Sodium in PDB 2z8f: The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose

The structure of The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose, PDB code: 2z8f was solved by R.Suzuki, J.Wada, T.Katayama, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.27 / 1.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	106.151, 143.050, 113.736, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.4

The structure of The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Sodium atom in the The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose (pdb code 2z8f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose, PDB code: 2z8f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na17 b:14.6 occ:1.00 O A:HOH916 2.1 42.0 1.0 O A:HOH915 2.1 29.4 1.0 O A:HOH914 2.1 24.9 1.0 O A:HOH913 2.2 32.6 1.0 OD2 A:ASP224 2.2 30.0 1.0 O A:HOH912 2.4 30.8 1.0 CG A:ASP224 3.2 28.6 1.0 OD1 A:ASP224 3.4 29.9 1.0 OG A:SER225 4.1 25.4 1.0 O A:LYS222 4.2 25.4 1.0 CB A:SER225 4.4 23.9 1.0 CB A:ASP224 4.6 26.3 1.0 N A:ASP224 4.8 25.1 1.0 N A:SER225 4.9 25.2 1.0

Sodium binding site 2 out of 3 in the The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na18 b:14.1 occ:1.00 O A:HOH910 1.8 32.7 1.0 O A:HOH911 1.9 34.4 1.0 OD2 A:ASP420 2.2 18.1 1.0 OD1 A:ASP420 2.4 17.7 1.0 CG A:ASP420 2.6 18.4 1.0 O A:HOH895 3.0 32.8 1.0 O A:HOH800 4.1 30.9 1.0 O A:HOH905 4.1 43.4 1.0 CB A:ASP420 4.1 14.7 1.0 CG2 A:THR403 4.3 17.8 1.0 OG1 A:THR403 4.3 19.0 1.0 CB A:ASP416 4.4 18.4 1.0 O A:ASP416 4.5 17.1 1.0 O A:HOH562 4.6 29.1 1.0 CB A:THR403 5.0 17.3 1.0 CG A:ASP416 5.0 24.0 1.0

Sodium binding site 3 out of 3 in the The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Tetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na16 b:15.5 occ:1.00 O B:HOH1325 1.6 23.8 1.0 OD1 B:ASP357 1.8 30.8 1.0 O B:HOH1326 2.1 35.8 1.0 O B:HOH1324 2.2 33.8 1.0 OE2 B:GLU359 2.3 17.8 1.0 CG B:ASP357 2.9 28.7 1.0 ZN B:ZN15 3.3 17.3 0.5 CD B:GLU359 3.3 21.9 1.0 OD2 B:ASP357 3.3 36.2 1.0 CG B:GLU359 3.6 21.0 1.0 O B:HOH1327 3.8 35.6 1.0 O B:ASP357 3.9 22.6 1.0 CB B:ASP357 4.2 27.1 1.0 N B:ASP357 4.2 24.7 1.0 C B:ASP357 4.4 23.3 1.0 O B:HOH1059 4.4 41.5 1.0 OE1 B:GLU359 4.4 24.1 1.0 CA B:ASP357 4.4 24.7 1.0 O B:HOH1319 4.5 37.7 1.0 O B:HOH1209 5.0 40.9 1.0

R.Suzuki, J.Wada, T.Katayama, S.Fushinobu, T.Wakagi, H.Shoun, H.Sugimoto, A.Tanaka, H.Kumagai, H.Ashida, M.Kitaoka, K.Yamamoto. Structural and Thermodynamic Analyses of Solute-Binding Protein From Bifidobacterium Longum Specific For Core 1 Disaccharide and Lacto-N-Biose I. J.Biol.Chem. V. 283 13165 2008.
ISSN: ISSN 0021-9258
PubMed: 18332142
DOI: 10.1074/JBC.M709777200