Sodium in PDB 9in8: True-Atomic Resolution Crystal Structure of the Open State of the Viral Channelrhodopsin OLPVR1

The structure of True-Atomic Resolution Crystal Structure of the Open State of the Viral Channelrhodopsin OLPVR1, PDB code: 9in8 was solved by S.Bukhdruker, D.Zabelskii, R.Astashkin, G.Bourenkov, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.11 / 1.34
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.427, 115.029, 53.337, 90, 90, 90
R / Rfree (%)	18.4 / 21.2

The binding sites of Sodium atom in the True-Atomic Resolution Crystal Structure of the Open State of the Viral Channelrhodopsin OLPVR1 (pdb code 9in8). 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 True-Atomic Resolution Crystal Structure of the Open State of the Viral Channelrhodopsin OLPVR1, PDB code: 9in8:

Sodium binding site 1 out of 1 in the True-Atomic Resolution Crystal Structure of the Open State of the Viral Channelrhodopsin OLPVR1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of True-Atomic Resolution Crystal Structure of the Open State of the Viral Channelrhodopsin OLPVR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:28.3 occ:0.70 O A:HOH512 2.0 33.8 0.3 OD2 A:ASP68 2.1 35.8 0.3 OE2 A:GLU132 2.1 25.9 0.3 O A:HOH494 2.3 26.4 1.0 OE2 A:GLU132 2.4 27.1 0.7 O A:GLU132 2.5 25.8 0.7 O A:HOH512 2.5 32.1 0.7 O A:HOH468 2.7 50.1 1.0 OD2 A:ASP68 2.8 35.8 0.7 CG A:ASP68 2.8 35.6 0.3 O A:GLU132 3.0 28.4 0.3 CG A:ASP68 3.1 35.6 0.7 CD A:GLU132 3.1 22.1 0.3 OD1 A:ASP68 3.2 35.0 0.7 OD1 A:ASP68 3.3 35.1 0.3 CD A:GLU132 3.4 25.4 0.7 CG A:GLU132 3.5 24.6 0.3 C A:GLU132 3.6 23.7 0.7 CG A:GLU132 3.8 25.4 0.7 CB A:ASP68 3.9 36.0 0.3 C A:GLU132 3.9 26.5 0.3 O A:HOH529 4.0 48.9 1.0 NZ A:LYS192 4.1 29.1 1.0 CB A:ASP68 4.1 36.0 0.7 O A:HOH403 4.1 30.4 1.0 OE1 A:GLU132 4.1 23.0 0.3 O A:HOH473 4.2 38.3 0.7 CA A:GLU132 4.3 23.6 0.3 CA A:GLU132 4.3 22.4 0.7 CG2 A:THR70 4.3 25.8 0.3 CB A:THR70 4.3 23.2 0.7 CB A:GLU132 4.5 20.8 0.3 OG1 A:THR70 4.5 20.0 0.7 OE1 A:GLU132 4.5 18.4 0.7 CB A:GLU132 4.6 25.5 0.7 O A:HOH486 4.6 28.6 1.0 O A:ASP68 4.6 35.2 0.7 O A:HOH516 4.6 54.6 1.0 N A:THR133 4.7 23.7 0.7 O A:ASP68 4.7 37.5 0.3 C A:ASP68 4.9 35.2 0.3 CA A:ASP68 5.0 35.7 0.3 CE A:LYS134 5.0 47.8 0.7 N A:THR133 5.0 23.8 0.3 CA A:THR133 5.0 20.9 0.7

D.Zabelskii, S.Bukhdruker, S.Bukhalovich, F.Tsybrov, G.H.U.Lamm, R.Astashkin, D.Doroginin, G.Matveev, V.Sudarev, A.Kuzmin, E.Zinovev, A.Vlasova, Y.Ryzhykau, N.Ilyinsky, I.Gushchin, G.Bourenkov, A.Alekseev, A.Round, J.Wachtveitl, E.Bamberg, V.Gordeliy. Ion Conducting and Gating Molecular Mechanisms of Channelrhodopsin Revealed By True-Atomic Resolution Structures of Open and Closed States Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985