Sodium in PDB 5kn7: Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii

The structure of Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii, PDB code: 5kn7 was solved by D.L.Dovala, Q.Hu, L.E.Metzger Iv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.67 / 1.99
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	58.770, 145.330, 87.210, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.7

The binding sites of Sodium atom in the Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii (pdb code 5kn7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii, PDB code: 5kn7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:48.5 occ:1.00 OH B:TYR271 2.4 31.4 1.0 O B:ALA55 2.7 35.8 1.0 CZ B:TYR271 3.4 33.5 1.0 CE1 B:TYR271 3.5 32.5 1.0 CD1 B:PHE205 3.6 30.7 1.0 C B:ALA55 3.9 32.0 1.0 CD B:PRO57 4.0 36.4 1.0 CE1 B:PHE205 4.3 31.2 1.0 CG B:PHE205 4.5 28.6 1.0 CB B:PHE205 4.6 28.9 1.0 CE2 B:TYR271 4.6 26.4 1.0 CA B:ALA55 4.7 33.5 1.0 NZ B:LYS309 4.7 49.0 1.0 CG B:PRO57 4.8 42.1 1.0 N B:LEU56 4.8 32.1 1.0 CD1 B:TYR271 4.9 28.1 1.0 CE1 B:TYR58 4.9 37.5 1.0 CA B:LEU56 5.0 37.5 1.0 CD2 B:LEU56 5.0 39.1 1.0

Sodium binding site 2 out of 3 in the Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:63.4 occ:1.00 OG1 B:THR254 3.1 32.8 1.0 CG2 B:THR254 3.6 38.2 1.0 CB B:THR254 3.8 35.6 1.0 OD1 B:ASP256 3.8 56.8 1.0 CB B:ASP256 3.9 38.0 1.0 CG B:ASP256 4.3 45.4 1.0 OD1 B:ASP257 4.4 40.7 1.0 OD2 B:ASP257 4.6 37.5 1.0 CG B:ASP257 4.7 42.1 1.0 O B:HOH550 4.7 40.6 1.0 O B:HOH526 5.0 49.5 1.0

Sodium binding site 3 out of 3 in the Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lipid A Secondary Acyltransferase Lpxm From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:53.4 occ:1.00 OD1 B:ASN130 2.6 48.8 1.0 OE1 B:GLU127 2.6 45.6 1.0 O B:GLU127 2.6 40.5 1.0 NH1 B:ARG159 3.0 55.5 1.0 CG B:ASN130 3.1 51.0 1.0 CB B:ASN130 3.3 41.9 1.0 OE1 B:GLU162 3.3 47.5 0.6 C B:GLU127 3.4 40.3 1.0 CB B:GLU127 3.4 31.8 1.0 CA B:GLU127 3.4 40.6 1.0 OE2 B:GLU162 3.5 48.6 0.6 NE1 B:TRP86 3.6 44.7 1.0 CD B:GLU127 3.7 46.9 1.0 CD B:GLU162 3.8 51.3 0.6 NH2 B:ARG159 3.8 59.6 1.0 CZ B:ARG159 3.8 53.0 1.0 ND2 B:ASN130 4.1 49.4 1.0 CD1 B:TRP86 4.1 34.9 1.0 CG B:GLU127 4.1 40.7 1.0 O B:HOH597 4.1 42.1 1.0 O3 B:GOL409 4.3 52.5 1.0 CG2 B:ILE85 4.5 39.0 1.0 CA B:ASN130 4.6 41.1 1.0 N B:ASN130 4.6 37.8 1.0 N B:VAL128 4.6 38.0 1.0 OE2 B:GLU162 4.7 44.3 0.4 OE2 B:GLU127 4.7 50.7 1.0 N B:GLU127 4.8 32.8 1.0 CE2 B:TRP86 4.8 41.1 1.0

D.Dovala, C.M.Rath, Q.Hu, W.S.Sawyer, S.Shia, R.A.Elling, M.S.Knapp, L.E.Metzger. Structure-Guided Enzymology of the Lipid A Acyltransferase Lpxm Reveals A Dual Activity Mechanism. Proc.Natl.Acad.Sci.Usa V. 113 E6064 2016.
ISSN: ESSN 1091-6490
PubMed: 27681620
DOI: 10.1073/PNAS.1610746113