Atomistry » Sodium » PDB 3lbg-3m9y » 3lu9
Atomistry »
  Sodium »
    PDB 3lbg-3m9y »
      3lu9 »

Sodium in PDB 3lu9: Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1

Enzymatic activity of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1

All present enzymatic activity of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1, PDB code: 3lu9 was solved by P.S.Gandhi, Z.Chen, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.07 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.334, 50.171, 85.502, 76.39, 83.93, 73.74
R / Rfree (%) 19.3 / 23.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1 (pdb code 3lu9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1, PDB code: 3lu9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3lu9

Go back to Sodium Binding Sites List in 3lu9
Sodium binding site 1 out of 2 in the Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:26.2
occ:1.00
O B:HOH520 2.3 11.7 1.0
O B:ARG221A 2.3 15.0 1.0
O B:LYS224 2.4 14.3 1.0
O B:HOH2 2.4 7.8 1.0
O B:HOH515 2.5 6.5 1.0
O B:HOH278 2.7 9.3 1.0
C B:ARG221A 3.4 16.2 1.0
C B:LYS224 3.5 14.4 1.0
N B:LYS224 3.8 15.8 1.0
N B:ARG221A 3.9 14.3 1.0
C B:ASP221 4.0 15.2 1.0
O B:HOH258 4.0 9.0 1.0
O B:HOH512 4.0 9.0 1.0
N B:GLY223 4.1 19.3 1.0
O B:TYR184A 4.2 15.2 1.0
CA B:LYS224 4.2 14.6 1.0
N B:ASP222 4.2 17.4 1.0
CA B:ARG221A 4.3 15.3 1.0
O B:HOH296 4.3 4.9 1.0
CA B:ASP222 4.3 19.2 1.0
CA B:ASP221 4.3 14.8 1.0
O B:HOH330 4.4 13.8 1.0
C B:ASP222 4.5 19.8 1.0
O B:ASP221 4.5 16.6 1.0
N B:TYR225 4.5 13.4 1.0
CB B:LYS224 4.6 15.0 1.0
OD1 B:ASP221 4.6 18.4 1.0
C B:GLY223 4.8 17.1 1.0
CA B:TYR225 4.8 12.2 1.0

Sodium binding site 2 out of 2 in 3lu9

Go back to Sodium Binding Sites List in 3lu9
Sodium binding site 2 out of 2 in the Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na401

b:27.6
occ:1.00
O E:ARG221A 2.3 18.5 1.0
O E:LYS224 2.4 19.3 1.0
O E:HOH513 2.4 11.2 1.0
O E:HOH508 2.5 17.0 1.0
O E:HOH510 2.5 9.6 1.0
O E:HOH597 2.6 15.4 1.0
C E:ARG221A 3.4 19.1 1.0
C E:LYS224 3.4 20.9 1.0
N E:LYS224 3.8 23.1 1.0
N E:ARG221A 3.9 16.4 1.0
O E:HOH600 4.0 13.4 1.0
O E:HOH509 4.0 6.5 1.0
O E:TYR184A 4.1 20.3 1.0
CA E:LYS224 4.1 22.6 1.0
C E:ASP221 4.1 17.0 1.0
N E:GLY223 4.1 24.4 1.0
O E:HOH253 4.2 9.2 1.0
N E:ASP222 4.2 20.4 1.0
CA E:ASP222 4.3 22.4 1.0
CA E:ARG221A 4.3 19.0 1.0
CA E:ASP221 4.4 15.1 1.0
C E:ASP222 4.5 23.8 1.0
N E:TYR225 4.5 21.0 1.0
CB E:LYS224 4.5 20.9 1.0
O E:HOH310 4.5 16.8 1.0
OD1 E:ASP221 4.6 17.5 1.0
O E:ASP221 4.6 17.1 1.0
C E:GLY223 4.8 25.4 1.0
CA E:TYR225 4.8 20.5 1.0
CA E:GLY223 5.0 26.6 1.0
CD1 E:TYR225 5.0 22.0 1.0

Reference:

P.S.Gandhi, Z.Chen, E.Di Cera. Crystal Structure of Thrombin Bound to the Uncleaved Extracellular Fragment of PAR1. J.Biol.Chem. V. 285 15393 2010.
ISSN: ISSN 0021-9258
PubMed: 20236938
DOI: 10.1074/JBC.M110.115337
Page generated: Thu Oct 29 04:36:34 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy