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Sodium in PDB 3vw7: Crystal Structure of Human Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom

Enzymatic activity of Crystal Structure of Human Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom

All present enzymatic activity of Crystal Structure of Human Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Human Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom, PDB code: 3vw7 was solved by C.Zhang, Y.Srinivasan, D.H.Arlow, J.J.Fung, D.Palmer, Y.Zheng, H.F.Green, A.Pandey, R.O.Dror, D.E.Shaw, W.I.Weis, S.R.Coughlin, B.K.Kobilka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.27 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.044, 71.460, 172.187, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 23.5

Other elements in 3vw7:

The structure of Crystal Structure of Human Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom (pdb code 3vw7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom, PDB code: 3vw7:

Sodium binding site 1 out of 1 in 3vw7

Go back to Sodium Binding Sites List in 3vw7
Sodium binding site 1 out of 1 in the Crystal Structure of Human Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom


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 Protease-Activated Receptor 1 (PAR1) Bound with Antagonist Vorapaxar at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2012

b:35.4
occ:1.00
O A:HOH3065 2.3 34.1 1.0
OD2 A:ASP367 2.4 39.1 1.0
O A:HOH3066 2.4 32.8 1.0
OG A:SER189 2.6 26.7 1.0
OD2 A:ASP148 2.8 28.1 1.0
CB A:SER189 3.2 24.8 1.0
CG A:ASP367 3.4 36.3 1.0
CD1 A:LEU144 3.4 22.8 1.0
CG A:ASP148 3.6 30.2 1.0
OD1 A:ASP148 3.6 28.9 1.0
OD1 A:ASP367 3.7 36.5 1.0
OD1 A:ASN185 4.1 34.5 1.0
OG A:SER363 4.3 31.8 1.0
CA A:SER189 4.4 24.4 1.0
CG A:LEU144 4.5 24.4 1.0
O A:SER363 4.5 35.8 1.0
ND2 A:ASN185 4.5 26.0 1.0
CZ A:PHE326 4.6 30.8 1.0
CB A:SER363 4.7 27.0 1.0
C A:SER363 4.7 33.2 1.0
CG A:ASN185 4.7 29.1 1.0
CB A:ASP367 4.7 28.0 1.0
SG A:CYS364 4.9 38.1 1.0
N A:CYS364 4.9 29.8 1.0
CA A:CYS364 5.0 30.8 1.0

Reference:

C.Zhang, Y.Srinivasan, D.H.Arlow, J.J.Fung, D.Palmer, Y.Zheng, H.F.Green, A.Pandey, R.O.Dror, D.E.Shaw, W.I.Weis, S.R.Coughlin, B.K.Kobilka. High-Resolution Crystal Structure of Human Protease-Activated Receptor 1 Nature V. 492 387 2012.
ISSN: ISSN 0028-0836
PubMed: 23222541
DOI: 10.1038/NATURE11701
Page generated: Tue Dec 15 06:29:17 2020

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