Sodium in PDB 6boc: Influenza A M2 Transmembrane Domain Bound to Rimantadine in the Inward(Open) Conformation

The structure of Influenza A M2 Transmembrane Domain Bound to Rimantadine in the Inward(Open) Conformation, PDB code: 6boc was solved by J.L.Thomaston, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.05 / 2.25
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	34.050, 34.020, 72.090, 90.00, 90.23, 90.00
R / Rfree (%)	26 / 28.2

The structure of Influenza A M2 Transmembrane Domain Bound to Rimantadine in the Inward(Open) Conformation also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Influenza A M2 Transmembrane Domain Bound to Rimantadine in the Inward(Open) Conformation (pdb code 6boc). 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 Influenza A M2 Transmembrane Domain Bound to Rimantadine in the Inward(Open) Conformation, PDB code: 6boc:

Sodium binding site 1 out of 1 in the Influenza A M2 Transmembrane Domain Bound to Rimantadine in the Inward(Open) Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Influenza A M2 Transmembrane Domain Bound to Rimantadine in the Inward(Open) Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:27.9 occ:1.00 O D:SER22 2.0 30.1 1.0 O C:SER22 2.1 26.8 1.0 O A:SER22 2.4 33.1 1.0 O B:SER22 2.6 31.5 1.0 O A:HOH202 3.0 52.5 1.0 C D:SER22 3.1 36.9 1.0 C C:SER22 3.2 36.4 1.0 CL A:CL101 3.2 38.1 1.0 C A:SER22 3.5 54.8 1.0 C B:SER22 3.6 39.8 1.0 CA C:SER23 3.8 42.3 1.0 N C:SER23 3.9 32.8 1.0 OG D:SER22 3.9 71.1 1.0 N D:SER23 3.9 34.2 1.0 CA D:SER23 3.9 41.5 1.0 OG D:SER23 4.0 34.1 1.0 N D:SER22 4.0 55.4 1.0 OG C:SER22 4.0 97.8 1.0 CA D:SER22 4.1 59.8 1.0 CA B:SER23 4.1 41.5 1.0 OG C:SER23 4.2 34.9 1.0 OG A:SER22 4.2 79.3 1.0 CA A:SER23 4.3 42.7 1.0 CA C:SER22 4.3 53.6 1.0 OG B:SER22 4.3 95.0 1.0 N B:SER23 4.3 33.7 1.0 N A:SER23 4.3 39.9 1.0 OG A:SER23 4.4 34.5 1.0 N A:SER22 4.4 46.3 1.0 N C:SER22 4.5 47.5 1.0 OG B:SER23 4.5 29.8 1.0 CB D:SER23 4.5 29.8 1.0 CA A:SER22 4.5 62.1 1.0 CB D:SER22 4.6 73.0 1.0 CB C:SER23 4.6 34.1 1.0 CA B:SER22 4.7 54.2 1.0 N B:SER22 4.7 51.4 1.0 CB C:SER22 4.7 64.6 1.0 CB B:SER23 4.8 31.4 1.0 CB A:SER23 4.9 35.2 1.0 C D:ACE21 4.9 53.8 1.0 CB A:SER22 5.0 65.8 1.0 C C:SER23 5.0 35.5 1.0

J.L.Thomaston, N.F.Polizzi, A.Konstantinidi, J.Wang, A.Kolocouris, W.F.Degrado. Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters. J. Am. Chem. Soc. V. 140 15219 2018.
ISSN: ESSN 1520-5126
PubMed: 30165017
DOI: 10.1021/JACS.8B06741