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Sodium in PDB 2zgb: Thrombin Inhibition

Enzymatic activity of Thrombin Inhibition

All present enzymatic activity of Thrombin Inhibition:
3.4.21.5;

Protein crystallography data

The structure of Thrombin Inhibition, PDB code: 2zgb was solved by B.Baum, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.760, 71.370, 72.570, 90.00, 100.28, 90.00
R / Rfree (%) 19.8 / 24.2

Other elements in 2zgb:

The structure of Thrombin Inhibition also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin Inhibition (pdb code 2zgb). 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 Inhibition, PDB code: 2zgb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zgb

Go back to Sodium Binding Sites List in 2zgb
Sodium binding site 1 out of 2 in the Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibition within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1802

b:21.5
occ:1.00
O H:HOH2116 2.2 23.0 1.0
O H:ARG221A 2.3 20.6 1.0
O H:HOH2057 2.4 22.5 1.0
O H:HOH2033 2.5 18.2 1.0
O H:LYS224 2.5 17.1 1.0
O H:HOH2052 2.7 24.5 1.0
C H:ARG221A 3.3 23.4 1.0
C H:LYS224 3.5 14.2 1.0
N H:ARG221A 3.8 20.3 1.0
N H:LYS224 3.9 19.9 1.0
O H:HOH2032 3.9 21.2 1.0
O H:HOH2050 4.0 31.8 1.0
C H:ASP221 4.0 21.8 1.0
O H:HOH2019 4.1 21.6 1.0
N H:ASP222 4.2 23.2 1.0
CA H:LYS224 4.2 16.4 1.0
CA H:ARG221A 4.2 25.2 1.0
O H:TYR184A 4.2 24.1 1.0
CA H:ASP221 4.3 14.8 1.0
CA H:ASP222 4.3 22.5 1.0
N H:GLY223 4.3 22.8 1.0
O H:ASP221 4.5 29.1 1.0
N H:TYR225 4.5 19.2 1.0
C H:ASP222 4.5 19.2 1.0
CB H:LYS224 4.6 19.1 1.0
OD1 H:ASP221 4.6 20.9 1.0
CA H:TYR225 4.8 18.4 1.0
O H:HOH2037 4.8 23.5 1.0
C H:GLY223 4.9 24.4 1.0
N H:ASP221 5.0 21.5 1.0

Sodium binding site 2 out of 2 in 2zgb

Go back to Sodium Binding Sites List in 2zgb
Sodium binding site 2 out of 2 in the Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibition within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1803

b:16.0
occ:1.00
O H:THR172 2.4 17.6 1.0
O H:LYS169 2.4 17.6 1.0
O H:HOH2028 2.4 19.8 1.0
O H:HOH2034 2.5 24.2 1.0
O H:HOH2078 2.7 24.0 1.0
C H:LYS169 3.5 16.4 1.0
C H:THR172 3.6 15.9 1.0
CA H:ASP170 4.0 18.8 1.0
N H:ASP170 4.2 18.3 1.0
O H:HOH2149 4.2 45.3 1.0
N H:THR172 4.3 16.8 1.0
C H:ASP170 4.4 18.8 1.0
CA H:LYS169 4.5 13.9 1.0
CA H:ARG173 4.5 22.6 1.0
N H:ARG173 4.5 17.5 1.0
CA H:THR172 4.5 18.2 1.0
OD1 H:ASP170 4.6 17.0 1.0
CG2 H:THR172 4.7 18.0 1.0
O H:ASP170 4.8 19.1 1.0
N H:SER171 4.9 14.1 1.0
CB H:LYS169 4.9 14.5 1.0
O H:HOH2049 5.0 30.4 1.0

Reference:

B.Baum, L.Muley, M.Smolinski, A.Heine, D.Hangauer, G.Klebe. Non-Additivity of Functional Group Contributions in Protein-Ligand Binding: A Comprehensive Study By Crystallography and Isothermal Titration Calorimetry. J.Mol.Biol. V. 397 1042 2010.
ISSN: ISSN 0022-2836
PubMed: 20156458
DOI: 10.1016/J.JMB.2010.02.007
Page generated: Tue Dec 15 06:01:06 2020

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