Sodium in PDB 3zxd: Wild-Type Lysenin

The structure of Wild-Type Lysenin, PDB code: 3zxd 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)	29.09 / 3.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.910, 85.560, 108.810, 98.88, 96.84, 90.04
R / Rfree (%)	21.3 / 23.6

The structure of Wild-Type Lysenin also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Wild-Type Lysenin (pdb code 3zxd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Wild-Type Lysenin, PDB code: 3zxd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Wild-Type Lysenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na467 b:25.6 occ:1.00 OG A:SER151 3.0 48.5 1.0 O A:ALA18 3.2 37.9 1.0 N A:ALA18 3.3 30.4 1.0 CG2 A:VAL17 3.9 31.7 1.0 CG1 A:VAL148 4.0 34.7 1.0 C A:ALA18 4.0 38.0 1.0 CG2 A:VAL148 4.1 33.1 1.0 CA A:VAL17 4.1 28.5 1.0 CA A:ALA18 4.1 31.6 1.0 C A:VAL17 4.2 34.0 1.0 CB A:SER151 4.2 35.9 1.0 CB A:ALA18 4.5 32.3 1.0 O A:VAL16 4.6 30.6 1.0 CB A:VAL17 4.6 31.4 1.0 CB A:VAL148 4.7 33.5 1.0

Sodium binding site 2 out of 6 in the Wild-Type Lysenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:59.6 occ:1.00 NE2 A:GLN143 3.2 56.6 1.0 OE2 A:GLU22 3.8 61.6 1.0 CD A:GLN143 4.5 67.4 1.0 CH2 A:TRP116 4.5 37.0 1.0 CD1 A:ILE145 4.6 70.9 1.0 CG1 A:ILE145 4.8 53.1 1.0 CD A:GLU22 5.0 71.6 1.0

Sodium binding site 3 out of 6 in the Wild-Type Lysenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:51.8 occ:1.00 OD1 A:ASP15 2.9 47.4 1.0 O A:GLU13 3.4 38.5 1.0 C A:GLU13 3.9 39.1 1.0 CG A:ASP15 4.0 43.2 1.0 CD A:ARG152 4.1 60.2 1.0 NE A:ARG152 4.2 71.8 1.0 O1 A:SO4466 4.2 0.1 1.0 CA A:VAL14 4.3 35.3 1.0 CG A:GLU13 4.3 40.7 1.0 N A:VAL14 4.3 36.6 1.0 N A:ASP15 4.3 32.6 1.0 OE1 A:GLU13 4.3 36.4 1.0 C A:VAL14 4.4 37.0 1.0 CB A:GLU13 4.4 35.7 1.0 CD A:GLU13 4.5 54.7 1.0 OD2 A:ASP15 4.7 44.2 1.0 CG A:ARG152 4.8 44.8 1.0 CA A:GLU13 4.8 33.8 1.0

Sodium binding site 4 out of 6 in the Wild-Type Lysenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:40.7 occ:1.00 OE2 A:GLU174 2.4 89.5 1.0 CD A:GLU174 3.1 93.8 1.0 OE1 A:GLU174 3.3 80.1 1.0 N A:LYS290 3.5 53.7 1.0 CA A:ASP289 3.7 52.6 1.0 CG A:LYS290 4.0 75.6 1.0 C A:ASP289 4.1 55.4 1.0 CB A:LYS290 4.2 57.1 1.0 CB A:ASP289 4.3 55.7 1.0 CG A:GLU174 4.3 72.0 1.0 O A:GLU288 4.4 54.4 1.0 CA A:LYS290 4.5 52.5 1.0 CG A:ASP289 4.5 67.6 1.0 CD A:LYS290 4.5 89.9 1.0 OD1 A:ASP289 4.6 68.2 1.0 N A:ASP289 4.8 51.6 1.0

Sodium binding site 5 out of 6 in the Wild-Type Lysenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na500 b:24.9 occ:1.00 O B:ALA18 3.2 34.2 1.0 OG B:SER151 3.4 46.4 1.0 CG1 B:VAL148 3.5 31.6 1.0 N B:ALA18 3.6 26.6 1.0 CG2 B:VAL148 4.0 30.0 1.0 CD A:PRO241 4.0 31.8 1.0 C B:ALA18 4.1 33.6 1.0 CG2 B:VAL17 4.1 29.9 1.0 CG A:PRO241 4.2 36.4 1.0 CA B:ALA18 4.3 26.9 1.0 CA B:VAL17 4.4 26.5 1.0 CB B:VAL148 4.4 30.3 1.0 C B:VAL17 4.5 30.7 1.0 CB B:SER151 4.5 33.5 1.0 CB B:ALA18 4.7 27.8 1.0 O B:VAL16 4.9 32.0 1.0 CB B:VAL17 4.9 29.5 1.0 CE1 A:TYR265 5.0 53.6 1.0

Sodium binding site 6 out of 6 in the Wild-Type Lysenin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ D:Na500 b:49.9 occ:1.00 O D:GLU102 3.4 44.0 1.0 C D:GLU102 4.6 41.2 1.0 CB D:HIS103 4.8 37.4 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