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Sodium in PDB 2pks: Thrombin in Complex with Inhibitor

Protein crystallography data

The structure of Thrombin in Complex with Inhibitor, PDB code: 2pks was solved by Y.Xue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.67 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.942, 71.843, 70.778, 90.00, 100.23, 90.00
R / Rfree (%) 18.5 / 25.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with Inhibitor (pdb code 2pks). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Thrombin in Complex with Inhibitor, PDB code: 2pks:

Sodium binding site 1 out of 1 in 2pks

Go back to Sodium Binding Sites List in 2pks
Sodium binding site 1 out of 1 in the Thrombin in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:49.2
occ:1.00
O C:LYS266 2.6 40.7 1.0
O C:ARG263 2.8 51.1 1.0
O C:HOH413 2.8 34.6 1.0
O C:HOH406 2.9 28.1 1.0
C C:LYS266 3.5 41.0 1.0
N C:ARG263 3.7 49.4 1.0
C C:ARG263 3.8 50.9 1.0
CA C:ASP262 4.0 47.5 1.0
C C:ASP262 4.1 48.6 1.0
N C:TYR267 4.2 37.9 1.0
CA C:TYR267 4.3 34.7 1.0
OD1 C:ASP262 4.3 44.0 1.0
CA C:LYS266 4.4 43.2 1.0
CA C:ARG263 4.4 50.0 1.0
CB C:LYS266 4.5 43.5 1.0
N C:LYS266 4.5 45.2 1.0
N C:ASP262 4.5 45.9 1.0
OD1 C:ASP229 4.7 44.6 1.0
O C:TYR220 4.7 44.6 1.0
O C:HOH410 4.8 30.2 1.0
O C:GLY228 4.8 43.2 1.0
N C:ASP264 4.8 51.4 1.0
CG C:ASP229 4.9 40.0 1.0
CB C:ASP229 4.9 40.4 1.0

Reference:

D.Blomberg, T.Fex, Y.Xue, K.Brickmann, J.Kihlberg. Design, Synthesis and Biological Evaluation of Thrombin Inhibitors Based on A Pyridine Scaffold. Org.Biomol.Chem. V. 5 2599 2007.
ISSN: ISSN 1477-0520
PubMed: 18019535
DOI: 10.1039/B705344D
Page generated: Tue Dec 15 05:53:59 2020

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