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

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

All present enzymatic activity of Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Butyl)-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-Butyl)-3-Phenyl- Propanamide, PDB code: 4ufe 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) 28.996 / 1.59
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.006, 71.360, 72.524, 90.00, 100.50, 90.00
R / Rfree (%) 15.78 / 18.17

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-Butyl)-3-Phenyl- Propanamide (pdb code 4ufe). 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-Butyl)-3-Phenyl- Propanamide, PDB code: 4ufe:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ufe

Go back to Sodium Binding Sites List in 4ufe
Sodium binding site 1 out of 2 in the Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Butyl)-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-Butyl)-3-Phenyl- Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1247

b:13.9
occ:1.00
 O H:THR172 2.4 15.5 1.0
O H:HOH2194 2.4 18.5 1.0
O H:LYS169 2.4 15.1 1.0
O H:HOH2187 2.5 25.8 1.0
O H:HOH2186 2.7 23.4 1.0
C H:LYS169 3.5 15.4 1.0
C H:THR172 3.6 14.1 1.0
CA H:ASP170 4.0 15.6 1.0
O H:HOH2196 4.1 35.8 1.0
N H:ASP170 4.2 14.7 1.0
CG H:LYS169 4.2 24.8 1.0
N H:THR172 4.3 14.2 1.0
CA H:ARG173 4.4 14.5 1.0
C H:ASP170 4.4 15.4 1.0
N H:ARG173 4.4 14.1 1.0
CA H:THR172 4.5 14.4 1.0
CA H:LYS169 4.5 13.2 1.0
NZ H:LYS169 4.6 35.8 1.0
OD1 H:ASP170 4.7 20.3 1.0
O H:ASP170 4.8 16.4 1.0
CG2 H:THR172 4.9 19.0 1.0
N H:SER171 4.9 15.7 1.0
CB H:LYS169 4.9 13.9 1.0
C H:ARG173 5.0 15.6 1.0

Sodium binding site 2 out of 2 in 4ufe

Go back to Sodium Binding Sites List in 4ufe
Sodium binding site 2 out of 2 in the Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Butyl)-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-Butyl)-3-Phenyl- Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1248

b:16.9
occ:1.00
 O H:HOH2224 2.3 16.8 1.0
O H:ARG221A 2.3 19.3 1.0
O H:HOH2239 2.4 19.0 1.0
O H:LYS224 2.4 16.7 1.0
O H:HOH2212 2.4 15.9 1.0
O H:HOH2213 2.6 18.6 1.0
C H:ARG221A 3.4 17.9 1.0
C H:LYS224 3.5 16.3 1.0
N H:LYS224 3.8 16.5 1.0
O H:HOH2223 3.8 22.7 1.0
O H:HOH2208 3.9 14.4 1.0
N H:ARG221A 4.0 17.9 1.0
O H:TYR184A 4.1 18.3 1.0
C H:ASP221 4.1 16.6 1.0
CA H:LYS224 4.1 18.9 1.0
N H:GLY223 4.2 24.3 1.0
O H:HOH2211 4.2 16.8 1.0
N H:ASP222 4.2 19.3 1.0
CA H:ASP222 4.3 24.6 1.0
CA H:ARG221A 4.3 23.1 1.0
CA H:ASP221 4.4 18.6 1.0
C H:ASP222 4.5 23.3 1.0
N H:TYR225 4.5 14.9 1.0
CB H:LYS224 4.5 15.6 1.0
OD1 H:ASP221 4.6 17.4 1.0
O H:ASP221 4.6 21.1 1.0
CA H:TYR225 4.8 13.2 1.0
C H:GLY223 4.8 19.2 1.0
O H:HOH2225 4.8 23.2 1.0

Reference:

E.H.Ruhmann, M.Rupp, M.Betz, A.Heine, G.Klebe. Boosting Affinity By Correct Ligand Preorganization For the S2 Pocket of Thrombin: A Study By Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures. Chemmedchem V. 11 309 2016.
ISSN: ISSN 1860-7179
PubMed: 26762840
DOI: 10.1002/CMDC.201500531
Page generated: Tue Dec 15 08:30:55 2020

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