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Sodium in PDB 4ufg: Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(( 1S)-2-((4-Carbamimidoylphenyl)Methylamino)-1-Methyl-2-Oxo- Ethyl)-N-Methyl-3-Phenyl-Propanamide Ethane

Enzymatic activity of Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(( 1S)-2-((4-Carbamimidoylphenyl)Methylamino)-1-Methyl-2-Oxo- Ethyl)-N-Methyl-3-Phenyl-Propanamide Ethane

All present enzymatic activity of Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(( 1S)-2-((4-Carbamimidoylphenyl)Methylamino)-1-Methyl-2-Oxo- Ethyl)-N-Methyl-3-Phenyl-Propanamide Ethane:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(( 1S)-2-((4-Carbamimidoylphenyl)Methylamino)-1-Methyl-2-Oxo- Ethyl)-N-Methyl-3-Phenyl-Propanamide Ethane, PDB code: 4ufg 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) 35.682 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.092, 71.249, 72.587, 90.00, 100.53, 90.00
R / Rfree (%) 16.18 / 18.65

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 4ufg

Go back to Sodium Binding Sites List in 4ufg
Sodium binding site 1 out of 2 in the Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(( 1S)-2-((4-Carbamimidoylphenyl)Methylamino)-1-Methyl-2-Oxo- Ethyl)-N-Methyl-3-Phenyl-Propanamide Ethane


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-(( 1S)-2-((4-Carbamimidoylphenyl)Methylamino)-1-Methyl-2-Oxo- Ethyl)-N-Methyl-3-Phenyl-Propanamide Ethane within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1247

b:14.4
occ:1.00
 O H:THR172 2.4 16.9 1.0
O H:LYS169 2.4 15.5 1.0
O H:HOH2142 2.8 21.0 1.0
C H:LYS169 3.5 15.5 1.0
C H:THR172 3.6 16.8 1.0
CA H:ASP170 4.0 15.9 1.0
O H:HOH2147 4.2 37.1 1.0
N H:ASP170 4.2 16.2 1.0
CG H:LYS169 4.2 23.6 1.0
N H:THR172 4.3 13.1 1.0
CA H:ARG173 4.4 14.1 1.0
C H:ASP170 4.4 14.1 1.0
N H:ARG173 4.5 16.1 1.0
CA H:LYS169 4.6 12.3 1.0
CA H:THR172 4.6 12.9 1.0
O H:ASP170 4.8 16.7 1.0
OD1 H:ASP170 4.8 18.7 1.0
CG2 H:THR172 4.9 17.0 1.0
N H:SER171 4.9 14.4 1.0
CB H:LYS169 4.9 14.1 1.0
C H:ARG173 5.0 17.2 1.0

Sodium binding site 2 out of 2 in 4ufg

Go back to Sodium Binding Sites List in 4ufg
Sodium binding site 2 out of 2 in the Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(( 1S)-2-((4-Carbamimidoylphenyl)Methylamino)-1-Methyl-2-Oxo- Ethyl)-N-Methyl-3-Phenyl-Propanamide Ethane


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-(( 1S)-2-((4-Carbamimidoylphenyl)Methylamino)-1-Methyl-2-Oxo- Ethyl)-N-Methyl-3-Phenyl-Propanamide Ethane within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1248

b:15.9
occ:1.00
 O H:HOH2171 2.3 14.1 1.0
O H:ARG221A 2.4 16.9 1.0
O H:HOH2190 2.4 15.7 1.0
O H:LYS224 2.4 13.8 1.0
O H:HOH2159 2.4 13.4 1.0
O H:HOH2161 2.6 17.4 1.0
C H:ARG221A 3.4 17.0 1.0
C H:LYS224 3.5 14.9 1.0
N H:LYS224 3.8 15.9 1.0
O H:HOH2169 3.9 18.9 1.0
O H:HOH2156 3.9 12.0 1.0
N H:ARG221A 4.0 16.2 1.0
O H:TYR184A 4.0 15.9 1.0
C H:ASP221 4.1 18.9 1.0
N H:GLY223 4.1 21.1 1.0
CA H:LYS224 4.1 14.9 1.0
O H:HOH2160 4.2 14.1 1.0
N H:ASP222 4.2 18.2 1.0
CA H:ASP222 4.3 22.1 1.0
CA H:ARG221A 4.3 17.8 1.0
CA H:ASP221 4.4 18.0 1.0
C H:ASP222 4.5 18.4 1.0
N H:TYR225 4.5 14.8 1.0
CB H:LYS224 4.6 15.0 1.0
O H:ASP221 4.6 20.3 1.0
OD1 H:ASP221 4.7 16.5 1.0
CA H:TYR225 4.7 13.7 1.0
C H:GLY223 4.8 19.4 1.0
O H:HOH2172 4.8 22.0 1.0
O H:HOH2170 5.0 18.1 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 08:31:06 2020

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