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Sodium in PDB 5afz: Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide

Enzymatic activity of Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide

All present enzymatic activity of Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide, PDB code: 5afz 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) 21.468 / 1.53
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.308, 71.643, 72.354, 90.00, 100.53, 90.00
R / Rfree (%) 14.5 / 17.41

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide (pdb code 5afz). 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 (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide, PDB code: 5afz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5afz

Go back to Sodium Binding Sites List in 5afz
Sodium binding site 1 out of 2 in the Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide


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 (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1246

b:22.6
occ:1.00
 O H:HOH2158 2.3 20.1 1.0
O H:ARG221A 2.3 25.5 1.0
O H:HOH2176 2.4 22.4 1.0
O H:LYS224 2.4 20.1 1.0
O H:HOH2147 2.5 19.4 1.0
O H:HOH2148 2.6 24.7 1.0
C H:ARG221A 3.4 25.7 1.0
C H:LYS224 3.5 19.7 1.0
N H:LYS224 3.8 22.0 1.0
O H:HOH2157 3.9 19.0 1.0
O H:HOH2156 3.9 25.3 1.0
N H:ARG221A 3.9 23.9 1.0
C H:ASP221 4.1 24.2 1.0
O H:TYR184A 4.1 24.2 1.0
CA H:LYS224 4.1 21.1 1.0
N H:GLY223 4.2 26.5 1.0
N H:ASP222 4.2 26.9 1.0
O H:HOH2146 4.3 19.8 1.0
CA H:ARG221A 4.3 25.4 1.0
CA H:ASP222 4.3 27.2 1.0
CA H:ASP221 4.4 23.2 1.0
C H:ASP222 4.5 26.4 1.0
N H:TYR225 4.5 18.4 1.0
O H:ASP221 4.5 26.0 1.0
CB H:LYS224 4.5 21.6 1.0
OD1 H:ASP221 4.6 22.7 1.0
CA H:TYR225 4.8 18.0 1.0
C H:GLY223 4.8 23.5 1.0
O H:HOH2159 4.8 23.2 1.0

Sodium binding site 2 out of 2 in 5afz

Go back to Sodium Binding Sites List in 5afz
Sodium binding site 2 out of 2 in the Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide


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 (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Propyl)-3-Phenyl- Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1247

b:18.2
occ:1.00
 O H:LYS169 2.4 20.6 1.0
O H:THR172 2.4 20.1 1.0
C H:LYS169 3.5 19.6 1.0
C H:THR172 3.6 19.3 1.0
CA H:ASP170 4.0 20.1 1.0
N H:ASP170 4.2 19.0 1.0
CG H:LYS169 4.2 26.1 1.0
N H:THR172 4.3 18.4 1.0
C H:ASP170 4.4 19.7 1.0
CA H:ARG173 4.4 20.4 1.0
N H:ARG173 4.5 19.8 1.0
CA H:LYS169 4.5 19.5 1.0
CA H:THR172 4.6 19.2 1.0
OD1 H:ASP170 4.7 23.8 1.0
O H:ASP170 4.8 19.2 1.0
N H:SER171 4.8 18.8 1.0
CG2 H:THR172 4.9 20.2 1.0
CB H:LYS169 4.9 21.9 1.0
C H:ARG173 5.0 20.5 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: Mon Oct 7 19:53:12 2024

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