Sodium in PDB 7q36: Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton

The structure of Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton, PDB code: 7q36 was solved by I.Melnikov, M.Rulev, R.Astashkin, K.Kovalev, P.Carpentier, V.Gordeliy, A.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	116.72 / 2.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	40.489, 82.18, 233.442, 90, 90, 90
R / Rfree (%)	21.6 / 26.9

The structure of Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton also contains other interesting chemical elements:

Krypton

(Kr)

11 atoms

The binding sites of Sodium atom in the Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton (pdb code 7q36). 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton, PDB code: 7q36:

Sodium binding site 1 out of 1 in the Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton


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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Na329 b:68.0 occ:1.00 O A:THR83 2.6 52.6 1.0 O A:PHE86 2.6 49.5 1.0 O A:HOH471 2.7 73.4 1.0 O A:HOH445 2.7 56.7 1.0 OH A:TYR25 2.9 45.8 1.0 O A:HOH432 3.6 54.0 1.0 C A:PHE86 3.7 50.5 1.0 C A:THR83 3.8 48.7 1.0 O A:HOH450 3.8 92.4 1.0 CZ A:TYR25 3.8 45.0 1.0 CA A:THR87 4.0 53.4 1.0 CG2 A:THR87 4.2 54.3 1.0 N A:THR87 4.3 52.4 1.0 CE1 A:TYR25 4.4 44.6 1.0 CA A:THR83 4.5 46.9 1.0 O A:HOH420 4.6 53.7 1.0 CE2 A:TYR95 4.6 49.7 1.0 CB A:THR87 4.7 54.2 1.0 CE2 A:TYR25 4.7 45.7 1.0 N A:SER84 4.8 48.8 1.0 CD2 A:TYR95 4.8 50.1 1.0 CB A:THR83 4.9 45.3 1.0 CA A:PHE86 4.9 49.8 1.0 N A:PHE86 5.0 49.0 1.0

I.Melnikov, P.Orekhov, M.Rulev, K.Kovalev, R.Astashkin, D.Bratanov, Y.Ryzhykau, T.Balandin, S.Bukhdruker, I.Okhrimenko, V.Borshchevskiy, G.Bourenkov, C.Mueller-Dieckmann, P.Van Der Linden, P.Carpentier, G.Leonard, V.Gordeliy, A.Popov. High-Pressure Crystallography Shows Noble Gas Intervention Into Protein-Lipid Interaction and Suggests A Model For Anaesthetic Action. Commun Biol V. 5 360 2022.
ISSN: ESSN 2399-3642
PubMed: 35422073
DOI: 10.1038/S42003-022-03233-Y