Sodium in PDB 1a61: Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor

All present enzymatic activity of Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor:
3.4.21.5;

The structure of Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor, PDB code: 1a61 was solved by R.St Charles, J.H.Matthews, E.Zhang, 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 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.850, 72.410, 72.970, 90.00, 101.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Sodium atom in the Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor (pdb code 1a61). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor, PDB code: 1a61:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na650 b:28.6 occ:0.73 O H:HOH561 2.1 27.7 0.8 O H:LYS224 2.3 26.8 1.0 O H:ARG221A 2.4 36.9 1.0 O H:HOH429 2.4 23.8 1.0 O H:HOH476 2.8 27.3 0.9 O H:HOH496 3.1 28.2 0.8 C H:LYS224 3.4 26.0 1.0 O H:HOH528 3.5 29.2 1.0 C H:ARG221A 3.6 34.1 1.0 N H:LYS224 3.8 27.1 1.0 O H:HOH459 4.0 26.2 0.7 O H:HOH497 4.1 28.9 1.0 CA H:LYS224 4.1 25.1 1.0 C H:ASP221 4.2 32.8 1.0 N H:ARG221A 4.2 34.0 1.0 O H:TYR184A 4.2 25.6 1.0 CA H:ASP222 4.3 38.9 1.0 N H:GLY223 4.3 36.0 1.0 N H:TYR225 4.3 25.7 1.0 O H:ASP221 4.3 33.9 1.0 N H:ASP222 4.4 37.3 1.0 CA H:ASP221 4.4 30.6 1.0 C H:ASP222 4.5 38.5 1.0 CB H:LYS224 4.6 25.5 1.0 CA H:ARG221A 4.6 34.9 1.0 CA H:TYR225 4.7 19.1 1.0 OD1 H:ASP221 4.7 31.1 1.0 C H:GLY223 4.8 29.5 1.0 CD2 H:TYR225 5.0 19.5 1.0

Sodium binding site 2 out of 2 in the Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Complexed with A Beta-Mimetic Thiazole-Containing Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na651 b:26.8 occ:0.95 O H:THR172 2.2 22.9 1.0 O H:HOH559 2.3 25.7 0.9 O H:HOH558 2.5 28.5 0.8 O H:LYS169 2.6 22.0 1.0 O H:HOH560 2.7 27.1 0.6 C H:THR172 3.4 21.6 1.0 C H:LYS169 3.7 21.2 1.0 CA H:ASP170 4.1 23.5 1.0 N H:THR172 4.1 19.5 1.0 N H:ARG173 4.3 23.4 1.0 CA H:ARG173 4.3 23.9 1.0 N H:ASP170 4.4 23.1 1.0 CA H:THR172 4.4 19.7 1.0 C H:ASP170 4.5 25.4 1.0 NZ H:LYS169 4.5 45.2 1.0 OD1 H:ASP170 4.7 24.5 1.0 CA H:LYS169 4.7 23.1 1.0 N H:SER171 4.7 21.6 1.0 CG2 H:THR172 4.7 18.7 1.0 C H:ARG173 4.9 25.4 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