Sodium in PDB 4cdb: Crystal Structure of Listeriolysin O

The structure of Crystal Structure of Listeriolysin O, PDB code: 4cdb was solved by S.Koester, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.638 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.720, 85.150, 229.900, 90.00, 90.00, 90.00
R / Rfree (%)	19.37 / 24.59

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Listeriolysin O (pdb code 4cdb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Crystal Structure of Listeriolysin O, PDB code: 4cdb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1531 b:73.6 occ:1.00 OD1 A:ASP207 2.5 69.5 1.0 N A:ASP208 2.8 47.9 1.0 NZ A:LYS220 3.1 75.5 1.0 CE A:LYS220 3.1 73.3 1.0 CA A:ASP207 3.2 47.9 1.0 O A:ASP208 3.2 47.0 1.0 OD1 A:ASP208 3.3 73.0 1.0 C A:ASP207 3.4 42.7 1.0 CG A:ASP207 3.4 66.7 1.0 CB A:ASP207 3.6 56.4 1.0 CA A:ASP208 3.9 50.7 1.0 C A:ASP208 3.9 48.8 1.0 O A:HOH2149 4.2 74.1 1.0 O A:TYR206 4.3 52.4 1.0 CG A:ASP208 4.3 70.1 1.0 N A:ASP207 4.4 44.3 1.0 OD2 A:ASP207 4.6 69.9 1.0 O A:ASP207 4.6 36.3 1.0 CD A:LYS220 4.7 68.2 1.0 CB A:ASP208 4.7 58.6 1.0 C A:TYR206 4.8 48.3 1.0

Sodium binding site 2 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1532 b:84.8 occ:1.00 O A:THR409 2.5 54.7 1.0 O A:HOH2154 2.5 70.0 1.0 O A:HOH2167 2.5 59.9 1.0 O A:HOH2216 3.5 54.5 1.0 CE1 A:TYR212 3.6 45.4 1.0 C A:THR409 3.7 54.3 1.0 CG A:GLN245 3.7 53.7 1.0 CG2 A:ILE239 3.9 46.5 1.0 O A:HOH2169 4.0 62.1 1.0 OE1 A:GLN245 4.0 52.9 1.0 O A:HOH2152 4.1 36.8 1.0 OH A:TYR212 4.1 49.6 1.0 O A:MET244 4.1 54.9 1.0 CD A:GLN245 4.2 56.4 1.0 CZ A:TYR212 4.3 47.5 1.0 CA A:THR410 4.4 56.0 1.0 O A:ILE239 4.4 46.8 1.0 N A:THR410 4.5 55.2 1.0 CB A:GLN245 4.5 55.1 1.0 CD1 A:TYR212 4.5 47.0 1.0 CA A:GLN245 4.6 55.2 1.0 CA A:THR409 4.7 49.1 1.0 CB A:THR409 4.7 45.5 1.0 N A:THR409 5.0 48.9 1.0

Sodium binding site 3 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1533 b:54.3 occ:1.00 OD1 A:ASN402 2.4 36.1 1.0 O A:HOH2111 2.9 35.2 1.0 O A:ILE218 2.9 33.4 1.0 O A:HOH2079 3.0 51.3 1.0 CG A:ASN402 3.5 33.3 1.0 CA A:GLY222 3.5 29.4 1.0 C A:ILE218 3.9 39.3 1.0 ND2 A:ASN402 4.0 32.3 1.0 C A:GLY222 4.1 32.5 1.0 N A:THR223 4.1 36.3 1.0 N A:GLY222 4.1 36.7 1.0 CB A:TYR78 4.1 34.3 1.0 CG2 A:ILE218 4.2 32.9 1.0 CA A:ALA219 4.2 35.8 1.0 CG A:TYR78 4.3 41.4 1.0 CD2 A:TYR78 4.4 44.0 1.0 N A:ALA219 4.5 36.1 1.0 CG2 A:ILE400 4.5 33.4 1.0 O A:ALA219 4.5 39.1 1.0 C A:ALA219 4.6 39.7 1.0 OG1 A:THR223 4.6 43.8 1.0 CB A:ASN402 4.7 31.0 1.0 CG1 A:VAL138 4.8 40.1 1.0 O A:GLY222 5.0 30.5 1.0

Sodium binding site 4 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1534 b:93.2 occ:1.00 OE2 A:GLU446 2.5 79.0 1.0 OH A:TYR440 2.6 55.2 1.0 O A:HOH2059 3.4 72.6 1.0 CZ A:TYR440 3.7 49.8 1.0 CD A:GLU446 3.7 76.3 1.0 CE1 A:TYR440 4.0 48.2 1.0 NH1 A:ARG89 4.3 49.7 1.0 CG A:GLU446 4.4 70.1 1.0 CG1 A:VAL438 4.5 64.9 1.0 OE1 A:GLU446 4.6 76.7 1.0 O A:HOH2218 4.8 71.3 1.0 CE2 A:TYR440 4.9 46.0 1.0 O A:HOH2143 5.0 62.5 1.0 O A:HOH2144 5.0 58.8 1.0

Sodium binding site 5 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1535 b:81.5 occ:1.00 O A:SER123 2.6 46.6 1.0 ND2 A:ASN179 2.6 52.2 1.0 OD1 A:ASN179 3.2 55.4 1.0 O A:HOH2101 3.3 41.1 1.0 CG A:ASN179 3.3 50.7 1.0 C A:SER123 3.3 46.0 1.0 CA A:SER123 3.5 40.9 1.0 O A:THR125 3.6 38.9 1.0 CB A:TYR126 4.1 29.2 1.0 CB A:SER123 4.2 45.3 1.0 CG A:LYS175 4.3 39.3 1.0 C A:THR125 4.3 37.3 1.0 O A:SER122 4.4 40.2 1.0 N A:LEU124 4.5 42.7 1.0 CD A:LYS175 4.6 46.1 1.0 CD1 A:TYR126 4.7 34.1 1.0 N A:THR125 4.7 34.4 1.0 CB A:ASN179 4.7 40.3 1.0 N A:SER123 4.7 39.1 1.0 CG A:TYR126 4.8 34.1 1.0 CA A:TYR126 4.8 31.9 1.0 N A:TYR126 4.9 37.5 1.0 C A:LEU124 5.0 35.2 1.0 O A:HOH2098 5.0 55.8 1.0

Sodium binding site 6 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1536 b:59.6 occ:1.00 OE1 A:GLU209 2.6 76.4 1.0 OH A:TYR406 2.8 46.3 1.0 NE2 A:GLN216 2.9 40.2 1.0 CD A:GLU209 3.1 72.0 1.0 O A:HOH2150 3.2 46.5 1.0 OE2 A:GLU209 3.3 72.9 1.0 CZ A:TYR406 3.5 44.1 1.0 O A:HOH2072 3.8 72.1 1.0 CE1 A:TYR406 3.8 41.2 1.0 CD A:GLN216 3.9 42.2 1.0 O A:HOH2213 3.9 58.4 1.0 CG A:GLN216 4.0 37.6 1.0 CD1 A:ILE108 4.2 68.3 1.0 CG A:GLU209 4.3 63.3 1.0 CE2 A:TYR406 4.5 43.0 1.0 CB A:ILE108 4.5 62.0 1.0 CG1 A:ILE108 4.8 66.3 1.0 CD1 A:TYR406 5.0 43.4 1.0

Sodium binding site 7 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1537 b:58.9 occ:1.00 OD1 A:ASN172 2.5 68.1 1.0 N A:ARG149 2.7 36.3 1.0 CA A:LYS148 3.3 42.5 1.0 CG A:ASN172 3.3 67.9 1.0 ND2 A:ASN172 3.4 72.5 1.0 C A:LYS148 3.5 39.9 1.0 O A:HOH2284 3.6 48.6 1.0 CA A:ARG149 3.7 37.4 1.0 CB A:ARG149 3.7 41.3 1.0 CB A:LYS148 3.7 46.7 1.0 O A:ARG149 3.9 38.9 1.0 CG2 A:THR174 3.9 48.5 1.0 CG A:ARG149 4.0 42.7 1.0 CG A:LYS148 4.0 55.1 1.0 C A:ARG149 4.3 38.9 1.0 O A:VAL147 4.5 43.1 1.0 O A:HOH2117 4.5 72.1 1.0 N A:LYS148 4.6 39.9 1.0 O A:LYS148 4.7 33.0 1.0 CB A:ASN172 4.8 60.3 1.0

Sodium binding site 8 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1538 b:79.5 occ:1.00 OH A:TYR126 2.6 38.7 1.0 O A:ALA173 2.9 52.4 1.0 O A:HOH2104 3.0 77.7 1.0 NH1 A:ARG149 3.2 33.5 1.0 CZ A:TYR126 3.6 41.2 1.0 CG A:ARG149 3.7 42.7 1.0 CE2 A:TYR126 3.8 38.2 1.0 CA A:THR174 4.0 44.3 1.0 C A:ALA173 4.0 47.7 1.0 O A:HOH2133 4.1 57.6 1.0 CD A:ARG149 4.1 44.5 1.0 C A:THR174 4.3 40.4 1.0 CZ A:ARG149 4.3 39.2 1.0 N A:LYS175 4.4 39.8 1.0 N A:THR174 4.5 44.2 1.0 O A:HOH2103 4.5 54.1 1.0 NE A:ARG149 4.7 44.0 1.0 CA A:ALA129 4.8 30.7 1.0 CE1 A:TYR126 4.9 35.9 1.0 O A:THR174 5.0 39.9 1.0

Sodium binding site 9 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1539 b:56.3 occ:1.00 OH A:TYR303 2.5 51.3 1.0 O A:HOH2086 2.6 41.0 1.0 O A:PHE221 2.8 39.3 1.0 OE1 A:GLN116 2.9 37.3 1.0 CZ A:TYR303 3.4 46.7 1.0 CE1 A:TYR303 3.4 38.9 1.0 CD A:GLN116 3.5 37.2 1.0 CG A:GLN116 3.6 32.5 1.0 CB A:PHE221 3.6 37.0 1.0 C A:PHE221 3.7 38.4 1.0 CA A:PHE221 3.9 34.6 1.0 OG A:SER250 4.2 54.0 1.0 CB A:GLN116 4.2 31.9 1.0 OE1 A:GLN301 4.2 52.7 1.0 O A:HOH2087 4.2 42.9 1.0 CD1 A:PHE221 4.3 40.2 1.0 NZ A:LYS252 4.4 41.2 1.0 CG A:PHE221 4.4 41.6 1.0 NE2 A:GLN116 4.6 41.9 1.0 O A:HOH2089 4.7 40.1 1.0 CE2 A:TYR303 4.7 46.5 1.0 CD1 A:TYR303 4.7 37.6 1.0 CB A:SER250 4.8 43.7 1.0 N A:GLY222 5.0 36.7 1.0 CB A:ALA224 5.0 36.9 1.0

Sodium binding site 10 out of 15 in the Crystal Structure of Listeriolysin O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Listeriolysin O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1540 b:63.5 occ:1.00 OE1 A:GLN278 2.5 60.8 1.0 O A:HOH2116 2.8 41.4 1.0 CD A:GLN278 3.4 61.1 1.0 CB A:GLN278 3.5 45.2 1.0 CG1 A:VAL147 3.6 58.3 1.0 CG A:GLN278 3.8 55.3 1.0 O A:HOH2185 3.9 72.1 1.0 O A:HOH2186 3.9 76.8 1.0 CG1 A:VAL274 4.2 31.6 1.0 CB A:VAL147 4.2 50.7 1.0 CG2 A:VAL274 4.4 36.0 1.0 NE2 A:GLN278 4.4 63.0 1.0 CA A:VAL147 4.5 48.6 1.0 CD1 A:LEU282 4.6 58.1 1.0 CB A:VAL274 4.7 35.9 1.0 CA A:GLN278 4.8 44.2 1.0 CA A:VAL274 4.8 38.6 1.0

S.Koester, K.V.Pee, M.Hudel, M.Leustik, D.Rhinow, W.Kuehlbrandt, T.Chakraborty, O.Yildiz. Crystal Structure of Listeriolysin O Reveals Molecular Details of Oligomerization and Pore Formation Nat.Commun. V. 5 3690 2014.
ISSN: ISSN 2041-1723
PubMed: 24751541
DOI: 10.1038/NCOMMS4690