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Zinc in PDB 2z8e: The Galacto-N-Biose-/Lacto-N-Biose I-Binding Protein (Gl-Bp) of the Abc Transporter From Bifidobacterium Longum in Complex with Galacto- N-Biose

Protein crystallography data

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 Galacto- N-Biose, PDB code: 2z8e 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) 39.13 / 1.99
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 106.410, 143.403, 115.469, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.6

Zinc Binding Sites:

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 Galacto- N-Biose (pdb code 2z8e). 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 Galacto- N-Biose, PDB code: 2z8e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2z8e

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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 Galacto- 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 Galacto- N-Biose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:27.2
occ:1.00
 OE1 A:GLU329 1.9 27.1 1.0
ND1 A:HIS326 2.0 31.1 1.0
OD2 A:ASP38 2.1 26.2 1.0
CG A:ASP38 2.8 25.2 1.0
CD A:GLU329 2.9 25.4 1.0
OD1 A:ASP38 2.9 19.8 1.0
CE1 A:HIS326 3.0 34.2 1.0
CG A:HIS326 3.1 29.4 1.0
OE2 A:GLU329 3.2 27.9 1.0
CB A:HIS326 3.4 26.8 1.0
CA A:HIS326 3.7 26.6 1.0
O A:HOH769 3.9 42.0 1.0
NE2 A:HIS326 4.1 35.1 1.0
CD2 A:HIS326 4.2 31.2 1.0
CG A:GLU329 4.2 25.1 1.0
CB A:ASP38 4.2 25.3 1.0
CG2 A:VAL42 4.2 27.1 1.0
O A:LYS325 4.2 28.6 1.0
C A:HIS326 4.6 25.3 1.0
N A:HIS326 4.8 27.7 1.0
CB A:GLU329 4.8 22.8 1.0
O A:HIS326 4.9 23.1 1.0
CG1 A:VAL42 4.9 30.1 1.0
C A:LYS325 4.9 29.5 1.0
N A:GLU329 5.0 21.6 1.0

Zinc binding site 2 out of 7 in 2z8e

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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 Galacto- 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 Galacto- N-Biose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:31.4
occ:1.00
 OD1 A:ASP72 2.0 26.3 1.0
O A:HOH528 2.1 22.5 1.0
ND1 A:HIS70 2.2 27.7 1.0
CG A:ASP72 2.8 25.4 1.0
OD2 A:ASP72 2.9 24.1 1.0
CE1 A:HIS70 3.1 28.4 1.0
CG A:HIS70 3.1 26.3 1.0
CB A:HIS70 3.4 24.8 1.0
CA A:HIS70 3.6 24.8 1.0
O A:GLN69 4.0 24.9 1.0
NE2 A:HIS70 4.2 26.2 1.0
CD2 A:HIS70 4.2 25.7 1.0
CB A:ASP72 4.2 24.6 1.0
C A:HIS70 4.4 24.8 1.0
N A:HIS70 4.6 24.6 1.0
C A:GLN69 4.6 25.5 1.0
N A:ASP72 4.7 24.4 1.0
N A:PRO71 4.8 24.4 1.0
CD A:PRO71 4.8 23.8 1.0

Zinc binding site 3 out of 7 in 2z8e

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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 Galacto- 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 Galacto- N-Biose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:30.1
occ:1.00
 OE1 B:GLU329 1.9 29.0 1.0
ND1 B:HIS326 2.0 19.3 1.0
OD1 B:ASP38 2.1 32.9 1.0
CD B:GLU329 2.9 27.2 1.0
CG B:ASP38 2.9 30.6 1.0
CE1 B:HIS326 2.9 27.4 1.0
CG B:HIS326 3.0 24.7 1.0
OD2 B:ASP38 3.1 30.1 1.0
OE2 B:GLU329 3.2 25.4 1.0
CB B:HIS326 3.3 24.1 1.0
CA B:HIS326 3.7 24.8 1.0
O B:HOH646 3.8 30.0 1.0
O B:HOH461 3.8 20.2 1.0
NE2 B:HIS326 4.1 26.2 1.0
CD2 B:HIS326 4.1 24.7 1.0
CG2 B:VAL42 4.1 28.6 1.0
CG B:GLU329 4.2 25.3 1.0
CB B:ASP38 4.2 29.3 1.0
O B:HOH455 4.3 25.0 1.0
O B:LYS325 4.4 27.1 1.0
C B:HIS326 4.6 24.3 1.0
CG1 B:VAL42 4.6 28.5 1.0
CB B:GLU329 4.8 24.1 1.0
N B:HIS326 4.8 25.6 1.0
O B:HIS326 4.9 24.8 1.0
CB B:VAL42 5.0 27.8 1.0
C B:LYS325 5.0 26.6 1.0

Zinc binding site 4 out of 7 in 2z8e

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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 Galacto- 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 Galacto- N-Biose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:32.8
occ:1.00
 ND1 B:HIS70 2.0 20.5 1.0
OD1 B:ASP72 2.0 24.1 1.0
O B:HOH563 2.3 26.3 1.0
CG B:ASP72 2.8 22.8 1.0
CE1 B:HIS70 2.9 23.0 1.0
OD2 B:ASP72 2.9 26.0 1.0
CG B:HIS70 3.0 20.6 1.0
CB B:HIS70 3.4 22.1 1.0
CA B:HIS70 3.7 21.3 1.0
NE2 B:HIS70 4.0 21.7 1.0
O B:GLN69 4.0 23.5 1.0
CD2 B:HIS70 4.1 22.0 1.0
CB B:ASP72 4.2 23.2 1.0
C B:HIS70 4.5 21.9 1.0
N B:ASP72 4.7 22.4 1.0
N B:HIS70 4.7 22.7 1.0
C B:GLN69 4.8 24.2 1.0
N B:PRO71 4.9 22.4 1.0
CA B:ASP72 5.0 22.5 1.0

Zinc binding site 5 out of 7 in 2z8e

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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 Galacto- 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 Galacto- N-Biose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:18.3
occ:0.50
 O B:HOH651 1.3 12.1 0.5
OE2 B:GLU359 2.2 16.4 1.0
OD2 B:ASP357 2.3 29.5 1.0
O B:HOH817 2.4 50.0 1.0
CG B:ASP357 2.8 29.0 1.0
OD1 B:ASP357 3.0 31.3 1.0
CD B:GLU359 3.2 18.8 1.0
ZN B:ZN6 3.4 39.2 1.0
OE1 B:GLU359 3.6 21.8 1.0
O B:HOH730 3.7 34.2 1.0
CB B:ASP357 4.0 24.7 1.0
O B:HOH828 4.3 32.2 1.0
CG B:GLU359 4.5 17.2 1.0
O B:HOH552 4.5 28.7 1.0
O B:HOH809 4.7 31.6 1.0

Zinc binding site 6 out of 7 in 2z8e

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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 Galacto- 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 Galacto- N-Biose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:39.2
occ:1.00
 OD1 B:ASP357 2.2 31.3 1.0
O B:HOH687 2.4 29.9 1.0
OE2 B:GLU359 2.5 16.4 1.0
CG B:ASP357 3.2 29.0 1.0
CD B:GLU359 3.3 18.8 1.0
ZN B:ZN5 3.4 18.3 0.5
CG B:GLU359 3.5 17.2 1.0
OD2 B:ASP357 3.6 29.5 1.0
O B:HOH688 3.8 28.7 1.0
O B:ASP357 3.9 20.9 1.0
O B:HOH651 4.2 12.1 0.5
OE1 B:GLU359 4.4 21.8 1.0
O B:HOH830 4.5 37.8 1.0
C B:ASP357 4.5 21.4 1.0
CB B:ASP357 4.5 24.7 1.0
N B:ASP357 4.5 22.5 1.0
CA B:ASP357 4.7 23.0 1.0

Zinc binding site 7 out of 7 in 2z8e

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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 Galacto- 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 Galacto- N-Biose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn7

b:44.8
occ:1.00
 O A:HOH845 2.2 33.9 1.0
O B:HOH849 2.4 34.7 1.0
O B:HOH827 2.4 28.0 1.0
OD2 A:ASP180 3.8 30.8 1.0
OD2 B:ASP240 3.9 29.5 1.0
O A:HOH631 4.0 31.8 1.0
OD1 B:ASP180 4.1 30.2 1.0
NE2 B:GLN244 4.2 20.8 1.0
OD2 B:ASP180 4.4 30.2 1.0
O A:HOH622 4.5 34.1 1.0
OD1 A:ASP180 4.6 27.7 1.0
CG A:ASP180 4.6 24.3 1.0
O B:HOH449 4.6 24.7 1.0
CG B:ASP180 4.7 28.1 1.0
CG B:ASP240 4.9 23.8 1.0

Reference:

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
Page generated: Thu Oct 24 10:40:30 2024

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