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Zinc in PDB 2xig: The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites

Protein crystallography data

The structure of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites, PDB code: 2xig was solved by C.Dian, S.Vitale, G.A.Leonard, F.Fauquant, C.Muller, C.Bahlawane, H.De Reuse, I.Michaud-Soret, L.Terradot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.097 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.150, 48.290, 72.250, 83.32, 77.82, 87.65
R / Rfree (%) 19.81 / 23.39

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites (pdb code 2xig). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites, PDB code: 2xig:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 2xig

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Zinc binding site 1 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1149

b:24.2
occ:1.00
NE2 A:HIS96 2.1 25.2 1.0
OD2 A:ASP98 2.1 22.4 1.0
NE2 A:HIS134 2.1 24.0 1.0
OE2 A:GLU117 2.1 23.6 1.0
OD1 A:ASP98 2.6 21.7 1.0
CG A:ASP98 2.7 24.4 1.0
CD A:GLU117 2.9 27.9 1.0
CE1 A:HIS96 3.0 27.2 1.0
OE1 A:GLU117 3.1 24.6 1.0
CE1 A:HIS134 3.1 22.3 1.0
CD2 A:HIS134 3.2 20.7 1.0
CD2 A:HIS96 3.2 27.1 1.0
O A:HOH2073 3.6 30.1 1.0
ND1 A:HIS96 4.1 24.5 1.0
CB A:ASP98 4.2 18.0 1.0
ND1 A:HIS134 4.2 20.4 1.0
CG A:HIS96 4.3 28.2 1.0
CG A:HIS134 4.3 20.1 1.0
CG A:GLU117 4.4 24.2 1.0
OE1 A:GLN120 4.5 35.8 1.0
NE2 A:GLN120 4.6 33.0 1.0
N A:ASP98 4.7 21.4 1.0
C A:HIS97 4.9 21.9 1.0
O A:HOH2064 4.9 23.1 1.0
CA A:ASP98 5.0 19.5 1.0
CD A:GLN120 5.0 32.0 1.0

Zinc binding site 2 out of 12 in 2xig

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Zinc binding site 2 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1150

b:26.9
occ:1.00
NE2 A:HIS42 2.1 24.6 1.0
NE2 A:HIS97 2.2 18.3 1.0
NE2 A:HIS99 2.2 24.3 1.0
OE1 A:GLU90 2.3 28.3 1.0
OE2 A:GLU90 2.5 28.2 1.0
OE2 A:GLU110 2.6 40.4 1.0
CD A:GLU90 2.7 29.4 1.0
CD2 A:HIS42 2.9 22.7 1.0
CD2 A:HIS99 3.1 23.0 1.0
CE1 A:HIS97 3.1 21.6 1.0
CD2 A:HIS97 3.2 21.6 1.0
CE1 A:HIS99 3.2 19.9 1.0
CE1 A:HIS42 3.3 24.1 1.0
CD A:GLU110 3.6 32.8 1.0
CG A:GLU110 4.0 22.8 1.0
CG A:GLU90 4.1 25.5 1.0
CG A:HIS42 4.2 23.2 1.0
ND1 A:HIS97 4.2 20.2 1.0
CG A:HIS99 4.3 19.3 1.0
ND1 A:HIS42 4.3 24.2 1.0
ND1 A:HIS99 4.3 22.0 1.0
CG A:HIS97 4.3 20.2 1.0
NZ A:LYS94 4.6 45.1 1.0
OE1 A:GLU110 4.7 34.5 1.0
CB A:GLU90 4.8 19.5 1.0
CE A:LYS94 4.9 44.3 1.0
O A:HOH2062 5.0 46.1 1.0

Zinc binding site 3 out of 12 in 2xig

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Zinc binding site 3 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1151

b:30.7
occ:1.00
SG A:CYS105 2.3 29.6 1.0
SG A:CYS145 2.3 26.9 1.0
SG A:CYS142 2.4 30.7 1.0
SG A:CYS102 2.4 24.3 1.0
CB A:CYS102 3.2 20.6 1.0
CB A:CYS145 3.3 25.4 1.0
CB A:CYS105 3.3 26.3 1.0
CB A:CYS142 3.4 30.3 1.0
N A:CYS105 3.8 38.6 1.0
N A:CYS142 4.0 25.1 1.0
CA A:CYS105 4.1 33.2 1.0
N A:CYS145 4.2 35.1 1.0
CA A:CYS142 4.2 27.8 1.0
CA A:CYS145 4.3 32.5 1.0
O A:HOH2094 4.4 44.2 1.0
CA A:CYS102 4.7 17.1 1.0
CB A:HIS104 4.7 29.1 1.0
CB A:LYS107 4.8 32.5 1.0
O A:CYS142 4.8 33.2 1.0
C A:CYS142 4.8 31.0 1.0
C A:HIS104 4.8 35.9 1.0
C A:CYS105 4.9 33.4 1.0
N A:GLY106 4.9 30.8 1.0
CE A:LYS107 4.9 39.2 1.0
CD A:LYS107 4.9 38.0 1.0

Zinc binding site 4 out of 12 in 2xig

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Zinc binding site 4 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1150

b:26.0
occ:1.00
NE2 B:HIS42 2.1 27.9 1.0
NE2 B:HIS97 2.1 28.5 1.0
OE2 B:GLU90 2.1 29.9 1.0
NE2 B:HIS99 2.2 25.5 1.0
OE1 B:GLU90 2.4 24.9 1.0
CD B:GLU90 2.6 27.4 1.0
CD2 B:HIS42 3.0 24.1 1.0
CD2 B:HIS99 3.0 26.4 1.0
CD2 B:HIS97 3.0 26.2 1.0
CE1 B:HIS97 3.1 28.8 1.0
CE1 B:HIS42 3.2 30.8 1.0
CE1 B:HIS99 3.3 27.8 1.0
CG B:GLU90 4.1 23.2 1.0
ND1 B:HIS97 4.2 26.1 1.0
CG B:HIS42 4.2 27.4 1.0
CG B:HIS97 4.2 25.9 1.0
ND1 B:HIS42 4.2 29.1 1.0
CG B:HIS99 4.2 24.4 1.0
OE2 B:GLU110 4.2 31.6 1.0
O B:HOH2025 4.3 34.9 1.0
ND1 B:HIS99 4.3 24.7 1.0
CG B:GLU110 4.4 34.6 1.0
CD B:GLU110 4.5 35.6 1.0
NZ B:LYS94 4.6 32.2 1.0
CB B:GLU90 4.8 19.5 1.0
O B:HOH2030 4.9 59.3 1.0

Zinc binding site 5 out of 12 in 2xig

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Zinc binding site 5 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1151

b:26.3
occ:1.00
NE2 B:HIS96 2.1 36.5 1.0
OE1 B:GLU117 2.1 23.8 1.0
NE2 B:HIS134 2.1 20.8 1.0
OD1 B:ASP98 2.2 23.2 1.0
OD2 B:ASP98 2.7 20.5 1.0
CG B:ASP98 2.7 23.4 1.0
CD B:GLU117 2.9 31.2 1.0
CE1 B:HIS96 2.9 32.5 1.0
CE1 B:HIS134 3.0 27.8 1.0
OE2 B:GLU117 3.1 29.6 1.0
CD2 B:HIS134 3.2 21.8 1.0
CD2 B:HIS96 3.2 32.3 1.0
O B:HOH2032 3.9 27.9 1.0
ND1 B:HIS96 4.1 25.4 1.0
ND1 B:HIS134 4.1 23.9 1.0
CB B:ASP98 4.2 21.9 1.0
CG B:HIS96 4.3 31.0 1.0
CG B:HIS134 4.3 22.9 1.0
CG B:GLU117 4.4 30.7 1.0
OE1 B:GLN120 4.4 35.6 1.0
N B:ASP98 4.6 20.9 1.0
C B:HIS97 4.8 22.2 1.0
CA B:ASP98 4.9 23.4 1.0
O B:HOH2033 4.9 23.8 1.0

Zinc binding site 6 out of 12 in 2xig

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Zinc binding site 6 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1152

b:35.6
occ:1.00
SG B:CYS142 2.2 29.4 1.0
SG B:CYS102 2.3 33.7 1.0
SG B:CYS145 2.4 39.0 1.0
SG B:CYS105 2.4 39.1 1.0
CB B:CYS145 3.2 53.3 1.0
CB B:CYS105 3.3 39.1 1.0
CB B:CYS102 3.3 21.2 1.0
CB B:CYS142 3.5 43.1 1.0
N B:CYS105 3.6 42.2 1.0
CA B:CYS105 4.0 40.9 1.0
N B:CYS142 4.1 33.0 1.0
CB B:HIS104 4.2 49.4 1.0
N B:CYS145 4.3 55.7 1.0
CA B:CYS145 4.3 53.3 1.0
CA B:CYS142 4.4 40.3 1.0
CE B:LYS107 4.5 40.2 1.0
C B:HIS104 4.7 49.0 1.0
CB B:LYS107 4.7 37.0 1.0
CA B:CYS102 4.7 25.6 1.0
N B:GLY106 4.7 35.5 1.0
C B:CYS105 4.8 42.6 1.0
CA B:HIS104 4.8 45.0 1.0
N B:HIS104 4.9 37.4 1.0
O B:CYS142 4.9 35.9 1.0
C B:CYS142 5.0 43.4 1.0
N B:LYS107 5.0 35.4 1.0

Zinc binding site 7 out of 12 in 2xig

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Zinc binding site 7 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1151

b:21.0
occ:1.00
OE2 C:GLU90 2.0 22.8 1.0
NE2 C:HIS97 2.1 15.8 1.0
NE2 C:HIS99 2.1 18.2 1.0
NE2 C:HIS42 2.2 16.8 1.0
OE1 C:GLU90 2.6 16.2 1.0
CD C:GLU90 2.6 23.0 1.0
CD2 C:HIS97 3.0 12.1 1.0
CD2 C:HIS99 3.1 15.4 1.0
CD2 C:HIS42 3.1 13.6 1.0
CE1 C:HIS99 3.1 19.4 1.0
CE1 C:HIS97 3.1 17.9 1.0
CE1 C:HIS42 3.2 18.1 1.0
O C:HOH2088 3.8 41.4 1.0
OE2 C:GLU110 3.9 31.5 1.0
CG C:GLU90 4.0 21.3 1.0
CG C:GLU110 4.1 21.6 1.0
CG C:HIS97 4.2 11.9 1.0
ND1 C:HIS99 4.2 20.7 1.0
CD C:GLU110 4.2 27.1 1.0
CG C:HIS99 4.2 19.0 1.0
ND1 C:HIS97 4.2 16.6 1.0
CG C:HIS42 4.3 20.1 1.0
O C:HOH2089 4.3 31.6 1.0
ND1 C:HIS42 4.3 20.8 1.0
NZ C:LYS94 4.4 22.0 1.0
CB C:GLU90 4.8 17.2 1.0

Zinc binding site 8 out of 12 in 2xig

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Zinc binding site 8 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1152

b:23.3
occ:1.00
SG C:CYS105 2.3 24.0 1.0
SG C:CYS102 2.4 19.4 1.0
SG C:CYS145 2.4 24.8 1.0
SG C:CYS142 2.4 23.5 1.0
CB C:CYS105 3.2 23.4 1.0
CB C:CYS102 3.2 17.2 1.0
CB C:CYS145 3.3 13.9 1.0
CB C:CYS142 3.5 24.8 1.0
N C:CYS105 3.7 28.9 1.0
CA C:CYS105 4.0 24.5 1.0
N C:CYS142 4.0 15.0 1.0
N C:CYS145 4.1 21.1 1.0
CA C:CYS142 4.3 23.1 1.0
CA C:CYS145 4.3 26.1 1.0
CB C:HIS104 4.6 22.0 1.0
CA C:CYS102 4.7 17.5 1.0
C C:HIS104 4.7 30.4 1.0
C C:CYS105 4.7 26.0 1.0
CB C:LYS107 4.8 26.3 1.0
C C:CYS142 4.8 26.1 1.0
CE C:LYS107 4.9 39.3 1.0
O C:CYS142 4.9 20.8 1.0
NZ C:LYS107 4.9 39.3 1.0
N C:GLY106 4.9 25.4 1.0
N C:HIS104 5.0 23.8 1.0

Zinc binding site 9 out of 12 in 2xig

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Zinc binding site 9 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1153

b:20.8
occ:1.00
OE2 C:GLU117 2.0 23.8 1.0
NE2 C:HIS134 2.0 16.2 1.0
OD2 C:ASP98 2.1 19.6 1.0
NE2 C:HIS96 2.1 23.5 1.0
OD1 C:ASP98 2.5 17.8 1.0
CG C:ASP98 2.7 15.4 1.0
CE1 C:HIS134 2.9 18.9 1.0
CD C:GLU117 2.9 22.8 1.0
CE1 C:HIS96 3.1 17.1 1.0
CD2 C:HIS134 3.1 19.9 1.0
OE1 C:GLU117 3.1 24.7 1.0
CD2 C:HIS96 3.2 20.6 1.0
O C:HOH2097 3.9 27.8 1.0
ND1 C:HIS134 4.1 20.4 1.0
CB C:ASP98 4.2 13.1 1.0
CG C:HIS134 4.2 19.7 1.0
ND1 C:HIS96 4.2 18.2 1.0
CG C:HIS96 4.3 22.7 1.0
CG C:GLU117 4.3 23.8 1.0
N C:ASP98 4.7 12.4 1.0
OE1 C:GLN120 4.8 34.1 1.0
C C:HIS97 4.8 12.9 1.0
CA C:ASP98 4.9 14.6 1.0
O C:HOH2098 5.0 19.4 1.0

Zinc binding site 10 out of 12 in 2xig

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Zinc binding site 10 out of 12 in the The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1149

b:39.6
occ:1.00
SG D:CYS105 2.3 40.2 1.0
SG D:CYS142 2.4 37.8 1.0
SG D:CYS145 2.4 40.1 1.0
SG D:CYS102 2.4 36.9 1.0
CB D:CYS105 3.2 40.3 1.0
CB D:CYS102 3.3 41.2 1.0
CB D:CYS145 3.4 43.3 1.0
CB D:CYS142 3.4 26.8 1.0
N D:CYS105 3.7 35.5 1.0
N D:CYS142 4.0 30.5 1.0
CA D:CYS105 4.0 38.5 1.0
CA D:CYS142 4.3 31.5 1.0
N D:CYS145 4.3 57.5 1.0
CA D:CYS145 4.4 50.8 1.0
O D:HOH2090 4.5 67.1 1.0
CE D:LYS107 4.7 44.3 1.0
C D:HIS104 4.7 45.6 1.0
CB D:HIS104 4.7 61.3 1.0
CB D:LYS107 4.7 27.9 1.0
CA D:CYS102 4.7 32.4 1.0
NZ D:LYS107 4.8 45.9 1.0
C D:CYS142 4.9 36.0 1.0
O D:CYS142 4.9 36.9 1.0
C D:CYS105 4.9 34.3 1.0
N D:GLY106 4.9 36.2 1.0

Reference:

C.Dian, S.Vitale, G.A.Leonard, C.Bahlawane, C.Fauquant, D.Leduc, C.Muller, H.De Reuse, I.Michaud-Soret, L.Terradot. The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites. Mol.Microbiol. V. 79 1260 2011.
ISSN: ISSN 0950-382X
PubMed: 21208302
DOI: 10.1111/J.1365-2958.2010.07517.X
Page generated: Wed Dec 16 03:59:58 2020

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