code: 1b5g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen within 5.0Å range: probe atom residue distance (Å) B Occ H:Na391 b:17.7 occ:0.75 O H:LYS224 2.1 26.9 1.0 O H:ARG221A 2.3 29.0 1.0 O H:HOH505 2.6 22.7 0.8 O H:HOH440 3.2 23.8 0.6 C H:LYS224 3.3 26.4 1.0 C H:ARG221A 3.4 29.5 1.0 O H:HOH471 3.6 22.0 0.9 N H:LYS224 3.8 28.0 1.0 N H:ARG221A 3.9 28.5 1.0 O H:HOH504 4.0 26.0 0.9 C H:ASP221 4.0 27.8 1.0 CA H:LYS224 4.1 27.1 1.0 CA H:ASP221 4.2 27.1 1.0 N H:ASP222 4.3 29.8 1.0 CA H:ASP222 4.3 30.7 1.0 N H:TYR225 4.3 24.9 1.0 N H:GLY223 4.3 30.5 1.0 CA H:ARG221A 4.3 29.4 1.0 O H:TYR184A 4.4 25.1 1.0 O H:HOH418 4.4 17.2 1.0 C H:ASP222 4.5 30.9 1.0 CB H:LYS224 4.5 27.8 1.0 O H:ASP221 4.6 28.2 1.0 OD1 H:ASP221 4.6 26.3 1.0 CA H:TYR225 4.7 23.6 1.0 O H:HOH425 4.8 32.1 1.0 N H:ASP221 4.9 26.6 1.0 C H:GLY223 4.9 28.9 1.0

Sodium binding site 2 out of 2 in the Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin Complexed with Novel Synthetic Peptide Mimetic Inhibitor and Hirugen within 5.0Å range: probe atom residue distance (Å) B Occ H:Na392 b:20.7 occ:0.83 O H:THR172 2.1 20.7 1.0 O H:LYS169 2.4 22.4 1.0 O H:HOH472 2.7 25.1 0.8 C H:THR172 3.3 21.4 1.0 C H:LYS169 3.5 21.7 1.0 N H:ARG173 4.1 22.9 1.0 CA H:ARG173 4.1 24.0 1.0 N H:ASP170 4.2 21.6 1.0 CA H:ASP170 4.2 22.2 1.0 N H:THR172 4.2 20.8 1.0 CA H:THR172 4.4 21.0 1.0 CA H:LYS169 4.5 22.0 1.0 C H:ASP170 4.6 21.7 1.0 OD1 H:ASP170 4.6 23.8 1.0 C H:ARG173 4.6 24.3 1.0 CG2 H:THR172 4.7 19.9 1.0 O H:ILE174 4.9 23.8 1.0 O H:ARG173 5.0 26.2 1.0 CB H:LYS169 5.0 24.2 1.0

R.St Charles, J.H.Matthews, E.Zhang, A.Tulinsky. Bound Structures of Novel P3-P1' Beta-Strand Mimetic Inhibitors of Thrombin. J.Med.Chem. V. 42 1376 1999.
ISSN: ISSN 0022-2623
PubMed: 10212123
DOI: 10.1021/JM980052N