Zinc in PDB 2z8d: The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Lacto-N- Biose

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- Biose, PDB code: 2z8d 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)	29.75 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	106.326, 143.551, 114.644, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.8

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- Biose (pdb code 2z8d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 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- Biose, PDB code: 2z8d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 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- Biose


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- Biose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:23.6 occ:1.00 OE1 A:GLU329 2.0 26.3 1.0 OD2 A:ASP38 2.0 21.3 1.0 ND1 A:HIS326 2.1 27.3 1.0 CG A:ASP38 2.8 22.3 1.0 CD A:GLU329 2.9 20.6 1.0 OD1 A:ASP38 3.0 23.2 1.0 CG A:HIS326 3.1 21.9 1.0 CE1 A:HIS326 3.1 26.3 1.0 OE2 A:GLU329 3.3 19.0 1.0 CB A:HIS326 3.3 22.0 1.0 CA A:HIS326 3.7 20.9 1.0 O A:HOH805 3.8 35.4 1.0 CB A:ASP38 4.2 22.1 1.0 CG A:GLU329 4.2 17.5 1.0 O A:LYS325 4.2 24.1 1.0 CG2 A:VAL42 4.2 22.6 1.0 CD2 A:HIS326 4.2 26.1 1.0 NE2 A:HIS326 4.2 28.5 1.0 C A:HIS326 4.5 20.0 1.0 N A:HIS326 4.7 22.8 1.0 CB A:GLU329 4.8 16.3 1.0 CG1 A:VAL42 4.8 25.2 1.0 O A:HIS326 4.8 19.1 1.0 C A:LYS325 4.9 24.6 1.0 N A:GLU329 5.0 16.9 1.0

Zinc binding site 2 out of 7 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- Biose


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- Biose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:24.4 occ:1.00 O A:HOH531 1.9 24.6 1.0 OD1 A:ASP72 1.9 22.0 1.0 ND1 A:HIS70 2.2 25.7 1.0 CG A:ASP72 2.8 21.6 1.0 OD2 A:ASP72 3.1 24.5 1.0 CG A:HIS70 3.1 22.2 1.0 CE1 A:HIS70 3.2 26.3 1.0 CB A:HIS70 3.4 20.8 1.0 CA A:HIS70 3.6 20.4 1.0 O A:GLN69 4.1 18.9 1.0 CB A:ASP72 4.2 20.8 1.0 CD2 A:HIS70 4.3 24.7 1.0 NE2 A:HIS70 4.3 23.8 1.0 C A:HIS70 4.4 19.5 1.0 N A:HIS70 4.6 19.5 1.0 N A:ASP72 4.6 20.8 1.0 C A:GLN69 4.7 19.9 1.0 N A:PRO71 4.8 20.2 1.0 CD A:PRO71 4.8 19.9 1.0 O A:HOH578 4.9 24.1 1.0 CA A:ASP72 4.9 20.1 1.0

Zinc binding site 3 out of 7 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- Biose


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- Biose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:25.1 occ:1.00 OE1 B:GLU329 1.9 26.9 1.0 OD1 B:ASP38 2.0 25.6 1.0 ND1 B:HIS326 2.1 21.1 1.0 CD B:GLU329 2.8 23.7 1.0 CG B:ASP38 2.9 24.1 1.0 OE2 B:GLU329 3.1 24.7 1.0 CG B:HIS326 3.1 24.5 1.0 OD2 B:ASP38 3.1 23.2 1.0 CE1 B:HIS326 3.1 27.7 1.0 CB B:HIS326 3.4 22.5 1.0 O B:HOH655 3.7 34.1 1.0 CA B:HIS326 3.8 22.8 1.0 O B:HOH460 4.0 24.9 1.0 CG2 B:VAL42 4.1 23.5 1.0 CG B:GLU329 4.2 20.1 1.0 CB B:ASP38 4.2 24.1 1.0 NE2 B:HIS326 4.2 24.8 1.0 CD2 B:HIS326 4.2 25.9 1.0 O B:HOH454 4.3 21.2 1.0 O B:LYS325 4.4 25.2 1.0 CG1 B:VAL42 4.5 25.3 1.0 C B:HIS326 4.6 21.2 1.0 CB B:GLU329 4.8 18.6 1.0 N B:HIS326 4.9 23.4 1.0 O B:HIS326 4.9 20.6 1.0 CB B:VAL42 4.9 23.6 1.0 N B:GLU329 5.0 17.3 1.0

Zinc binding site 4 out of 7 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- Biose


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- Biose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:24.4 occ:1.00 ND1 B:HIS70 2.0 15.0 1.0 O B:HOH566 2.1 20.0 1.0 OD1 B:ASP72 2.2 15.5 1.0 O B:HOH707 2.3 32.6 1.0 CG B:ASP72 2.8 20.8 1.0 CE1 B:HIS70 2.9 18.6 1.0 OD2 B:ASP72 3.0 24.8 1.0 CG B:HIS70 3.1 17.5 1.0 CB B:HIS70 3.5 18.0 1.0 CA B:HIS70 3.7 19.1 1.0 NE2 B:HIS70 4.0 18.7 1.0 O B:GLN69 4.1 23.2 1.0 CD2 B:HIS70 4.2 18.7 1.0 CB B:ASP72 4.2 20.4 1.0 C B:HIS70 4.5 20.3 1.0 N B:ASP72 4.7 20.2 1.0 N B:HIS70 4.7 21.6 1.0 C B:GLN69 4.8 22.9 1.0 N B:PRO71 5.0 20.6 1.0 CD B:PRO71 5.0 20.3 1.0

Zinc binding site 5 out of 7 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- Biose


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- Biose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn5 b:17.5 occ:0.50 O B:HOH865 1.6 26.4 1.0 O B:HOH662 1.8 7.0 0.5 OE2 B:GLU359 2.3 10.6 1.0 OD2 B:ASP357 2.3 29.8 1.0 CG B:ASP357 3.0 28.2 1.0 CD B:GLU359 3.1 19.7 1.0 OE1 B:GLU359 3.3 18.8 1.0 OD1 B:ASP357 3.3 23.7 1.0 ZN B:ZN6 3.4 32.2 1.0 O B:HOH753 3.8 23.4 1.0 CB B:ASP357 4.0 26.8 1.0 O B:HOH554 4.4 20.4 1.0 CG B:GLU359 4.5 18.9 1.0 O B:HOH879 4.5 27.2 1.0 O B:HOH856 4.9 28.5 1.0

Zinc binding site 6 out of 7 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- Biose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 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- Biose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn6 b:32.2 occ:1.00 OD1 B:ASP357 2.0 23.7 1.0 OE2 B:GLU359 2.2 10.6 1.0 O B:HOH708 2.4 26.5 1.0 CG B:ASP357 3.0 28.2 1.0 CD B:GLU359 3.2 19.7 1.0 OD2 B:ASP357 3.3 29.8 1.0 ZN B:ZN5 3.4 17.5 0.5 CG B:GLU359 3.5 18.9 1.0 O B:HOH709 3.6 30.9 1.0 O B:ASP357 3.9 21.7 1.0 CB B:ASP357 4.3 26.8 1.0 OE1 B:GLU359 4.3 18.8 1.0 O B:HOH865 4.4 26.4 1.0 N B:ASP357 4.4 24.7 1.0 C B:ASP357 4.5 23.4 1.0 O B:HOH880 4.5 35.3 1.0 CA B:ASP357 4.6 24.8 1.0 O B:HOH662 4.9 7.0 0.5

Zinc binding site 7 out of 7 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- Biose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 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- Biose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn7 b:49.1 occ:1.00 O A:HOH894 2.2 31.5 1.0 O B:HOH878 2.3 32.3 1.0 O A:HOH901 2.3 29.8 1.0 O B:HOH893 2.7 42.2 1.0 O B:HOH904 3.0 44.0 1.0 OD2 A:ASP180 3.8 32.2 1.0 OD2 B:ASP240 3.9 34.4 1.0 OD1 B:ASP180 4.1 30.7 1.0 NE2 B:GLN244 4.3 26.5 1.0 OD2 B:ASP180 4.3 30.4 1.0 OD1 A:ASP180 4.5 29.0 1.0 CG A:ASP180 4.5 27.2 1.0 O B:HOH633 4.6 39.3 1.0 O B:HOH448 4.6 33.3 1.0 CG B:ASP180 4.7 28.7 1.0 CG B:ASP240 4.9 28.4 1.0 O B:HOH673 4.9 41.5 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