Sodium in PDB 2r5o: Crystal Structure of the C-Terminal Domain of Wzt

The structure of Crystal Structure of the C-Terminal Domain of Wzt, PDB code: 2r5o was solved by M.S.Kimber, L.Cuthbertson, C.Whitfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.30
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.081, 106.081, 70.351, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.2

The structure of Crystal Structure of the C-Terminal Domain of Wzt also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of the C-Terminal Domain of Wzt (pdb code 2r5o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the C-Terminal Domain of Wzt, PDB code: 2r5o:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the C-Terminal Domain of Wzt


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 the C-Terminal Domain of Wzt within 5.0Å range: probe atom residue distance (Å) B Occ A:Na11 b:21.1 occ:1.00 OH A:TYR284 2.5 19.2 1.0 CZ A:TYR284 3.4 15.9 1.0 CE1 A:TYR284 3.4 14.8 1.0 CB A:TRP286 3.9 12.6 1.0 O A:HOH491 4.5 21.9 1.0 CE2 A:TYR284 4.6 18.0 1.0 CD1 A:TYR284 4.7 14.8 1.0 CA A:TRP286 4.8 12.6 1.0 O A:ARG285 4.9 12.8 1.0 CG A:TRP286 5.0 13.4 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the C-Terminal Domain of Wzt


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 the C-Terminal Domain of Wzt within 5.0Å range: probe atom residue distance (Å) B Occ A:Na13 b:17.6 occ:1.00 OH A:TYR345 2.7 14.1 1.0 OD1 B:ASP422 2.7 14.6 1.0 O B:HOH447 2.7 14.2 1.0 O A:HOH434 2.7 12.0 1.0 O B:HOH591 3.3 23.0 1.0 CZ A:TYR345 3.5 14.2 1.0 CE1 A:TYR345 3.6 14.0 1.0 CA B:LYS424 3.7 13.4 1.0 N B:LYS424 3.7 12.3 1.0 CG B:ASP422 3.7 15.0 1.0 N B:SER425 3.9 12.3 1.0 CB B:PHE417 4.0 13.6 1.0 OD2 B:ASP422 4.1 14.9 1.0 C B:LYS424 4.2 13.2 1.0 OG1 A:THR347 4.4 14.7 1.0 O B:ASP416 4.5 15.5 1.0 O B:HOH548 4.6 28.6 1.0 CB A:THR347 4.7 15.2 1.0 O B:SER425 4.7 13.5 1.0 CA A:ALA352 4.8 15.4 1.0 CE2 A:TYR345 4.9 14.3 1.0 CD1 A:TYR345 4.9 14.5 1.0 C B:LEU423 4.9 13.6 1.0 CG B:PHE417 4.9 13.6 1.0 CB B:LYS424 4.9 14.4 1.0 CB B:ASP422 5.0 14.2 1.0 N B:LEU423 5.0 13.2 1.0 CA B:SER425 5.0 12.7 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the C-Terminal Domain of Wzt


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 the C-Terminal Domain of Wzt within 5.0Å range: probe atom residue distance (Å) B Occ B:Na9 b:18.6 occ:1.00 OG B:SER385 2.7 14.3 1.0 OD1 B:ASP405 2.8 16.1 1.0 O B:LEU383 2.9 14.4 1.0 O B:LEU335 3.3 14.9 1.0 C B:LEU383 3.5 13.8 1.0 N B:SER385 3.5 12.8 1.0 CG B:LYS337 3.5 17.1 0.7 CD B:LYS337 3.6 18.1 0.3 CB B:SER385 3.6 14.2 1.0 C B:LEU384 3.6 13.4 1.0 CG B:LYS337 3.7 17.5 0.3 CD B:LYS337 3.8 19.0 0.7 CE B:LYS337 3.8 20.0 0.7 CA B:LEU384 3.9 13.7 1.0 N B:LEU384 3.9 13.5 1.0 C B:LEU335 3.9 14.4 1.0 CG B:LEU335 3.9 14.9 0.7 N B:LYS337 3.9 15.4 1.0 CG B:ASP405 4.0 16.1 1.0 CB B:LYS337 4.0 16.8 0.3 CB B:LEU383 4.0 14.4 1.0 CD2 B:LEU335 4.0 16.8 0.7 CB B:LYS337 4.0 17.1 0.7 N B:ASP405 4.1 15.1 1.0 CA B:SER385 4.1 13.2 1.0 CB B:LEU335 4.2 15.1 0.3 O B:LEU384 4.2 14.1 1.0 CB B:LEU335 4.2 15.1 0.7 CA B:ASP405 4.3 15.0 1.0 CA B:ILE336 4.3 15.0 1.0 N B:ILE336 4.4 15.1 1.0 C B:ILE336 4.4 14.8 1.0 CA B:LEU383 4.4 14.2 1.0 CA B:LYS337 4.6 16.3 1.0 CE1 B:TYR404 4.7 19.0 0.3 CA B:LEU335 4.7 14.9 1.0 CD1 B:TYR404 4.7 17.7 0.3 CB B:ASP405 4.7 15.5 1.0 NZ B:LYS337 4.8 21.0 0.7 OD2 B:ASP405 4.9 19.1 1.0 CE B:LYS337 4.9 20.3 0.3 CD1 B:LEU335 4.9 17.7 0.3

Sodium binding site 4 out of 5 in the Crystal Structure of the C-Terminal Domain of Wzt


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 the C-Terminal Domain of Wzt within 5.0Å range: probe atom residue distance (Å) B Occ B:Na10 b:23.1 occ:1.00 OH B:TYR284 2.5 21.9 1.0 O B:HOH446 2.6 14.0 1.0 CZ B:TYR284 3.3 20.0 1.0 CE1 B:TYR284 3.4 18.2 1.0 CB B:TRP286 3.8 15.0 1.0 CE2 B:TYR284 4.6 21.2 1.0 O B:ARG285 4.7 14.0 1.0 CD1 B:TYR284 4.8 16.3 1.0 CG B:TRP286 4.8 16.4 1.0 CA B:TRP286 4.8 13.8 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the C-Terminal Domain of Wzt


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 the C-Terminal Domain of Wzt within 5.0Å range: probe atom residue distance (Å) B Occ B:Na12 b:23.1 occ:1.00 OH B:TYR345 2.6 15.3 1.0 OD1 A:ASP422 2.7 14.2 1.0 O B:HOH599 2.7 25.4 1.0 O A:HOH551 2.9 22.3 1.0 O A:HOH585 3.0 56.4 1.0 CE1 B:TYR345 3.4 14.6 1.0 CZ B:TYR345 3.4 15.1 1.0 CG A:ASP422 3.7 15.4 1.0 CA A:LYS424 3.7 12.3 1.0 N A:LYS424 3.8 11.8 1.0 OD2 A:ASP422 3.9 18.4 1.0 N A:SER425 4.0 12.1 1.0 CD2 A:PHE417 4.2 22.0 0.3 C A:LYS424 4.3 13.2 1.0 OG1 B:THR347 4.4 17.8 1.0 CB B:THR347 4.6 16.4 1.0 CE2 A:PHE417 4.6 21.8 0.3 CD1 B:TYR345 4.7 14.7 1.0 O A:SER425 4.8 13.4 1.0 CE2 B:TYR345 4.8 15.6 1.0 CG A:PHE417 4.8 20.8 0.3 CD2 A:PHE417 4.9 13.3 0.7 CB A:LYS424 5.0 13.4 1.0 CB A:ASP422 5.0 15.2 1.0

L.Cuthbertson, M.S.Kimber, C.Whitfield. Substrate Binding By A Bacterial Abc Transporter Involved in Polysaccharide Export. Proc.Natl.Acad.Sci.Usa V. 104 19529 2007.
ISSN: ISSN 0027-8424
PubMed: 18032609
DOI: 10.1073/PNAS.0705709104