Sodium in PDB 6rf5: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 6.0

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 6.0, PDB code: 6rf5 was solved by K.Kovalev, V.Polovinkin, I.Gushchin, V.Borshchevskiy, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	40.334, 81.246, 233.359, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.9

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 6.0 (pdb code 6rf5). 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 the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 6.0, PDB code: 6rf5:

Sodium binding site 1 out of 1 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 6.0


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 the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:58.9 occ:1.00 O A:PHE86 2.4 44.8 1.0 O A:THR83 2.5 47.3 1.0 O A:HOH445 2.6 76.1 1.0 O A:HOH443 2.7 65.3 1.0 OH A:TYR25 2.8 44.6 1.0 C A:PHE86 3.6 42.4 1.0 C A:THR83 3.6 38.8 1.0 CZ A:TYR25 3.7 40.2 1.0 CA A:THR87 4.0 45.2 1.0 O A:HOH433 4.2 47.5 1.0 CE1 A:TYR25 4.2 35.9 1.0 N A:THR87 4.2 43.8 1.0 CA A:THR83 4.3 39.5 1.0 OG1 A:THR87 4.4 47.3 1.0 O A:HOH423 4.4 54.3 1.0 CB A:THR87 4.4 46.2 1.0 CB A:THR83 4.7 42.0 1.0 N A:SER84 4.7 36.1 1.0 N A:PHE86 4.7 38.2 1.0 CE2 A:TYR25 4.7 40.3 1.0 CA A:PHE86 4.7 39.9 1.0 CD2 A:TYR95 4.9 47.9 1.0 CE2 A:TYR95 4.9 43.7 1.0

K.Kovalev, V.Polovinkin, I.Gushchin, A.Alekseev, V.Shevchenko, V.Borshchevskiy, R.Astashkin, T.Balandin, D.Bratanov, S.Vaganova, A.Popov, V.Chupin, G.Buldt, E.Bamberg, V.Gordeliy. Structure and Mechanisms of Sodium-Pumping KR2 Rhodopsin. Sci Adv V. 5 V2671 2019.
ISSN: ESSN 2375-2548
PubMed: 30989112
DOI: 10.1126/SCIADV.AAV2671