Sodium in PDB 1ca8: Thrombin Inhibitors with Rigid Tripeptidyl Aldehydes

All present enzymatic activity of Thrombin Inhibitors with Rigid Tripeptidyl Aldehydes:
3.4.21.5;

The structure of Thrombin Inhibitors with Rigid Tripeptidyl Aldehydes, PDB code: 1ca8 was solved by R.Krishnan, E.Zhang, K.Hakansson, R.K.Arni, A.Tulinsky, M.S.L.Lim-Wilby, O.E.Levy, J.E.Semple, T.K.Brunck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.130, 72.120, 73.140, 90.00, 100.80, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Sodium atom in the Thrombin Inhibitors with Rigid Tripeptidyl Aldehydes (pdb code 1ca8). 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 Inhibitors with Rigid Tripeptidyl Aldehydes, PDB code: 1ca8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin Inhibitors with Rigid Tripeptidyl Aldehydes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibitors with Rigid Tripeptidyl Aldehydes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:28.3 occ:0.75 O B:HOH518 2.3 30.5 0.8 O B:HOH501 2.3 24.8 0.8 O B:LYS224 2.3 29.0 1.0 O B:ARG221A 2.5 32.9 1.0 O B:HOH428 2.5 22.5 0.8 O B:HOH473 2.6 27.2 0.9 C B:LYS224 3.4 26.6 1.0 C B:ARG221A 3.6 33.8 1.0 N B:LYS224 3.7 28.4 1.0 O B:HOH496 3.9 34.3 0.8 O B:HOH485 4.0 22.1 0.8 N B:ARG221A 4.0 33.2 1.0 O B:TYR184A 4.1 27.8 1.0 CA B:LYS224 4.1 26.9 1.0 O B:HOH462 4.2 21.8 0.7 C B:ASP221 4.3 31.3 1.0 N B:TYR225 4.3 25.7 1.0 N B:GLY223 4.4 34.0 1.0 CA B:ASP222 4.4 34.8 1.0 N B:ASP222 4.4 33.4 1.0 CA B:ARG221A 4.4 33.1 1.0 CA B:ASP221 4.6 28.9 1.0 C B:ASP222 4.6 35.0 1.0 OD1 B:ASP221 4.7 31.8 1.0 CA B:TYR225 4.7 23.7 1.0 O B:HOH536 4.7 23.4 0.8 O B:ASP221 4.7 32.1 1.0 CB B:LYS224 4.7 27.7 1.0 C B:GLY223 4.8 30.8 1.0 CD1 B:TYR225 5.0 23.0 1.0

Sodium binding site 2 out of 2 in the Thrombin Inhibitors with Rigid Tripeptidyl Aldehydes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibitors with Rigid Tripeptidyl Aldehydes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:25.7 occ:0.75 O B:THR172 2.2 26.8 1.0 O B:HOH595 2.3 27.0 0.7 O B:HOH596 2.4 26.9 0.7 O B:LYS169 2.4 27.3 1.0 O B:HOH446 2.7 28.8 0.7 C B:THR172 3.5 25.5 1.0 C B:LYS169 3.6 24.7 1.0 CA B:ASP170 4.1 26.8 1.0 N B:ASP170 4.2 25.6 1.0 N B:THR172 4.2 23.3 1.0 N B:ARG173 4.3 26.4 1.0 CA B:ARG173 4.4 29.3 1.0 C B:ASP170 4.4 26.1 1.0 CA B:THR172 4.5 23.6 1.0 OD1 B:ASP170 4.6 26.9 1.0 CA B:LYS169 4.7 25.9 1.0 C B:ARG173 4.8 28.4 1.0 N B:SER171 4.8 25.9 1.0 O B:ILE174 4.9 25.2 1.0 O B:ASP170 4.9 27.1 1.0 CG2 B:THR172 4.9 22.0 1.0 CB B:LYS169 5.0 29.7 1.0

R.Krishnan, E.Zhang, K.Hakansson, R.K.Arni, A.Tulinsky, M.S.Lim-Wilby, O.E.Levy, J.E.Semple, T.K.Brunck. Highly Selective Mechanism-Based Thrombin Inhibitors: Structures of Thrombin and Trypsin Inhibited with Rigid Peptidyl Aldehydes Biochemistry V. 37 12094 1998.
ISSN: ISSN 0006-2960
PubMed: 9724521
DOI: 10.1021/BI980840E