Sodium in PDB 6mbn: Lptb E163Q in Complex with Atp

The structure of Lptb E163Q in Complex with Atp, PDB code: 6mbn was solved by T.W.Owens, N.Ruiz, D.Kahne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.85 / 1.96
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	65.351, 137.585, 100.971, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.9

The binding sites of Sodium atom in the Lptb E163Q in Complex with Atp (pdb code 6mbn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Lptb E163Q in Complex with Atp, PDB code: 6mbn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Lptb E163Q in Complex with Atp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lptb E163Q in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:21.3 occ:1.00 O3G A:ATP302 2.3 20.5 1.0 OE1 A:GLN85 2.3 20.4 1.0 OG1 A:THR43 2.3 19.3 1.0 O2B A:ATP302 2.4 17.3 1.0 O A:HOH429 2.5 21.1 1.0 O A:HOH440 2.5 25.5 1.0 HB A:THR43 3.3 21.0 1.0 CD A:GLN85 3.4 27.1 1.0 CB A:THR43 3.4 17.4 1.0 PG A:ATP302 3.4 17.2 1.0 H A:THR43 3.5 21.8 1.0 HE22 A:GLN85 3.5 39.0 1.0 PB A:ATP302 3.6 20.1 1.0 OE1 A:GLN163 3.7 28.7 1.0 O3B A:ATP302 3.7 16.6 1.0 NE2 A:GLN85 3.9 32.5 1.0 O2A A:ATP302 4.0 17.2 1.0 O1G A:ATP302 4.0 19.4 1.0 O A:HOH423 4.1 19.6 1.0 N A:THR43 4.2 18.1 1.0 HB2 A:LYS42 4.2 18.7 1.0 OD1 A:ASP162 4.2 23.7 1.0 HE2 A:LYS42 4.3 22.6 1.0 HG21 A:THR43 4.3 24.2 1.0 CA A:THR43 4.3 16.1 1.0 HB2 A:GLN85 4.4 28.3 1.0 CG2 A:THR43 4.5 20.1 1.0 OD2 A:ASP162 4.5 18.9 1.0 O1B A:ATP302 4.6 17.6 1.0 HG3 A:GLN163 4.6 29.7 1.0 HA A:THR43 4.6 19.4 1.0 O2G A:ATP302 4.7 18.8 1.0 CG A:GLN85 4.7 30.9 1.0 O3A A:ATP302 4.7 20.2 1.0 HB3 A:GLN85 4.7 28.3 1.0 HE21 A:GLN85 4.7 39.0 1.0 HE2 A:HIS195 4.8 25.3 1.0 CG A:ASP162 4.8 23.7 1.0 CD A:GLN163 4.8 27.2 1.0 CB A:GLN85 4.8 23.5 1.0 HG23 A:THR43 4.9 24.2 1.0 PA A:ATP302 4.9 16.0 1.0 HZ1 A:LYS42 4.9 19.7 1.0

Sodium binding site 2 out of 2 in the Lptb E163Q in Complex with Atp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lptb E163Q in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:24.7 occ:1.00 O3G B:ATP302 2.2 20.3 1.0 OG1 B:THR43 2.3 21.8 1.0 OE1 B:GLN85 2.4 32.5 1.0 O2B B:ATP302 2.4 19.0 1.0 O B:HOH428 2.5 28.2 1.0 O B:HOH411 2.5 21.4 1.0 HB B:THR43 3.4 24.3 1.0 CB B:THR43 3.4 20.2 1.0 CD B:GLN85 3.4 40.5 1.0 PG B:ATP302 3.4 20.8 1.0 HE22 B:GLN85 3.5 54.0 1.0 H B:THR43 3.6 26.4 1.0 PB B:ATP302 3.6 19.1 1.0 O B:HOH409 3.7 31.0 1.0 O3B B:ATP302 3.8 19.2 1.0 NE2 B:GLN85 3.8 44.9 1.0 O2A B:ATP302 4.0 21.5 1.0 OE1 B:GLN163 4.0 36.0 1.0 O1G B:ATP302 4.0 19.9 1.0 O B:HOH424 4.1 22.7 1.0 HB2 B:LYS42 4.2 28.4 1.0 N B:THR43 4.2 21.9 1.0 OD1 B:ASP162 4.2 27.3 1.0 HE2 B:LYS42 4.2 29.0 1.0 HG23 B:THR43 4.3 26.7 1.0 CA B:THR43 4.4 19.8 1.0 OD2 B:ASP162 4.4 26.4 1.0 CG2 B:THR43 4.5 22.1 1.0 HB2 B:GLN85 4.5 34.8 1.0 O1B B:ATP302 4.5 20.1 1.0 HE2 B:HIS195 4.6 32.5 1.0 HA B:THR43 4.6 23.9 1.0 O2G B:ATP302 4.7 17.9 1.0 O3A B:ATP302 4.7 25.4 1.0 HE21 B:GLN85 4.7 54.0 1.0 HZ3 B:LYS42 4.7 26.2 1.0 CG B:GLN85 4.8 36.7 1.0 CG B:ASP162 4.8 27.1 1.0 HB3 B:GLN85 4.8 34.8 1.0 HG3 B:GLN163 4.8 41.8 1.0 HG22 B:THR43 4.8 26.7 1.0 PA B:ATP302 4.9 21.6 1.0 CB B:GLN85 4.9 28.9 1.0 HZ2 B:LYS42 5.0 26.2 1.0

B.W.Simpson, K.S.Pahil, T.W.Owens, E.A.Lundstedt, R.M.Davis, D.Kahne, N.Ruiz. Combining Mutations That Inhibit Two Distinct Steps of the Atp Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows That Atp Binding Triggers Transport. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 31431556
DOI: 10.1128/MBIO.01931-19