Sodium in PDB 6nc6: Lipid II Flippase Murj, Inward Closed Conformation

The structure of Lipid II Flippase Murj, Inward Closed Conformation, PDB code: 6nc6 was solved by A.C.Y.Kuk, S.-Y.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.63 / 3.20
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.134, 101.759, 158.516, 90.00, 90.00, 90.00
R / Rfree (%)	25.5 / 27.8

The structure of Lipid II Flippase Murj, Inward Closed Conformation also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the Lipid II Flippase Murj, Inward Closed Conformation (pdb code 6nc6). 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 Lipid II Flippase Murj, Inward Closed Conformation, PDB code: 6nc6:

Sodium binding site 1 out of 1 in the Lipid II Flippase Murj, Inward Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lipid II Flippase Murj, Inward Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:18.5 occ:1.00 OG1 A:THR394 2.4 19.5 1.0 OD1 A:ASP378 2.4 26.1 1.0 O A:VAL390 2.4 20.5 1.0 OD1 A:ASP235 2.4 29.0 1.0 OD1 A:ASN374 2.5 20.9 1.0 HG13 A:VAL390 2.6 22.4 1.0 HB3 A:ALA393 2.8 27.8 1.0 H A:THR394 2.8 26.6 1.0 HG12 A:VAL390 3.1 22.4 1.0 CG A:ASP378 3.2 25.5 1.0 N A:THR394 3.2 21.9 1.0 OD2 A:ASP378 3.2 26.0 1.0 HD21 A:ASN374 3.3 36.1 1.0 CG A:ASP235 3.3 25.9 1.0 C A:VAL390 3.3 20.2 1.0 CG1 A:VAL390 3.3 18.3 1.0 CG A:ASN374 3.4 22.8 1.0 HA A:VAL390 3.5 25.9 1.0 CB A:THR394 3.5 19.1 1.0 HA A:THR394 3.6 24.8 1.0 OD2 A:ASP235 3.7 25.8 1.0 CB A:ALA393 3.7 22.8 1.0 CA A:THR394 3.7 20.3 1.0 ND2 A:ASN374 3.7 29.8 1.0 HB1 A:ALA393 3.8 27.8 1.0 CA A:VAL390 3.9 21.3 1.0 C A:ALA393 3.9 20.8 1.0 HB A:THR394 4.0 23.3 1.0 HG11 A:VAL390 4.0 22.4 1.0 CB A:VAL390 4.2 18.2 1.0 HA A:ALA391 4.2 23.6 1.0 CA A:ALA393 4.3 21.0 1.0 N A:ALA391 4.3 18.5 1.0 HA A:ASP235 4.3 27.7 1.0 HB2 A:ALA393 4.4 27.8 1.0 HB3 A:ASP235 4.4 28.1 1.0 CB A:ASP235 4.4 23.1 1.0 O A:ASN374 4.5 21.5 1.0 H A:ALA393 4.5 23.6 1.0 HD22 A:ASN374 4.6 36.1 1.0 HG22 A:VAL390 4.6 23.1 1.0 CB A:ASP378 4.6 22.9 1.0 CA A:ALA391 4.6 19.4 1.0 N A:ALA393 4.7 19.3 1.0 HA A:ASP378 4.7 29.1 1.0 HG23 A:THR394 4.7 21.9 1.0 CG2 A:THR394 4.7 18.0 1.0 O A:ALA391 4.7 18.0 1.0 HA A:ASN374 4.8 26.8 1.0 O A:ALA393 4.8 20.9 1.0 CB A:ASN374 4.8 22.3 1.0 C A:ALA391 4.9 20.0 1.0 CA A:ASP235 4.9 22.7 1.0 HB A:VAL390 4.9 22.2 1.0 HG21 A:THR394 5.0 21.9 1.0 CG2 A:VAL390 5.0 18.9 1.0

A.C.Y.Kuk, A.Hao, Z.Guan, S.Y.Lee. Visualizing Conformation Transitions of the Lipid II Flippase Murj. Nat Commun V. 10 1736 2019.
ISSN: ESSN 2041-1723
PubMed: 30988294
DOI: 10.1038/S41467-019-09658-0