Zinc 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:

Sodium

(Na)

3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 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 Zinc with other atoms in the Zn 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:Zn11 b:22.4 occ:1.00 OE1 A:GLU329 1.9 22.2 1.0 ND1 A:HIS326 2.0 22.7 1.0 OD2 A:ASP38 2.1 20.6 1.0 CD A:GLU329 2.8 19.3 1.0 CG A:ASP38 2.9 22.9 1.0 CE1 A:HIS326 3.0 24.6 1.0 CG A:HIS326 3.0 22.0 1.0 OD1 A:ASP38 3.1 25.0 1.0 OE2 A:GLU329 3.1 21.3 1.0 CB A:HIS326 3.4 21.4 1.0 CA A:HIS326 3.7 21.1 1.0 O A:HOH548 3.7 26.4 1.0 NE2 A:HIS326 4.1 24.1 1.0 CG A:GLU329 4.1 19.9 1.0 CD2 A:HIS326 4.2 23.9 1.0 CG2 A:VAL42 4.2 21.6 1.0 O A:LYS325 4.2 24.3 1.0 CB A:ASP38 4.2 22.5 1.0 O A:HOH474 4.3 21.2 1.0 C A:HIS326 4.5 20.1 1.0 CG1 A:VAL42 4.7 24.4 1.0 CB A:GLU329 4.7 18.1 1.0 N A:HIS326 4.8 22.3 1.0 C A:LYS325 4.9 23.8 1.0 O A:HIS326 4.9 19.6 1.0 N A:GLU329 5.0 18.3 1.0 O A:HOH634 5.0 44.9 1.0

Zinc binding site 2 out of 5 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 Zinc with other atoms in the Zn 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:Zn13 b:23.1 occ:1.00 OD1 A:ASP72 1.9 20.9 1.0 O A:HOH522 2.1 20.8 1.0 ND1 A:HIS70 2.1 22.4 1.0 CG A:ASP72 2.8 19.6 1.0 OD2 A:ASP72 2.9 20.8 1.0 CE1 A:HIS70 3.1 21.2 1.0 CG A:HIS70 3.1 19.9 1.0 CB A:HIS70 3.4 19.9 1.0 CA A:HIS70 3.6 19.1 1.0 O A:GLN69 4.1 21.1 1.0 NE2 A:HIS70 4.2 21.4 1.0 CB A:ASP72 4.2 20.3 1.0 CD2 A:HIS70 4.2 20.5 1.0 C A:HIS70 4.4 20.2 1.0 N A:HIS70 4.6 19.4 1.0 N A:ASP72 4.7 19.9 1.0 C A:GLN69 4.7 20.1 1.0 N A:PRO71 4.9 20.8 1.0 CD A:PRO71 4.9 21.7 1.0 O A:HOH930 5.0 25.8 1.0 CA A:ASP72 5.0 19.2 1.0 O A:HIS70 5.0 19.5 1.0

Zinc binding site 3 out of 5 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 Zinc with other atoms in the Zn 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:Zn12 b:23.9 occ:1.00 OE1 B:GLU329 1.9 24.1 1.0 OD1 B:ASP38 2.0 23.3 1.0 ND1 B:HIS326 2.1 24.3 1.0 CD B:GLU329 2.8 23.2 1.0 CG B:ASP38 2.9 25.0 1.0 CE1 B:HIS326 3.0 27.2 1.0 CG B:HIS326 3.1 23.2 1.0 OD2 B:ASP38 3.1 25.1 1.0 OE2 B:GLU329 3.1 22.5 1.0 CB B:HIS326 3.4 23.2 1.0 CA B:HIS326 3.7 23.1 1.0 O B:HOH1040 3.9 39.5 1.0 CG2 B:VAL42 4.1 23.5 1.0 NE2 B:HIS326 4.1 24.8 1.0 CG B:GLU329 4.2 21.6 1.0 CD2 B:HIS326 4.2 25.3 1.0 CB B:ASP38 4.2 23.9 1.0 O B:LYS325 4.3 24.6 1.0 C B:HIS326 4.6 22.6 1.0 CG1 B:VAL42 4.7 25.5 1.0 CB B:GLU329 4.8 20.9 1.0 N B:HIS326 4.8 23.7 1.0 O B:HIS326 4.9 23.3 1.0 N B:GLU329 4.9 20.2 1.0 C B:LYS325 5.0 24.7 1.0

Zinc binding site 4 out of 5 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 Zinc with other atoms in the Zn binding site number 4 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:Zn14 b:24.9 occ:1.00 ND1 B:HIS70 2.0 20.9 1.0 OD1 B:ASP72 2.1 20.6 1.0 CG B:ASP72 2.8 18.8 1.0 OD2 B:ASP72 2.9 22.3 1.0 CE1 B:HIS70 2.9 21.8 1.0 CG B:HIS70 3.1 21.7 1.0 CB B:HIS70 3.5 21.6 1.0 CA B:HIS70 3.7 21.9 1.0 O B:GLN69 4.0 23.6 1.0 NE2 B:HIS70 4.1 21.3 1.0 O B:HOH1147 4.1 34.5 1.0 CD2 B:HIS70 4.2 22.1 1.0 CB B:ASP72 4.2 21.1 1.0 C B:HIS70 4.5 21.7 1.0 O B:HOH1177 4.6 34.6 1.0 N B:HIS70 4.7 22.4 1.0 N B:ASP72 4.7 22.0 1.0 C B:GLN69 4.7 22.9 1.0 N B:PRO71 4.9 22.2 1.0 CD B:PRO71 5.0 22.4 1.0

Zinc binding site 5 out of 5 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 Zinc with other atoms in the Zn binding site number 5 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:Zn15 b:17.3 occ:0.50 O B:HOH1059 2.0 41.5 1.0 OE2 B:GLU359 2.1 17.8 1.0 O B:HOH1209 2.1 40.9 1.0 OD2 B:ASP357 2.6 36.2 1.0 CD B:GLU359 3.0 21.9 1.0 CG B:ASP357 3.0 28.7 1.0 OD1 B:ASP357 3.1 30.8 1.0 NA B:NA16 3.3 15.5 1.0 OE1 B:GLU359 3.3 24.1 1.0 O B:HOH1094 4.0 32.9 1.0 CB B:ASP357 4.1 27.1 1.0 O B:HOH962 4.2 21.2 1.0 O B:HOH1325 4.2 23.8 1.0 CG B:GLU359 4.3 21.0 1.0 O B:HOH1326 4.8 35.8 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