Sodium in PDB 6ek4: Paxb From Photorhabdus Luminescens

The structure of Paxb From Photorhabdus Luminescens, PDB code: 6ek4 was solved by B.Braeuning, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.590, 70.180, 136.890, 90.00, 108.41, 90.00
R / Rfree (%)	24.1 / 26.8

The binding sites of Sodium atom in the Paxb From Photorhabdus Luminescens (pdb code 6ek4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Paxb From Photorhabdus Luminescens, PDB code: 6ek4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Paxb From Photorhabdus Luminescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Paxb From Photorhabdus Luminescens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:81.5 occ:1.00 OD1 A:ASP56 2.7 65.6 1.0 OE1 A:GLU59 3.1 69.7 1.0 OD1 B:ASP139 3.2 73.5 1.0 CG A:ASP56 3.8 65.8 1.0 CD A:GLU59 4.0 68.6 1.0 OH B:TYR53 4.0 71.3 1.0 O B:HOH517 4.0 85.4 1.0 OE2 A:GLU59 4.0 69.1 1.0 CE D:LYS266 4.2 76.4 1.0 OD2 A:ASP56 4.3 66.1 1.0 CG B:ASP139 4.3 72.9 1.0 NZ D:LYS266 4.4 76.3 1.0 O B:HOH540 4.5 70.3 1.0 CZ B:TYR53 4.7 70.2 1.0 CB A:ASP56 4.9 65.6 1.0 OD2 B:ASP139 4.9 73.2 1.0

Sodium binding site 2 out of 4 in the Paxb From Photorhabdus Luminescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Paxb From Photorhabdus Luminescens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:82.5 occ:1.00 OD1 B:ASP56 2.7 70.2 1.0 OE1 B:GLU59 2.8 79.4 1.0 OD1 A:ASP139 3.2 74.0 1.0 CG B:ASP56 3.6 70.5 1.0 CD B:GLU59 3.9 79.0 1.0 NZ C:LYS266 4.1 83.5 1.0 CG A:ASP139 4.1 73.0 1.0 OD2 B:ASP56 4.2 70.7 1.0 OE2 B:GLU59 4.2 80.3 1.0 OD2 A:ASP139 4.5 72.4 1.0 OH A:TYR53 4.5 69.3 1.0 CB B:ASP56 4.6 70.2 1.0 CA B:ASP56 4.8 70.5 1.0

Sodium binding site 3 out of 4 in the Paxb From Photorhabdus Luminescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Paxb From Photorhabdus Luminescens within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:75.5 occ:1.00 OE1 C:GLU59 2.7 64.3 1.0 OD1 C:ASP56 2.9 58.1 1.0 OD1 D:ASP139 3.1 64.0 1.0 CG C:ASP56 3.8 58.4 1.0 CD C:GLU59 3.8 63.8 1.0 CG D:ASP139 4.1 62.9 1.0 NZ B:LYS266 4.2 71.5 1.0 OE2 C:GLU59 4.2 64.8 1.0 OD2 C:ASP56 4.4 58.8 1.0 OD2 D:ASP139 4.4 63.8 1.0 CB C:ASP56 4.7 57.8 1.0 CA C:ASP56 4.8 57.3 1.0 OH D:TYR53 4.9 65.3 1.0

Sodium binding site 4 out of 4 in the Paxb From Photorhabdus Luminescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Paxb From Photorhabdus Luminescens within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:78.5 occ:1.00 OD1 D:ASP56 2.6 64.3 1.0 OE1 D:GLU59 2.7 72.9 1.0 O C:HOH521 3.0 75.8 1.0 O D:HOH551 3.1 62.9 1.0 CG D:ASP56 3.7 63.9 1.0 OD1 C:ASP139 3.8 64.8 1.0 CD D:GLU59 3.9 72.3 1.0 O D:HOH512 4.0 57.9 1.0 NZ A:LYS266 4.3 74.1 1.0 OH C:TYR53 4.4 64.8 1.0 OE2 D:GLU59 4.4 73.6 1.0 OD2 D:ASP56 4.5 64.1 1.0 CB D:ASP56 4.5 62.9 1.0 CG C:ASP139 4.5 63.2 1.0 OD2 C:ASP139 4.7 63.1 1.0 CA D:ASP56 4.7 62.6 1.0 O D:HOH553 4.9 58.4 1.0

B.Brauning, E.Bertosin, F.Praetorius, C.Ihling, A.Schatt, A.Adler, K.Richter, A.Sinz, H.Dietz, M.Groll. Structure and Mechanism of the Two-Component Alpha-Helical Pore-Forming Toxin Yaxab. Nat Commun V. 9 1806 2018.
ISSN: ESSN 2041-1723
PubMed: 29728606
DOI: 10.1038/S41467-018-04139-2