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

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

All present enzymatic activity of Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Ethyl)-N-Methyl- 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-Ethyl)-N-Methyl- 3-Phenyl-Propanamide, PDB code: 4uff 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) 35.620 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.429, 71.562, 72.450, 90.00, 100.49, 90.00
R / Rfree (%) 16 / 18.74

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-Ethyl)-N-Methyl- 3-Phenyl-Propanamide (pdb code 4uff). 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-Ethyl)-N-Methyl- 3-Phenyl-Propanamide, PDB code: 4uff:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4uff

Go back to Sodium Binding Sites List in 4uff
Sodium binding site 1 out of 2 in the Thrombin in Complex with (2R)-2-(Benzylsulfonylamino)-N-(2-( (4-Carbamimidoylphenyl)Methylamino)-2-Oxo-Ethyl)-N-Methyl- 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-Ethyl)-N-Methyl- 3-Phenyl-Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1246

b:16.2
occ:1.00
 O H:HOH2150 2.3 19.1 1.0
O H:THR172 2.4 18.1 1.0
O H:LYS169 2.4 18.1 1.0
O H:HOH2145 2.5 25.3 1.0
O H:HOH2146 2.7 27.4 1.0
C H:LYS169 3.5 18.3 1.0
C H:THR172 3.6 19.1 1.0
CA H:ASP170 4.0 17.8 1.0
N H:ASP170 4.2 18.1 1.0
CG H:LYS169 4.2 28.6 1.0
N H:THR172 4.3 15.8 1.0
O H:HOH2152 4.4 34.9 1.0
C H:ASP170 4.4 18.3 1.0
CA H:ARG173 4.4 18.5 1.0
N H:ARG173 4.5 17.9 1.0
CA H:LYS169 4.5 16.5 1.0
CA H:THR172 4.6 15.5 1.0
OD1 H:ASP170 4.7 21.4 1.0
O H:ASP170 4.8 17.7 1.0
CG2 H:THR172 4.8 20.8 1.0
N H:SER171 4.9 18.0 1.0
NZ H:LYS169 4.9 52.3 1.0
CB H:LYS169 4.9 17.4 1.0
C H:ARG173 5.0 17.8 1.0

Sodium binding site 2 out of 2 in 4uff

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

b:19.4
occ:1.00
 O H:HOH2171 2.3 17.8 1.0
O H:ARG221A 2.3 20.2 1.0
O H:HOH2184 2.4 20.3 1.0
O H:LYS224 2.5 19.0 1.0
O H:HOH2162 2.5 17.6 1.0
O H:HOH2163 2.6 21.8 1.0
C H:ARG221A 3.4 20.3 1.0
C H:LYS224 3.5 19.4 1.0
O H:HOH2158 3.9 15.3 1.0
N H:LYS224 3.9 19.2 1.0
O H:HOH2170 3.9 22.6 1.0
N H:ARG221A 3.9 20.5 1.0
C H:ASP221 4.1 22.9 1.0
O H:TYR184A 4.1 21.2 1.0
N H:GLY223 4.2 24.9 1.0
CA H:LYS224 4.2 18.8 1.0
N H:ASP222 4.2 24.3 1.0
O H:HOH2161 4.2 16.9 1.0
CA H:ASP222 4.3 28.6 1.0
CA H:ARG221A 4.3 20.7 1.0
CA H:ASP221 4.4 20.3 1.0
C H:ASP222 4.5 22.3 1.0
N H:TYR225 4.5 17.5 1.0
O H:ASP221 4.5 23.9 1.0
CB H:LYS224 4.6 17.9 1.0
OD1 H:ASP221 4.6 21.3 1.0
CA H:TYR225 4.8 16.8 1.0
O H:HOH2172 4.8 20.0 1.0
C H:GLY223 4.8 22.5 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 18:39:43 2024

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