Atomistry » Sodium » PDB 5abd-5azp » 5ahg
Atomistry »
  Sodium »
    PDB 5abd-5azp »
      5ahg »

Sodium in PDB 5ahg: Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine

Enzymatic activity of Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine

All present enzymatic activity of Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine, PDB code: 5ahg was solved by E.Ruehmann, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.41 / 1.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.222, 71.263, 72.216, 90.00, 100.48, 90.00
R / Rfree (%) 12.3 / 14.4

Other elements in 5ahg:

The structure of Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine (pdb code 5ahg). 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 ((4-Chlorophenyl)Sulfamoyl))Diemethylamine, PDB code: 5ahg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ahg

Go back to Sodium Binding Sites List in 5ahg
Sodium binding site 1 out of 2 in the Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine


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 ((4-Chlorophenyl)Sulfamoyl))Diemethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1247

b:13.0
occ:1.00
O H:THR172 2.3 13.4 1.0
O H:LYS169 2.4 13.8 1.0
O H:HOH2200 2.4 21.3 1.0
O H:HOH2199 2.6 19.9 1.0
HA H:ASP170 3.3 15.1 1.0
C H:LYS169 3.5 12.7 1.0
H H:THR172 3.5 15.1 1.0
C H:THR172 3.5 12.8 1.0
HA H:ARG173 3.6 16.4 1.0
CA H:ASP170 4.0 12.6 1.0
N H:ASP170 4.2 12.6 1.0
HG21 H:THR172 4.2 16.7 1.0
N H:THR172 4.3 12.6 1.0
C H:ASP170 4.4 13.5 1.0
CA H:ARG173 4.4 13.6 1.0
N H:ARG173 4.4 12.8 1.0
O H:HOH2206 4.4 39.1 1.0
CA H:THR172 4.5 13.1 1.0
CA H:LYS169 4.5 13.1 1.0
HG23 H:THR172 4.6 16.7 1.0
OD1 H:ASP170 4.7 17.5 1.0
O H:ASP170 4.8 14.1 1.0
CG2 H:THR172 4.8 13.9 1.0
N H:SER171 4.8 12.8 1.0
CB H:LYS169 4.9 15.5 1.0
H H:SER171 4.9 15.4 1.0
C H:ARG173 4.9 13.5 1.0
O H:ILE174 5.0 14.1 1.0
H H:ASP170 5.0 15.1 1.0

Sodium binding site 2 out of 2 in 5ahg

Go back to Sodium Binding Sites List in 5ahg
Sodium binding site 2 out of 2 in the Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine


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 ((4-Chlorophenyl)Sulfamoyl))Diemethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1248

b:16.1
occ:1.00
O H:ARG221A 2.3 16.1 1.0
O H:HOH2228 2.3 16.2 1.0
O H:LYS224 2.4 13.9 1.0
O H:HOH2251 2.4 15.9 1.0
O H:HOH2218 2.4 14.0 1.0
O H:HOH2219 2.7 17.4 1.0
H H:LYS224 3.2 17.7 1.0
C H:ARG221A 3.4 16.4 1.0
C H:LYS224 3.4 13.4 1.0
HA H:ASP221 3.7 20.3 1.0
HA H:ASP222 3.7 21.9 1.0
HB2 H:LYS224 3.8 18.3 1.0
N H:LYS224 3.8 14.8 1.0
H H:GLY223 3.9 19.7 1.0
O H:HOH2214 3.9 14.4 1.0
N H:ARG221A 3.9 17.3 1.0
H H:ARG221A 3.9 20.7 1.0
O H:HOH2226 4.0 20.9 1.0
HA H:TYR225 4.0 14.6 1.0
C H:ASP221 4.1 16.9 1.0
O H:TYR184A 4.1 15.5 1.0
CA H:LYS224 4.1 14.1 1.0
O H:HOH2217 4.2 14.6 1.0
N H:ASP222 4.2 17.9 1.0
N H:GLY223 4.2 16.4 1.0
CA H:ARG221A 4.3 17.6 1.0
CA H:ASP222 4.3 18.2 1.0
CA H:ASP221 4.4 16.9 1.0
N H:TYR225 4.4 12.9 1.0
CB H:LYS224 4.5 15.3 1.0
C H:ASP222 4.5 17.2 1.0
O H:ASP221 4.5 18.8 1.0
OD1 H:ASP221 4.6 17.6 1.0
CA H:TYR225 4.7 12.1 1.0
HB2 H:ARG221A 4.8 21.4 1.0
C H:GLY223 4.8 15.4 1.0
O H:HOH2227 4.9 17.8 1.0
HA3 H:GLY184 4.9 14.0 1.0
HA H:ARG221A 5.0 21.1 1.0
HB3 H:LYS224 5.0 18.3 1.0
H H:ASP221 5.0 18.5 1.0
HB2 H:ASP189 5.0 16.3 1.0

Reference:

E.Ruehmann, M.Betz, A.Heine, G.Klebe. Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why. J.Med.Chem. V. 58 6960 2015.
ISSN: ISSN 0022-2623
PubMed: 26270568
DOI: 10.1021/ACS.JMEDCHEM.5B00812
Page generated: Tue Dec 15 10:23:16 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy