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Sodium in PDB 4ufd: Thrombin in Complex with 4-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine

Enzymatic activity of Thrombin in Complex with 4-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine

All present enzymatic activity of Thrombin in Complex with 4-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with 4-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine, PDB code: 4ufd 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) 49.660 / 1.43
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.000, 71.600, 71.900, 90.00, 100.00, 90.00
R / Rfree (%) 13.36 / 15.87

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with 4-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine (pdb code 4ufd). 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-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine, PDB code: 4ufd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ufd

Go back to Sodium Binding Sites List in 4ufd
Sodium binding site 1 out of 2 in the Thrombin in Complex with 4-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine


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-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1247

b:14.8
occ:1.00
 O H:THR172 2.3 13.4 1.0
O H:LYS169 2.3 14.6 1.0
O H:HOH2209 2.4 15.8 1.0
O H:HOH2204 2.4 24.7 1.0
O H:HOH2203 2.6 22.8 1.0
C H:LYS169 3.5 14.2 1.0
C H:THR172 3.5 13.9 1.0
CA H:ASP170 4.1 14.7 1.0
N H:ASP170 4.2 13.7 1.0
CG H:LYS169 4.2 20.3 1.0
N H:THR172 4.2 14.1 1.0
O H:HOH2212 4.3 33.3 1.0
C H:ASP170 4.4 14.6 1.0
CA H:ARG173 4.4 15.1 1.0
N H:ARG173 4.4 14.4 1.0
CA H:THR172 4.5 14.1 1.0
CA H:LYS169 4.5 14.2 1.0
OD1 H:ASP170 4.8 20.2 1.0
CG2 H:THR172 4.8 14.8 1.0
O H:ASP170 4.8 15.1 1.0
N H:SER171 4.8 14.2 1.0
CB H:LYS169 4.9 16.0 1.0
C H:ARG173 5.0 15.1 1.0

Sodium binding site 2 out of 2 in 4ufd

Go back to Sodium Binding Sites List in 4ufd
Sodium binding site 2 out of 2 in the Thrombin in Complex with 4-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine


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-(((1-((2S)-1-((2R)-2-( Benzylsulfonylamino)-3-Phenyl-Propanoyl)Pyrrolidin-2-Yl)-1- Oxo-Ethyl)Amino)Methyl)Benzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1248

b:16.8
occ:1.00
 O H:ARG221A 2.3 17.8 1.0
O H:HOH2236 2.3 16.2 1.0
O H:HOH2257 2.4 17.8 1.0
O H:LYS224 2.4 15.8 1.0
O H:HOH2225 2.5 15.4 1.0
O H:HOH2226 2.6 18.2 1.0
C H:ARG221A 3.4 18.2 1.0
C H:LYS224 3.5 14.9 1.0
N H:LYS224 3.9 16.8 1.0
O H:HOH2221 3.9 15.2 1.0
O H:HOH2235 3.9 21.2 1.0
N H:ARG221A 4.0 16.9 1.0
O H:TYR184A 4.1 19.1 1.0
C H:ASP221 4.1 17.0 1.0
N H:GLY223 4.2 21.3 1.0
CA H:LYS224 4.2 16.0 1.0
N H:ASP222 4.2 20.4 1.0
O H:HOH2224 4.3 15.4 1.0
CA H:ASP222 4.3 21.4 1.0
CA H:ARG221A 4.3 18.2 1.0
CA H:ASP221 4.4 16.5 1.0
C H:ASP222 4.5 21.5 1.0
N H:TYR225 4.5 13.5 1.0
CB H:LYS224 4.5 17.2 1.0
O H:ASP221 4.6 19.0 1.0
OD1 H:ASP221 4.6 17.2 1.0
CA H:TYR225 4.8 12.7 1.0
O H:HOH2237 4.8 19.3 1.0
C H:GLY223 4.8 18.2 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: Mon Oct 7 18:39:35 2024

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