Magnesium 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:

Chlorine	(Cl)	1 atom
Sodium	(Na)	6 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg470 b:55.5 occ:1.00 O3 A:SO4468 2.4 0.2 1.0 S A:SO4468 3.7 0.0 1.0 CG2 A:VAL19 3.7 46.2 1.0 O4 A:SO4468 4.1 0.5 1.0 O2 A:SO4468 4.4 0.9 1.0 CB A:VAL19 4.8 45.1 1.0 O1 A:SO4468 4.8 0.5 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg470 b:27.3 occ:0.98 O3 B:SO4465 2.3 36.4 0.6 S B:SO4465 3.7 35.8 0.6 O B:GLU13 4.0 34.4 1.0 O4 B:SO4465 4.3 40.0 0.6 CG2 B:ILE12 4.6 40.9 1.0 O2 B:SO4465 4.6 34.8 0.6 O1 B:SO4465 4.6 31.5 0.6 CG2 B:THR63 4.9 61.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg472 b:30.1 occ:1.00 OG1 B:THR66 3.2 35.3 1.0 CB B:SER59 3.3 42.5 1.0 N B:SER59 3.5 34.1 1.0 OG B:SER59 3.5 52.6 1.0 CA B:SER59 3.9 34.9 1.0 N B:THR66 4.0 33.4 1.0 C B:HIS58 4.4 36.0 1.0 CB B:THR66 4.4 36.9 1.0 CA B:SER65 4.6 38.7 1.0 CA B:HIS58 4.6 32.4 1.0 C B:SER65 4.7 37.4 1.0 CA B:THR66 4.8 32.1 1.0 CB B:SER65 4.8 48.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg546 b:44.3 occ:1.00 OD1 C:ASP257 2.1 98.9 1.0 CB C:LYS249 3.0 88.5 1.0 CG C:ASP257 3.2 93.9 1.0 CG C:LYS249 3.3 1.0 1.0 CB C:ASP257 3.7 82.2 1.0 O C:HOH2002 3.9 18.6 1.0 CD C:LYS249 3.9 0.8 1.0 OD1 C:ASP68 4.1 80.5 1.0 OD2 C:ASP257 4.2 95.8 1.0 NZ C:LYS249 4.3 0.3 1.0 O C:SER250 4.3 87.5 1.0 CD2 C:LEU253 4.4 92.0 1.0 CG C:ASP68 4.4 78.7 1.0 CA C:LYS249 4.4 84.7 1.0 CA C:ASP68 4.5 63.0 1.0 CE C:LYS249 4.7 1.0 1.0 CA C:LEU253 4.8 86.0 1.0 N C:ARG254 4.8 85.7 1.0 OD2 C:ASP68 4.8 85.2 1.0 C C:LYS249 4.9 88.4 1.0 CB C:ASP68 4.9 65.5 1.0 CG1 C:VAL259 4.9 81.0 1.0 CA C:ASP257 5.0 81.0 1.0 O C:PRO252 5.0 89.3 1.0 O C:GLY67 5.0 64.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg547 b:36.2 occ:0.97 OE1 C:GLU22 3.2 69.0 1.0 OE2 C:GLU22 3.6 56.7 1.0 CD C:GLU22 3.8 66.3 1.0 NZ C:LYS112 4.3 42.8 1.0 CG1 C:VAL25 4.7 32.6 1.0 CG2 C:VAL25 4.8 31.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Wild-Type Lysenin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg470 b:32.2 occ:1.00 O3 D:SO4467 2.1 80.5 0.8 O D:VAL25 3.1 32.8 1.0 N D:VAL25 3.2 25.3 1.0 CG1 D:VAL25 3.4 28.2 1.0 S D:SO4467 3.5 78.8 0.8 C D:VAL25 3.9 29.9 1.0 CA D:VAL25 3.9 24.7 1.0 C D:TYR24 4.1 28.2 1.0 CA D:TYR24 4.1 28.4 1.0 O1 D:SO4467 4.2 81.7 0.8 O4 D:SO4467 4.2 79.8 0.8 CB D:VAL25 4.3 26.9 1.0 CD2 D:TYR24 4.4 34.4 1.0 O2 D:SO4467 4.6 74.3 0.8 CG D:TYR24 4.7 31.6 1.0 CE2 D:TYR24 4.9 36.3 1.0 CB D:TYR24 4.9 29.6 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