Atomistry » Zinc » PDB 2z57-2zep » 2z8e
Atomistry »
  Zinc »
    PDB 2z57-2zep »
      2z8e »

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

Go back to Zinc Binding Sites List in 2z8e
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

Go back to Zinc Binding Sites List in 2z8e
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

Go back to Zinc Binding Sites List in 2z8e
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

Go back to Zinc Binding Sites List in 2z8e
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

Go back to Zinc Binding Sites List in 2z8e
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

Go back to Zinc Binding Sites List in 2z8e
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

Go back to Zinc Binding Sites List in 2z8e
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: Wed Aug 20 07:23:50 2025

Last articles

Zn in 3RAM
Zn in 3RDR
Zn in 3RCM
Zn in 3RC6
Zn in 3RC5
Zn in 3RBU
Zn in 3RC4
Zn in 3RAY
Zn in 3R3Q
Zn in 3R68
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy