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

Protein crystallography data

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

Other elements in 6boc:

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

Sodium Binding Sites:

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 6boc

Go back to Sodium Binding Sites List in 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

Reference:

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
Page generated: Tue Dec 15 11:59:34 2020

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