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Sodium in PDB 4ban: Thrombin in Complex with Inhibitor

Enzymatic activity of Thrombin in Complex with Inhibitor

All present enzymatic activity of Thrombin in Complex with Inhibitor:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with Inhibitor, PDB code: 4ban was solved by Y.Xue, D.Musil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.36 / 1.87
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.410, 71.510, 72.160, 90.00, 100.34, 90.00
R / Rfree (%) 16.7 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with Inhibitor (pdb code 4ban). 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 in Complex with Inhibitor, PDB code: 4ban:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ban

Go back to Sodium Binding Sites List in 4ban
Sodium binding site 1 out of 2 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
B:Na1288

b:15.5
occ:1.00
O B:HOH2206 2.2 18.3 1.0
O B:HOH2200 2.3 27.0 1.0
O B:THR207 2.3 19.6 1.0
O B:LYS204 2.4 21.4 1.0
O B:HOH2199 2.9 28.1 1.0
C B:LYS204 3.5 21.8 1.0
C B:THR207 3.5 19.0 1.0
CA B:ASP205 4.1 17.6 1.0
N B:ASP205 4.2 18.3 1.0
N B:THR207 4.3 15.0 1.0
CA B:ARG208 4.4 19.4 1.0
N B:ARG208 4.4 18.4 1.0
O B:HOH2208 4.4 31.8 1.0
CG B:LYS204 4.4 38.3 1.0
C B:ASP205 4.5 19.4 1.0
CA B:THR207 4.5 15.5 1.0
CA B:LYS204 4.6 17.8 1.0
OD1 B:ASP205 4.7 22.1 1.0
NZ B:LYS204 4.7 58.4 1.0
O B:ASP205 4.9 17.3 1.0
CG2 B:THR207 4.9 16.7 1.0
C B:ARG208 4.9 24.0 1.0
N B:SER206 5.0 14.9 1.0

Sodium binding site 2 out of 2 in 4ban

Go back to Sodium Binding Sites List in 4ban
Sodium binding site 2 out of 2 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 2 of Thrombin in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1289

b:22.3
occ:1.00
O B:ARG263 2.3 23.3 1.0
O B:LYS266 2.3 19.1 1.0
O B:HOH2234 2.4 21.6 1.0
O B:HOH2253 2.4 22.1 1.0
O B:HOH2223 2.6 16.5 1.0
O B:HOH2224 2.6 25.1 1.0
C B:ARG263 3.3 25.1 1.0
C B:LYS266 3.5 20.4 1.0
O B:HOH2233 3.8 23.2 1.0
N B:LYS266 3.8 18.4 1.0
N B:ARG263 3.9 21.1 1.0
O B:HOH2219 4.0 18.6 1.0
C B:ASP262 4.1 24.3 1.0
O B:TYR220 4.1 20.9 1.0
N B:ASP264 4.1 23.3 1.0
CA B:LYS266 4.2 17.5 1.0
CA B:ASP264 4.2 23.2 1.0
O B:HOH2222 4.3 15.3 1.0
CA B:ARG263 4.3 21.1 1.0
N B:GLY265 4.3 21.5 1.0
CA B:ASP262 4.4 19.4 1.0
C B:ASP264 4.5 24.8 1.0
O B:ASP262 4.5 23.4 1.0
CB B:LYS266 4.5 19.6 1.0
N B:TYR267 4.5 16.4 1.0
OD1 B:ASP262 4.6 20.9 1.0
O B:HOH2235 4.6 24.4 1.0
CA B:TYR267 4.8 15.6 1.0
C B:GLY265 4.9 24.5 1.0

Reference:

J.Winquist, S.Geschwindner, Y.Xue, L.Gustavsson, D.Musil, J.Deinum, U.H.Danielson. Identification of Structure-Kinetic and Structure-Thermodynamic Relationships For Thrombin Inhibitors. Biochemistry V. 52 613 2013.
ISSN: ISSN 0006-2960
PubMed: 23290007
DOI: 10.1021/BI301333Z
Page generated: Tue Dec 15 06:33:45 2020

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