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Sodium in PDB 5ndd: Crystal Structure of A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution

Enzymatic activity of Crystal Structure of A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution

All present enzymatic activity of Crystal Structure of A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution, PDB code: 5ndd was solved by R.K.Y.Cheng, C.Fiez-Vandal, O.Schlenker, K.Edman, B.Aggeler, D.G.Brown, G.Brown, R.M.Cooke, C.E.Dumelin, A.S.Dore, S.Geschwindner, C.Grebner, N.-O.Hermansson, A.Jazayeri, P.Johansson, L.Leong, R.Prihandoko, M.Rappas, H.Soutter, A.Snijder, L.Sundstrom, B.Tehan, P.Thornton, D.Troast, G.Wiggin, A.Zhukov, F.H.Marshall, N.Dekker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.34 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.109, 62.264, 87.341, 104.88, 90.88, 96.89
R / Rfree (%) 22.2 / 26.4

Other elements in 5ndd:

The structure of Crystal Structure of A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution also contains other interesting chemical elements:

Fluorine (F) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution (pdb code 5ndd). 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 A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution, PDB code: 5ndd:

Sodium binding site 1 out of 1 in 5ndd

Go back to Sodium Binding Sites List in 5ndd
Sodium binding site 1 out of 1 in the Crystal Structure of A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution


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 A Thermostabilised Human Protease-Activated Receptor-2 (PAR2) in Complex with AZ8838 at 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2202

b:49.6
occ:1.00
 OD1 A:ASP121 2.2 44.0 1.0
OD1 A:ASN336 2.3 45.8 1.0
OG A:SER162 2.4 43.6 1.0
OD2 A:ASP340 2.5 48.3 1.0
OD1 A:ASN158 2.6 55.7 1.0
O A:HOH2307 3.1 46.4 1.0
CG A:ASP121 3.2 45.2 1.0
CB A:SER162 3.4 46.1 1.0
CG A:ASN336 3.5 47.1 1.0
OD2 A:ASP121 3.7 49.5 1.0
CG A:ASN158 3.7 47.0 1.0
CG A:ASP340 3.7 51.6 1.0
ND2 A:ASN158 4.1 44.7 1.0
O A:LEU117 4.2 47.1 1.0
OD1 A:ASP340 4.3 52.4 1.0
O A:ASN158 4.3 46.4 1.0
ND2 A:ASN336 4.4 47.8 1.0
CA A:SER162 4.4 46.6 1.0
N A:SER337 4.4 44.3 1.0
CB A:ASP121 4.5 45.9 1.0
CB A:ASN336 4.5 46.0 1.0
CA A:SER337 4.5 44.8 1.0
C A:ASN336 4.5 47.8 1.0
N A:ASP121 4.5 44.8 1.0
CA A:ASP121 4.6 44.8 1.0
O A:ASN336 4.6 48.5 1.0
CB A:SER337 4.6 42.8 1.0
CD1 A:LEU117 4.7 49.5 1.0
CG A:LEU117 4.7 51.9 1.0
CB A:ASP340 4.9 47.5 1.0
CB A:ALA120 5.0 44.4 1.0

Reference:

R.K.Y.Cheng, C.Fiez-Vandal, O.Schlenker, K.Edman, B.Aggeler, D.G.Brown, G.A.Brown, R.M.Cooke, C.E.Dumelin, A.S.Dore, S.Geschwindner, C.Grebner, N.O.Hermansson, A.Jazayeri, P.Johansson, L.Leong, R.Prihandoko, M.Rappas, H.Soutter, A.Snijder, L.Sundstrom, B.Tehan, P.Thornton, D.Troast, G.Wiggin, A.Zhukov, F.H.Marshall, N.Dekker. Structural Insight Into Allosteric Modulation of Protease-Activated Receptor 2. Nature V. 545 112 2017.
ISSN: ESSN 1476-4687
PubMed: 28445455
DOI: 10.1038/NATURE22309
Page generated: Mon Oct 7 22:55:52 2024

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