Sodium in PDB 1k21: Human Thrombin-Inhibitor Complex

All present enzymatic activity of Human Thrombin-Inhibitor Complex:
3.4.21.5;

The structure of Human Thrombin-Inhibitor Complex, PDB code: 1k21 was solved by M.T.Stubbs, D.Musil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	500.00 / 1.86
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.619, 71.546, 71.821, 90.00, 100.12, 90.00
R / Rfree (%)	21.6 / 25.6

The binding sites of Sodium atom in the Human Thrombin-Inhibitor Complex (pdb code 1k21). 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-Inhibitor Complex, PDB code: 1k21:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na391 b:27.9 occ:1.00 O H:HOH445 2.3 28.5 1.0 O H:HOH434 2.3 29.0 1.0 O H:ARG221A 2.3 35.3 1.0 O H:LYS224 2.4 31.3 1.0 O H:HOH419 2.6 25.2 1.0 O H:HOH438 2.7 36.1 1.0 C H:ARG221A 3.3 35.4 1.0 C H:LYS224 3.4 30.7 1.0 N H:ARG221A 3.7 33.2 1.0 N H:LYS224 3.8 30.9 1.0 O H:HOH432 3.9 28.0 1.0 C H:ASP221 4.0 32.1 1.0 O H:HOH461 4.0 30.3 1.0 CA H:LYS224 4.1 31.0 1.0 N H:ASP222 4.1 35.7 1.0 CA H:ARG221A 4.2 35.2 1.0 O H:TYR184A 4.2 31.7 1.0 O H:HOH409 4.2 24.9 1.0 CA H:ASP222 4.3 35.7 1.0 CA H:ASP221 4.3 31.6 1.0 CB H:LYS224 4.4 32.8 1.0 N H:GLY223 4.4 34.6 1.0 N H:TYR225 4.4 29.1 1.0 O H:ASP221 4.5 32.0 1.0 C H:ASP222 4.5 35.4 1.0 OD1 H:ASP221 4.6 31.5 1.0 CA H:TYR225 4.7 27.7 1.0 C H:GLY223 4.9 32.8 1.0 O H:HOH524 4.9 32.5 1.0 O H:HOH519 5.0 31.3 1.0

Sodium binding site 2 out of 2 in the Human Thrombin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na392 b:24.5 occ:1.00 O H:HOH574 2.3 31.0 1.0 O H:THR172 2.3 26.6 1.0 O H:LYS169 2.3 28.8 1.0 O H:HOH518 2.7 32.3 1.0 C H:LYS169 3.4 28.2 1.0 C H:THR172 3.5 26.0 1.0 CA H:ASP170 4.0 27.5 1.0 N H:ASP170 4.1 27.6 1.0 CG H:LYS169 4.2 34.9 1.0 N H:THR172 4.3 25.6 1.0 C H:ASP170 4.4 27.3 1.0 CA H:ARG173 4.4 26.2 1.0 N H:ARG173 4.4 25.5 1.0 CA H:THR172 4.5 26.1 1.0 CA H:LYS169 4.5 28.3 1.0 OD2 H:ASP170 4.7 29.5 1.0 N H:SER171 4.8 26.4 1.0 O H:ASP170 4.9 26.8 1.0 CG2 H:THR172 4.9 25.8 1.0 CB H:LYS169 4.9 30.0 1.0 C H:ARG173 4.9 26.6 1.0 NZ H:LYS169 5.0 42.5 1.0

F.Dullweber, M.T.Stubbs, D.Musil, J.Sturzebecher, G.Klebe. Factorising Ligand Affinity: A Combined Thermodynamic and Crystallographic Study of Trypsin and Thrombin Inhibition. J.Mol.Biol. V. 313 593 2001.
ISSN: ISSN 0022-2836
PubMed: 11676542
DOI: 10.1006/JMBI.2001.5062