Atomistry » Sodium » PDB 5jid-5k8r » 5k2c
Atomistry »
  Sodium »
    PDB 5jid-5k8r »
      5k2c »

Sodium in PDB 5k2c: 1.9 Angstrom A2A Adenosine Receptor Structure with Sulfur Sad Phasing and Phase Extension Using Xfel Data

Protein crystallography data

The structure of 1.9 Angstrom A2A Adenosine Receptor Structure with Sulfur Sad Phasing and Phase Extension Using Xfel Data, PDB code: 5k2c was solved by A.Batyuk, L.Galli, A.Ishchenko, G.W.Han, C.Gati, P.Popov, M.-Y.Lee, B.Stauch, T.A.White, A.Barty, A.Aquila, M.S.Hunter, M.Liang, S.Boutet, M.Pu, Z.-J.Liu, G.Nelson, D.James, C.Li, Y.Zhao, J.C.H.Spence, W.Liu, P.Fromme, V.Katritch, U.Weierstall, R.C.Stevens, V.Cherezov, Gpcr Network(Gpcr), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.44 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 40.360, 180.740, 142.800, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.8

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.9 Angstrom A2A Adenosine Receptor Structure with Sulfur Sad Phasing and Phase Extension Using Xfel Data (pdb code 5k2c). 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 1.9 Angstrom A2A Adenosine Receptor Structure with Sulfur Sad Phasing and Phase Extension Using Xfel Data, PDB code: 5k2c:

Sodium binding site 1 out of 1 in 5k2c

Go back to Sodium Binding Sites List in 5k2c
Sodium binding site 1 out of 1 in the 1.9 Angstrom A2A Adenosine Receptor Structure with Sulfur Sad Phasing and Phase Extension Using Xfel Data


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.9 Angstrom A2A Adenosine Receptor Structure with Sulfur Sad Phasing and Phase Extension Using Xfel Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1202

b:35.3
occ:1.00
OD1 A:ASP52 2.4 30.8 1.0
O A:HOH1332 2.4 34.0 1.0
O A:HOH1381 2.4 36.9 1.0
O A:HOH1315 2.5 34.8 1.0
OG A:SER91 2.5 30.7 1.0
CG A:ASP52 3.3 31.0 1.0
CB A:SER91 3.4 28.9 1.0
OD2 A:ASP52 3.6 32.1 1.0
ND2 A:ASN280 3.9 29.0 1.0
CD1 A:LEU48 4.2 40.0 1.0
OG A:SER281 4.3 32.7 1.0
O A:HOH1351 4.3 38.7 1.0
O A:HOH1321 4.5 34.1 1.0
O A:HOH1355 4.6 50.0 1.0
CB A:ASP52 4.6 26.9 1.0
CE2 A:PHE242 4.7 30.2 1.0
N A:ASP52 4.7 30.2 1.0
CB A:ALA51 4.7 30.5 1.0
CA A:SER91 4.8 26.0 1.0
O A:LEU87 4.8 33.4 1.0
CA A:ASP52 4.8 28.8 1.0
O A:LEU48 4.8 33.4 1.0
CD2 A:PHE242 4.9 29.0 1.0

Reference:

A.Batyuk, L.Galli, A.Ishchenko, G.W.Han, C.Gati, P.A.Popov, M.Y.Lee, B.Stauch, T.A.White, A.Barty, A.Aquila, M.S.Hunter, M.Liang, S.Boutet, M.Pu, Z.J.Liu, G.Nelson, D.James, C.Li, Y.Zhao, J.C.Spence, W.Liu, P.Fromme, V.Katritch, U.Weierstall, R.C.Stevens, V.Cherezov. Native Phasing of X-Ray Free-Electron Laser Data For A G Protein-Coupled Receptor. Sci Adv V. 2 00292 2016.
ISSN: ESSN 2375-2548
PubMed: 27679816
DOI: 10.1126/SCIADV.1600292
Page generated: Tue Dec 15 11:09:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy