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Sodium in PDB 4baq: 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: 4baq 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) 18.54 / 1.89
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 (%) 18.7 / 22.1

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 4baq

Go back to Sodium Binding Sites List in 4baq
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:26.6
occ:1.00
O B:THR207 2.2 30.7 1.0
O B:HOH2122 2.2 28.6 1.0
O B:LYS204 2.3 30.9 1.0
O B:HOH2119 2.3 40.8 1.0
O B:HOH2118 2.6 38.0 1.0
C B:THR207 3.4 29.1 1.0
C B:LYS204 3.5 31.5 1.0
CA B:ASP205 4.2 26.6 1.0
N B:ASP205 4.2 27.3 1.0
N B:THR207 4.3 24.9 1.0
N B:ARG208 4.3 28.2 1.0
CA B:ARG208 4.3 29.8 1.0
O B:HOH2124 4.3 50.3 1.0
NZ B:LYS204 4.4 78.6 1.0
CA B:THR207 4.4 26.3 1.0
C B:ASP205 4.5 30.1 1.0
CA B:LYS204 4.5 27.3 1.0
OD1 B:ASP205 4.7 33.1 1.0
C B:ARG208 4.7 34.9 1.0
CG B:LYS204 4.8 60.9 1.0
CG2 B:THR207 4.8 32.0 1.0
O B:ILE209 4.8 34.0 1.0
O B:ASP205 4.9 29.4 1.0
N B:SER206 5.0 25.6 1.0

Sodium binding site 2 out of 2 in 4baq

Go back to Sodium Binding Sites List in 4baq
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:36.8
occ:1.00
O B:LYS266 2.3 34.2 1.0
O B:ARG263 2.3 39.9 1.0
O B:HOH2143 2.4 38.4 1.0
O B:HOH2134 2.6 30.4 1.0
O B:HOH2156 2.6 37.9 1.0
O B:HOH2135 2.6 40.4 1.0
C B:ARG263 3.4 42.0 1.0
C B:LYS266 3.4 33.9 1.0
N B:LYS266 3.8 31.9 1.0
N B:ARG263 3.9 36.4 1.0
O B:HOH2130 4.0 30.9 1.0
CA B:LYS266 4.1 30.6 1.0
O B:TYR220 4.1 40.2 1.0
C B:ASP262 4.1 39.5 1.0
N B:ASP264 4.1 40.7 1.0
CA B:ASP264 4.2 40.9 1.0
O B:HOH2133 4.3 29.0 1.0
N B:GLY265 4.3 36.6 1.0
CA B:ARG263 4.3 36.7 1.0
N B:TYR267 4.4 28.5 1.0
C B:ASP264 4.4 42.3 1.0
CA B:ASP262 4.4 33.2 1.0
CB B:LYS266 4.5 32.4 1.0
OD1 B:ASP262 4.5 39.7 1.0
O B:ASP262 4.6 39.5 1.0
O B:HOH2142 4.7 36.6 1.0
CA B:TYR267 4.7 28.3 1.0
C B:GLY265 4.8 38.4 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: Mon Oct 7 14:29:21 2024

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