Sodium in PDB 4p33: Crystal Structure of E. Coli Lptb-E163Q in Complex with Atp-Sodium

The structure of Crystal Structure of E. Coli Lptb-E163Q in Complex with Atp-Sodium, PDB code: 4p33 was solved by D.J.Sherman, M.B.Lazarus, L.Murphy, C.Liu, S.Walker, N.Ruiz, D.Kahne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.86 / 1.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	66.620, 138.360, 101.280, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21

The binding sites of Sodium atom in the Crystal Structure of E. Coli Lptb-E163Q in Complex with Atp-Sodium (pdb code 4p33). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of E. Coli Lptb-E163Q in Complex with Atp-Sodium, PDB code: 4p33:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of E. Coli Lptb-E163Q in Complex with Atp-Sodium


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 E. Coli Lptb-E163Q in Complex with Atp-Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:16.4 occ:1.00 O1G A:ATP402 2.2 13.6 1.0 O1B A:ATP402 2.3 14.0 1.0 OG1 A:THR43 2.3 14.1 1.0 OE1 A:GLN85 2.4 22.4 1.0 O A:HOH532 2.4 21.3 1.0 O A:HOH507 2.6 17.0 1.0 CB A:THR43 3.4 12.7 1.0 PG A:ATP402 3.5 13.6 1.0 CD A:GLN85 3.5 27.4 1.0 PB A:ATP402 3.5 14.3 1.0 O3B A:ATP402 3.7 12.8 1.0 O A:HOH518 3.9 32.9 1.0 OE1 A:GLN163 3.9 27.7 1.0 NE2 A:GLN85 4.0 31.8 1.0 O1A A:ATP402 4.1 16.1 1.0 O3G A:ATP402 4.1 16.6 1.0 OD1 A:ASP162 4.1 18.9 1.0 N A:THR43 4.2 14.5 1.0 CA A:THR43 4.3 13.3 1.0 CG2 A:THR43 4.4 13.6 1.0 OD2 A:ASP162 4.5 19.9 1.0 O3A A:ATP402 4.5 14.7 1.0 O2B A:ATP402 4.7 16.6 1.0 O2G A:ATP402 4.7 13.2 1.0 CG A:ASP162 4.7 19.8 1.0 CG A:GLN85 4.8 23.6 1.0 PA A:ATP402 4.8 15.0 1.0 CB A:GLN85 5.0 20.0 1.0 CE A:LYS42 5.0 17.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of E. Coli Lptb-E163Q in Complex with Atp-Sodium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of E. Coli Lptb-E163Q in Complex with Atp-Sodium within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:12.6 occ:1.00 O3G B:ATP402 2.3 10.6 1.0 O2B B:ATP402 2.4 9.4 1.0 OG1 B:THR43 2.4 10.8 1.0 OE1 B:GLN85 2.4 26.6 1.0 O B:HOH556 2.4 18.0 1.0 O B:HOH511 2.5 15.1 1.0 CB B:THR43 3.4 10.1 1.0 PG B:ATP402 3.4 10.0 1.0 PB B:ATP402 3.5 9.9 1.0 CD B:GLN85 3.5 29.6 1.0 O3B B:ATP402 3.6 9.5 1.0 OE1 B:GLN163 3.8 23.1 1.0 NE2 B:GLN85 4.0 33.6 1.0 O2A B:ATP402 4.1 11.9 1.0 O B:HOH537 4.1 30.6 1.0 O2G B:ATP402 4.1 12.4 1.0 N B:THR43 4.2 9.8 1.0 OD1 B:ASP162 4.2 15.8 1.0 O B:HOH514 4.3 13.7 1.0 CA B:THR43 4.3 10.4 1.0 CG2 B:THR43 4.5 11.1 1.0 O3A B:ATP402 4.5 9.4 1.0 OD2 B:ASP162 4.5 14.2 1.0 O1G B:ATP402 4.7 9.8 1.0 O1B B:ATP402 4.7 9.1 1.0 CG B:ASP162 4.8 14.9 1.0 CG B:GLN85 4.8 23.8 1.0 PA B:ATP402 4.8 10.4 1.0 CB B:GLN85 4.9 19.4 1.0 CD B:GLN163 4.9 19.5 1.0

D.J.Sherman, M.B.Lazarus, L.Murphy, C.Liu, S.Walker, N.Ruiz, D.Kahne. Decoupling Catalytic Activity From Biological Function of the Atpase That Powers Lipopolysaccharide Transport. Proc.Natl.Acad.Sci.Usa V. 111 4982 2014.
ISSN: ESSN 1091-6490
PubMed: 24639492
DOI: 10.1073/PNAS.1323516111