Sodium in PDB 3zx7: Complex of Lysenin with Phosphocholine

The structure of Complex of Lysenin with Phosphocholine, PDB code: 3zx7 was solved by L.De Colibus, A.F.P.Sonnen, K.J.Morris, C.A.Siebert, P.Abrusci, J.Plitzko, V.Hodnik, M.Leippe, E.Volpi, G.Anderluh, R.J.C.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.70 / 2.84
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.110, 98.110, 184.170, 90.00, 90.00, 120.00
R / Rfree (%)	22.35 / 26.4

The binding sites of Sodium atom in the Complex of Lysenin with Phosphocholine (pdb code 3zx7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Complex of Lysenin with Phosphocholine, PDB code: 3zx7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Complex of Lysenin with Phosphocholine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Lysenin with Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:52.8 occ:1.00 O1 A:PO4884 3.0 98.0 0.9 N A:TRP206 3.3 36.1 1.0 CA A:ASP205 3.7 33.7 1.0 CB A:ASP205 3.7 36.4 1.0 C A:ASP205 3.9 39.3 1.0 CD1 A:TRP206 4.0 43.2 1.0 CA A:TRP206 4.2 36.7 1.0 CB A:TRP206 4.3 37.8 1.0 P A:PO4884 4.3 95.7 0.9 CG A:TRP206 4.6 39.8 1.0 O2 A:PO4884 4.6 96.1 0.9 O A:ASP205 5.0 40.0 1.0 O A:GLU204 5.0 41.8 1.0

Sodium binding site 2 out of 3 in the Complex of Lysenin with Phosphocholine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of Lysenin with Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:66.4 occ:1.00 O A:GLY276 3.0 71.6 1.0 OD2 A:ASP275 3.5 88.6 1.0 CG A:ASP275 3.7 85.5 1.0 OD1 A:ASP275 3.8 94.6 1.0 N A:GLY276 3.9 58.4 1.0 O A:THR279 3.9 54.8 1.0 C A:GLY276 4.0 68.0 1.0 CB A:ASN280 4.1 52.0 1.0 CA A:ASP275 4.1 61.3 1.0 O A:ALA278 4.2 67.8 1.0 C A:ASP275 4.2 65.1 1.0 C A:THR279 4.4 55.7 1.0 ND2 A:ASN280 4.5 51.2 1.0 CB A:ASP275 4.5 67.6 1.0 CA A:GLY276 4.5 58.1 1.0 C A:ALA278 4.6 65.7 1.0 CG A:ASN280 4.7 59.2 1.0 N A:ASN280 4.9 51.8 1.0 CA A:ASN280 4.9 49.9 1.0 C A:PRO277 4.9 74.1 1.0 N A:THR279 5.0 58.1 1.0 N A:ALA278 5.0 64.0 1.0

Sodium binding site 3 out of 3 in the Complex of Lysenin with Phosphocholine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex of Lysenin with Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na905 b:50.3 occ:1.00 OD2 A:ASP235 3.0 40.8 1.0 CD2 A:TYR225 3.6 37.1 1.0 ND2 A:ASN240 3.6 35.8 1.0 CG A:TYR225 3.7 35.4 1.0 NE2 A:GLN243 3.9 50.9 1.0 CG A:ASP235 3.9 46.4 1.0 CG A:ASN240 4.0 42.8 1.0 CB A:TYR225 4.0 34.0 1.0 CB A:ASP235 4.0 42.9 1.0 CB A:ASN240 4.1 34.8 1.0 CE2 A:TYR225 4.2 39.3 1.0 CB A:LYS242 4.2 35.0 1.0 CD1 A:TYR225 4.3 38.0 1.0 CB A:GLN243 4.5 37.0 1.0 N A:GLN243 4.6 34.1 1.0 CZ A:TYR225 4.6 41.5 1.0 OD1 A:ASN240 4.7 31.3 1.0 CE1 A:TYR225 4.7 40.5 1.0 OG1 A:THR238 4.8 38.6 1.0 CD A:GLN243 4.9 53.1 1.0 CG A:GLN243 4.9 37.0 1.0 C A:LYS242 4.9 35.0 1.0

L.De Colibus, A.F.P.Sonnen, K.J.Morris, C.A.Siebert, P.Abrusci, J.Plitzko, V.Hodnik, M.Leippe, E.Volpi, G.Anderluh, R.J.C.Gilbert. Structures of Lysenin Reveal A Shared Evolutionary Origin For Pore-Forming Proteins and Its Mode of Sphingomyelin Recognition. Structure V. 20 1498 2012.
ISSN: ISSN 0969-2126
PubMed: 22819216
DOI: 10.1016/J.STR.2012.06.011