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Sodium in PDB 4udw: Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide

Enzymatic activity of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide, PDB code: 4udw 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) 71.13 / 1.16
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.640, 71.106, 72.327, 90.00, 100.44, 90.00
R / Rfree (%) 12.4 / 14.1

Other elements in 4udw:

The structure of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide (pdb code 4udw). 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 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide, PDB code: 4udw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4udw

Go back to Sodium Binding Sites List in 4udw
Sodium binding site 1 out of 2 in the Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide


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 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1247

b:16.6
occ:1.00
O H:ARG221A 2.3 18.0 1.0
O H:HOH2235 2.3 17.8 1.0
O H:LYS224 2.4 15.2 1.0
O H:HOH2253 2.4 17.6 1.0
O H:HOH2225 2.5 15.3 1.0
O H:HOH2227 2.7 19.9 1.0
H H:LYS224 3.2 20.8 1.0
C H:ARG221A 3.4 18.2 1.0
C H:LYS224 3.4 14.9 1.0
HA H:ASP221 3.7 20.2 1.0
HA H:ASP222 3.7 24.8 1.0
HB2 H:LYS224 3.8 20.4 1.0
N H:LYS224 3.8 17.3 1.0
O H:HOH2222 3.8 15.7 1.0
H H:GLY223 3.8 23.8 1.0
N H:ARG221A 3.9 17.5 1.0
H H:ARG221A 4.0 21.0 1.0
HA H:TYR225 4.0 16.1 1.0
O H:HOH2234 4.0 21.3 1.0
C H:ASP221 4.1 17.3 1.0
CA H:LYS224 4.1 16.4 1.0
O H:TYR184A 4.1 16.8 1.0
N H:GLY223 4.2 19.9 1.0
N H:ASP222 4.2 19.8 1.0
CA H:ARG221A 4.2 18.4 1.0
O H:HOH2226 4.3 15.9 1.0
CA H:ASP222 4.3 20.7 1.0
CA H:ASP221 4.4 16.9 1.0
N H:TYR225 4.4 14.0 1.0
CB H:LYS224 4.5 17.0 1.0
C H:ASP222 4.5 20.6 1.0
O H:ASP221 4.5 18.8 1.0
OD1 H:ASP221 4.6 17.9 1.0
CA H:TYR225 4.7 13.4 1.0
HB2 H:ARG221A 4.8 22.6 1.0
C H:GLY223 4.8 17.2 1.0
O H:HOH2236 4.8 17.4 1.0
H H:ASP221 4.9 18.9 1.0
HB2 H:ASP189 4.9 17.4 1.0
HA H:ARG221A 4.9 22.1 1.0
HA3 H:GLY184 5.0 16.0 1.0
HB3 H:LYS224 5.0 20.4 1.0

Sodium binding site 2 out of 2 in 4udw

Go back to Sodium Binding Sites List in 4udw
Sodium binding site 2 out of 2 in the Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide


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 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1248

b:14.8
occ:1.00
O H:THR172 2.3 15.3 1.0
O H:LYS169 2.3 14.9 1.0
O H:HOH2209 2.4 18.4 1.0
O H:HOH2205 2.4 27.7 1.0
O H:HOH2204 2.9 23.6 1.0
HA H:ASP170 3.2 17.9 1.0
HG2 H:LYS169 3.4 21.1 0.5
C H:LYS169 3.4 14.2 1.0
HG2 H:LYS169 3.5 21.6 0.5
H H:THR172 3.5 17.3 1.0
C H:THR172 3.5 14.1 1.0
HA H:ARG173 3.6 18.5 1.0
HZ1 H:LYS169 3.8 29.8 0.5
CA H:ASP170 4.0 14.9 1.0
HG3 H:LYS169 4.1 21.1 0.5
N H:ASP170 4.2 14.6 1.0
CG H:LYS169 4.2 17.6 0.5
N H:THR172 4.2 14.4 1.0
HG21 H:THR172 4.3 19.4 1.0
C H:ASP170 4.3 15.1 1.0
CG H:LYS169 4.4 18.0 0.5
O H:HOH2212 4.4 35.2 1.0
CA H:ARG173 4.4 15.4 1.0
N H:ARG173 4.4 14.8 1.0
HA H:LYS169 4.5 16.5 0.5
HA H:LYS169 4.5 16.5 0.5
HG3 H:LYS169 4.5 21.6 0.5
CA H:THR172 4.5 14.4 1.0
CA H:LYS169 4.5 13.8 0.5
CA H:LYS169 4.5 13.8 0.5
HE2 H:LYS169 4.6 25.5 0.5
NZ H:LYS169 4.6 24.9 0.5
O H:ASP170 4.7 16.0 1.0
OD1 H:ASP170 4.7 18.9 1.0
HG23 H:THR172 4.7 19.4 1.0
N H:SER171 4.8 14.2 1.0
HZ3 H:LYS169 4.9 29.8 0.5
H H:SER171 4.9 17.1 1.0
CG2 H:THR172 4.9 16.1 1.0
CB H:LYS169 4.9 14.6 0.5
CB H:LYS169 5.0 14.8 0.5
HE3 H:LYS169 5.0 25.5 0.5
H H:ASP170 5.0 17.6 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: Tue Dec 15 08:06:48 2020

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