Sodium in PDB 1r4p: Shiga Toxin Type 2

All present enzymatic activity of Shiga Toxin Type 2:
3.2.2.22;

The structure of Shiga Toxin Type 2, PDB code: 1r4p was solved by M.E.Fraser, M.Fujinaga, M.M.Cherney, A.R.Melton-Celsa, E.M.Twiddy, A.D.O'brien, M.N.G.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.10 / 1.77
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	143.960, 143.960, 59.300, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 18.4

The binding sites of Sodium atom in the Shiga Toxin Type 2 (pdb code 1r4p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Shiga Toxin Type 2, PDB code: 1r4p:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Shiga Toxin Type 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Shiga Toxin Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4001 b:20.8 occ:1.00 O A:HOH4110 2.2 22.1 1.0 O A:THR22 2.2 16.4 1.0 O A:HOH4168 2.3 29.0 1.0 O A:SER25 2.4 15.2 1.0 O A:HOH4173 2.4 27.6 1.0 O A:HOH4021 2.4 22.5 1.0 C A:THR22 3.4 15.7 1.0 C A:SER25 3.5 13.2 1.0 CA A:THR22 4.0 16.0 1.0 CG2 A:THR22 4.1 18.2 0.7 O A:HOH4063 4.1 19.1 1.0 OG1 A:THR26 4.2 16.9 1.0 CA A:THR26 4.3 13.9 1.0 N A:SER25 4.3 11.4 1.0 N A:THR26 4.4 12.9 1.0 N A:GLU23 4.5 16.5 1.0 OD1 A:ASN42 4.5 19.7 1.0 CA A:SER25 4.5 11.9 1.0 O A:ARG21 4.6 13.1 1.0 C A:GLU23 4.6 18.6 1.0 O A:GLU23 4.7 18.2 1.0 CA A:GLU23 4.7 17.8 1.0 CB A:THR22 4.7 17.6 1.0 CD A:PRO27 4.8 15.6 1.0 CB A:THR26 4.9 15.8 1.0

Sodium binding site 2 out of 5 in the Shiga Toxin Type 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Shiga Toxin Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4002 b:30.2 occ:1.00 OD1 A:ASN279 2.2 22.2 1.0 O C:HOH3065 2.2 26.2 1.0 O1 A:FMT3004 2.3 28.1 1.0 O A:ARG266 2.5 17.0 1.0 O A:HOH4035 2.6 21.4 1.0 C A:FMT3004 2.8 26.8 1.0 O A:HOH4142 3.2 20.4 1.0 OG A:SER278 3.2 17.3 1.0 CG A:ASN279 3.3 18.6 1.0 C A:ARG266 3.4 15.5 1.0 ND2 A:ASN279 3.7 16.8 1.0 CA A:PRO267 3.7 14.5 1.0 O A:PRO267 3.8 12.7 1.0 N A:PRO267 3.9 15.0 1.0 ND2 A:ASN207 4.0 16.2 1.0 O2 A:FMT3004 4.1 29.7 1.0 C A:PRO267 4.1 14.0 1.0 N A:ARG266 4.1 14.6 1.0 O A:THR263 4.2 14.8 1.0 OG1 C:THR45 4.2 19.4 0.7 N A:ASN279 4.3 9.3 1.0 CA A:ARG266 4.4 15.0 1.0 CB A:SER278 4.4 11.0 1.0 CB A:ASN279 4.6 11.9 1.0 N A:SER278 4.6 10.7 1.0 CG A:GLU277 4.7 12.1 1.0 O A:HOH4012 4.7 30.2 1.0 O A:HOH4118 4.8 20.7 1.0 CA A:SER278 4.9 11.7 1.0 CA A:ASN279 5.0 10.4 1.0

Sodium binding site 3 out of 5 in the Shiga Toxin Type 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Shiga Toxin Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4003 b:40.7 occ:1.00 O A:HOH4078 2.2 22.4 1.0 OG A:SER19 2.2 22.5 1.0 O A:HOH4217 2.3 41.5 1.0 O A:HOH4153 2.4 29.5 1.0 O A:SER15 2.5 11.9 1.0 OG A:SER15 2.5 15.2 1.0 C A:SER15 3.2 11.0 1.0 CB A:SER19 3.3 19.4 1.0 CB A:SER15 3.6 13.3 1.0 CA A:SER15 3.7 11.2 1.0 O A:HOH4224 3.7 46.8 1.0 O A:HOH4108 3.8 21.1 1.0 N A:SER19 3.9 16.3 1.0 CA A:SER19 4.0 16.7 1.0 N A:SER16 4.1 9.9 1.0 O A:HOH4083 4.3 31.4 1.0 CA A:SER16 4.6 10.6 1.0 O A:HOH4047 4.8 25.4 1.0 C A:ASN18 4.9 15.1 1.0 C1 A:EDO2004 4.9 39.8 1.0 CB A:ASN18 5.0 16.8 1.0

Sodium binding site 4 out of 5 in the Shiga Toxin Type 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Shiga Toxin Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na4005 b:52.3 occ:1.00 O B:THR55 2.3 48.9 1.0 O B:GLY61 2.4 24.8 1.0 OG B:SER60 2.6 38.7 1.0 OG B:SER53 2.6 37.2 1.0 OG1 B:THR55 3.3 49.8 1.0 C B:THR55 3.3 47.7 1.0 CB B:SER60 3.4 34.3 1.0 CB B:SER53 3.5 33.8 1.0 C B:GLY61 3.6 24.8 1.0 N B:GLY61 3.7 27.5 1.0 N B:THR55 4.0 44.8 1.0 CA B:THR55 4.0 47.8 1.0 C B:SER60 4.1 30.8 1.0 O B:HOH4038 4.2 40.3 1.0 CB B:THR55 4.2 48.2 1.0 CA B:GLY61 4.2 26.0 1.0 N B:CYS56 4.3 47.2 1.0 CA B:SER60 4.3 33.3 1.0 CA B:CYS56 4.5 47.1 1.0 N B:PHE62 4.6 18.4 1.0 O B:SER60 4.7 27.4 1.0 CA B:SER53 4.8 32.9 1.0 CA B:PHE62 4.8 16.1 1.0 N B:SER54 4.9 38.7 1.0

Sodium binding site 5 out of 5 in the Shiga Toxin Type 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Shiga Toxin Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na4004 b:30.9 occ:1.00 O F:GLY61 2.2 20.3 1.0 O F:THR55 2.3 32.5 1.0 OG F:SER53 2.4 24.8 1.0 OG F:SER60 2.5 29.1 1.0 CB F:SER53 3.1 21.7 1.0 CB F:SER60 3.3 24.6 1.0 C F:GLY61 3.3 20.1 1.0 C F:THR55 3.4 31.9 1.0 N F:GLY61 3.4 21.6 1.0 CB F:THR55 3.6 34.6 1.0 CA F:THR55 3.9 32.6 1.0 C F:SER60 3.9 23.0 1.0 CA F:GLY61 3.9 21.5 1.0 N F:THR55 4.0 31.6 1.0 O F:HOH4019 4.0 31.0 1.0 CG2 F:THR55 4.2 37.0 1.0 CA F:SER60 4.2 24.1 1.0 N F:PHE62 4.4 18.1 1.0 N F:CYS56 4.5 30.2 1.0 O F:SER60 4.5 21.3 1.0 CA F:SER53 4.6 22.9 1.0 CA F:PHE62 4.7 17.2 1.0 OG1 F:THR55 4.8 37.8 1.0 CD1 F:TYR28 4.8 24.3 1.0 CA F:CYS56 4.9 30.7 1.0 C F:SER53 5.0 25.2 1.0 N F:SER54 5.0 27.1 1.0 CB F:PHE62 5.0 16.3 1.0

M.E.Fraser, M.Fujinaga, M.M.Cherney, A.R.Melton-Celsa, E.M.Twiddy, A.D.O'brien, M.N.G.James. Structure of Shiga Toxin Type 2 (STX2) From Escherichia Coli O157:H7. J.Biol.Chem. V. 279 27511 2004.
ISSN: ISSN 0021-9258
PubMed: 15075327
DOI: 10.1074/JBC.M401939200