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Iron in PDB 3bvk: Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin

Enzymatic activity of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin

All present enzymatic activity of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin, PDB code: 3bvk was solved by K.H.Kim, K.J.Cho, J.H.Lee, H.J.Shin, I.S.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.61 / 1.50
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 128.454, 128.454, 165.334, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.4

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iron atom in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin (pdb code 3bvk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin, PDB code: 3bvk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in 3bvk

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Iron binding site 1 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1006

b:34.9
occ:0.50
 FE A:FE1007 2.4 23.6 0.5
OE2 A:GLU17 2.6 17.3 1.0
OE1 A:GLN127 2.8 14.9 1.0
OE1 A:GLU50 3.1 22.4 1.0
ND1 A:HIS53 3.3 17.3 1.0
O A:HOH1152 3.4 27.3 1.0
OE1 A:GLU17 3.4 18.4 1.0
CD A:GLU17 3.4 16.2 1.0
OE1 A:GLU130 3.5 17.4 1.0
OE2 A:GLU50 3.5 22.2 1.0
CD A:GLU50 3.5 20.5 1.0
CG2 A:ILE97 3.7 13.8 1.0
CE1 A:HIS53 3.8 17.1 1.0
CD A:GLN127 3.9 14.3 1.0
CE1 A:TYR123 4.1 13.5 1.0
CG A:HIS53 4.4 15.1 1.0
OH A:TYR123 4.5 14.2 1.0
CD A:GLU130 4.5 15.7 1.0
OE2 A:GLU94 4.5 16.3 1.0
NE2 A:GLN127 4.7 14.4 1.0
CZ A:TYR123 4.7 13.5 1.0
CG A:GLN127 4.8 14.4 1.0
CG A:GLU50 4.8 17.0 1.0
CB A:GLN127 4.8 13.8 1.0
OE2 A:GLU130 4.8 17.8 1.0
CB A:ILE97 4.8 13.5 1.0
CG A:GLU17 4.9 13.8 1.0
CB A:HIS53 4.9 13.3 1.0
NE2 A:HIS53 5.0 18.0 1.0

Iron binding site 2 out of 14 in 3bvk

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Iron binding site 2 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1007

b:23.6
occ:0.50
 OE1 A:GLN127 2.3 14.9 1.0
OE1 A:GLU130 2.3 17.4 1.0
OE2 A:GLU94 2.3 16.3 1.0
OE1 A:GLU50 2.4 22.4 1.0
FE A:FE1006 2.4 34.9 0.5
CD A:GLU94 3.2 15.4 1.0
CD A:GLN127 3.3 14.3 1.0
CD A:GLU50 3.3 20.5 1.0
OE1 A:GLU94 3.4 16.0 1.0
OE2 A:GLU50 3.5 22.2 1.0
CD A:GLU130 3.6 15.7 1.0
NE2 A:GLN127 3.6 14.4 1.0
O A:HOH1152 3.6 27.3 1.0
CE1 A:HIS46 3.9 14.3 1.0
CB A:GLU130 4.0 14.4 1.0
NE2 A:HIS46 4.1 14.6 1.0
CG2 A:ILE97 4.3 13.8 1.0
CG A:GLU130 4.4 15.5 1.0
OE2 A:GLU130 4.4 17.8 1.0
CG A:GLU94 4.6 13.7 1.0
CG A:GLN127 4.7 14.4 1.0
CG A:GLU50 4.7 17.0 1.0
CB A:ILE97 4.8 13.5 1.0
CE1 A:HIS53 4.8 17.1 1.0
ND1 A:HIS53 4.9 17.3 1.0
OE2 A:GLU17 4.9 17.3 1.0
CA A:GLN127 5.0 13.8 1.0

Iron binding site 3 out of 14 in 3bvk

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Iron binding site 3 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1008

b:60.1
occ:0.50
 ND1 D:HIS149 4.2 23.5 1.0
O B:HOH1154 4.2 38.0 1.0
ND1 A:HIS149 4.3 24.3 1.0
CD1 A:LEU153 4.5 16.5 1.0
ND1 B:HIS149 4.6 23.2 1.0
CD1 D:LEU153 4.7 16.9 1.0
CD1 B:LEU153 4.8 16.6 1.0

Iron binding site 4 out of 14 in 3bvk

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Iron binding site 4 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1006

b:36.6
occ:0.50
 FE B:FE1007 2.5 22.6 0.5
OE2 B:GLU17 2.7 17.9 1.0
OE1 B:GLN127 2.7 15.5 1.0
OE1 B:GLU50 3.2 21.6 1.0
O B:HOH1153 3.2 37.0 1.0
ND1 B:HIS53 3.3 15.2 1.0
OE1 B:GLU130 3.5 16.6 1.0
CD B:GLU17 3.5 16.5 1.0
OE1 B:GLU17 3.5 18.9 1.0
CG2 B:ILE97 3.7 12.8 1.0
CD B:GLU50 3.7 19.9 1.0
CE1 B:HIS53 3.7 14.7 1.0
OE2 B:GLU50 3.8 21.6 1.0
CD B:GLN127 3.8 14.1 1.0
CE1 B:TYR123 4.0 13.3 1.0
OH B:TYR123 4.4 13.5 1.0
CG B:HIS53 4.4 13.2 1.0
CD B:GLU130 4.5 15.3 1.0
OE2 B:GLU94 4.6 17.0 1.0
NE2 B:GLN127 4.6 14.4 1.0
CG B:GLN127 4.6 13.5 1.0
CZ B:TYR123 4.7 12.9 1.0
CB B:GLN127 4.7 13.0 1.0
OE2 B:GLU130 4.8 17.7 1.0
CB B:ILE97 4.8 12.6 1.0
CD1 B:TYR123 4.9 13.2 1.0
CB B:HIS53 4.9 11.9 1.0
CG B:GLU17 4.9 13.6 1.0
NE2 B:HIS53 5.0 15.9 1.0
CG B:GLU50 5.0 16.1 1.0

Iron binding site 5 out of 14 in 3bvk

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Iron binding site 5 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1007

b:22.6
occ:0.50
 OE1 B:GLN127 2.3 15.5 1.0
OE1 B:GLU130 2.3 16.6 1.0
OE2 B:GLU94 2.3 17.0 1.0
OE1 B:GLU50 2.4 21.6 1.0
FE B:FE1006 2.5 36.6 0.5
CD B:GLU94 3.2 15.2 1.0
CD B:GLN127 3.2 14.1 1.0
OE1 B:GLU94 3.4 16.2 1.0
CD B:GLU50 3.4 19.9 1.0
NE2 B:GLN127 3.5 14.4 1.0
CD B:GLU130 3.5 15.3 1.0
O B:HOH1153 3.6 37.0 1.0
OE2 B:GLU50 3.6 21.6 1.0
CE1 B:HIS46 4.0 15.2 1.0
CB B:GLU130 4.0 13.5 1.0
NE2 B:HIS46 4.1 15.2 1.0
CG2 B:ILE97 4.3 12.8 1.0
CG B:GLU130 4.4 14.8 1.0
OE2 B:GLU130 4.4 17.7 1.0
CG B:GLN127 4.6 13.5 1.0
CG B:GLU94 4.6 13.5 1.0
CG B:GLU50 4.8 16.1 1.0
CB B:ILE97 4.8 12.6 1.0
CE1 B:HIS53 4.8 14.7 1.0
ND1 B:HIS53 4.9 15.2 1.0
CA B:GLN127 4.9 12.7 1.0
OE2 B:GLU17 4.9 17.9 1.0

Iron binding site 6 out of 14 in 3bvk

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Iron binding site 6 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1006

b:40.1
occ:0.50
 FE C:FE1007 2.5 25.1 0.5
OE2 C:GLU17 2.6 18.0 1.0
OE1 C:GLN127 2.7 15.5 1.0
O C:HOH1146 3.1 42.2 1.0
OE1 C:GLU50 3.2 22.3 1.0
ND1 C:HIS53 3.2 16.8 1.0
CD C:GLU17 3.4 17.0 1.0
OE1 C:GLU130 3.4 18.7 1.0
OE1 C:GLU17 3.5 19.0 1.0
OE2 C:GLU50 3.6 21.4 1.0
CD C:GLU50 3.7 19.9 1.0
CE1 C:HIS53 3.7 17.3 1.0
CG2 C:ILE97 3.7 14.1 1.0
CD C:GLN127 3.8 14.6 1.0
CE1 C:TYR123 4.0 14.7 1.0
OH C:TYR123 4.4 15.2 1.0
CG C:HIS53 4.4 15.0 1.0
CD C:GLU130 4.4 16.9 1.0
OE2 C:GLU94 4.6 17.5 1.0
CG C:GLN127 4.6 14.2 1.0
NE2 C:GLN127 4.6 14.7 1.0
CZ C:TYR123 4.7 14.3 1.0
CB C:GLN127 4.7 13.8 1.0
OE2 C:GLU130 4.7 19.6 1.0
CB C:ILE97 4.9 13.9 1.0
CG C:GLU17 4.9 15.1 1.0
NE2 C:HIS53 4.9 17.9 1.0
CB C:HIS53 4.9 13.2 1.0
CD1 C:TYR123 5.0 14.8 1.0
CG C:GLU50 5.0 16.6 1.0

Iron binding site 7 out of 14 in 3bvk

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Iron binding site 7 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1007

b:25.1
occ:0.50
 OE1 C:GLU130 2.3 18.7 1.0
OE1 C:GLN127 2.3 15.5 1.0
OE2 C:GLU94 2.3 17.5 1.0
OE1 C:GLU50 2.4 22.3 1.0
FE C:FE1006 2.5 40.1 0.5
CD C:GLU94 3.2 16.8 1.0
CD C:GLN127 3.3 14.6 1.0
CD C:GLU50 3.3 19.9 1.0
OE1 C:GLU94 3.4 17.9 1.0
O C:HOH1146 3.5 42.2 1.0
CD C:GLU130 3.5 16.9 1.0
OE2 C:GLU50 3.5 21.4 1.0
NE2 C:GLN127 3.5 14.7 1.0
CE1 C:HIS46 3.9 15.4 1.0
CB C:GLU130 4.0 15.6 1.0
NE2 C:HIS46 4.0 14.9 1.0
CG C:GLU130 4.3 16.7 1.0
CG2 C:ILE97 4.4 14.1 1.0
OE2 C:GLU130 4.4 19.6 1.0
CG C:GLU94 4.6 15.0 1.0
CG C:GLN127 4.7 14.2 1.0
CG C:GLU50 4.8 16.6 1.0
CE1 C:HIS53 4.8 17.3 1.0
CB C:ILE97 4.9 13.9 1.0
ND1 C:HIS53 4.9 16.8 1.0
OE2 C:GLU17 4.9 18.0 1.0
CA C:GLN127 5.0 13.8 1.0

Iron binding site 8 out of 14 in 3bvk

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Iron binding site 8 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1006

b:37.2
occ:0.50
 FE D:FE1007 2.6 23.6 0.5
OE2 D:GLU17 2.6 17.3 1.0
OE1 D:GLN127 2.8 15.1 1.0
ND1 D:HIS53 3.1 16.2 1.0
OE1 D:GLU50 3.3 22.1 1.0
O D:HOH1153 3.3 30.1 1.0
CD D:GLU17 3.4 16.4 1.0
OE1 D:GLU17 3.4 18.3 1.0
OE1 D:GLU130 3.5 17.1 1.0
CE1 D:HIS53 3.6 16.3 1.0
OE2 D:GLU50 3.6 21.4 1.0
CD D:GLU50 3.7 19.9 1.0
CG2 D:ILE97 3.8 13.1 1.0
CD D:GLN127 3.9 14.2 1.0
CE1 D:TYR123 3.9 13.1 1.0
OH D:TYR123 4.3 14.2 1.0
CG D:HIS53 4.3 14.3 1.0
CD D:GLU130 4.5 15.6 1.0
CZ D:TYR123 4.5 12.9 1.0
OE2 D:GLU94 4.7 16.6 1.0
CG D:GLN127 4.7 13.3 1.0
CB D:GLN127 4.7 13.1 1.0
NE2 D:GLN127 4.7 14.0 1.0
OE2 D:GLU130 4.8 18.4 1.0
CB D:HIS53 4.8 12.8 1.0
CG D:GLU17 4.8 13.9 1.0
NE2 D:HIS53 4.8 16.9 1.0
CD1 D:TYR123 4.9 12.9 1.0
CB D:ILE97 4.9 13.3 1.0

Iron binding site 9 out of 14 in 3bvk

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Iron binding site 9 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1007

b:23.6
occ:0.50
 OE1 D:GLN127 2.3 15.1 1.0
OE2 D:GLU94 2.3 16.6 1.0
OE1 D:GLU130 2.3 17.1 1.0
OE1 D:GLU50 2.5 22.1 1.0
FE D:FE1006 2.6 37.2 0.5
CD D:GLU94 3.2 15.5 1.0
CD D:GLN127 3.3 14.2 1.0
OE1 D:GLU94 3.3 16.4 1.0
CD D:GLU50 3.4 19.9 1.0
O D:HOH1153 3.5 30.1 1.0
OE2 D:GLU50 3.5 21.4 1.0
CD D:GLU130 3.6 15.6 1.0
NE2 D:GLN127 3.6 14.0 1.0
CE1 D:HIS46 3.9 14.7 1.0
CB D:GLU130 4.1 13.7 1.0
NE2 D:HIS46 4.1 14.1 1.0
CG D:GLU130 4.4 15.1 1.0
CG2 D:ILE97 4.4 13.1 1.0
OE2 D:GLU130 4.4 18.4 1.0
CG D:GLU94 4.6 14.0 1.0
CG D:GLN127 4.7 13.3 1.0
CE1 D:HIS53 4.8 16.3 1.0
CG D:GLU50 4.8 16.4 1.0
CB D:ILE97 4.9 13.3 1.0
ND1 D:HIS53 4.9 16.2 1.0
OE2 D:GLU17 4.9 17.3 1.0

Iron binding site 10 out of 14 in 3bvk

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Iron binding site 10 out of 14 in the Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1006

b:36.7
occ:0.50
 OE2 E:GLU17 2.5 17.0 1.0
FE E:FE1007 2.6 21.9 0.5
OE1 E:GLN127 2.9 14.4 1.0
OE1 E:GLU50 3.2 20.0 1.0
ND1 E:HIS53 3.2 15.1 1.0
O E:HOH1159 3.2 28.3 1.0
CD E:GLU17 3.3 15.8 1.0
OE1 E:GLU17 3.3 18.3 1.0
OE1 E:GLU130 3.5 15.4 1.0
OE2 E:GLU50 3.6 19.4 1.0
CD E:GLU50 3.6 18.1 1.0
CE1 E:HIS53 3.7 14.8 1.0
CG2 E:ILE97 3.8 11.8 1.0
CD E:GLN127 4.0 13.0 1.0
CE1 E:TYR123 4.0 12.3 1.0
OH E:TYR123 4.3 13.2 1.0
CG E:HIS53 4.4 12.8 1.0
CD E:GLU130 4.5 14.4 1.0
CZ E:TYR123 4.6 12.6 1.0
OE2 E:GLU94 4.7 15.7 1.0
CG E:GLU17 4.7 12.7 1.0
OE2 E:GLU130 4.8 16.9 1.0
CG E:GLN127 4.8 12.9 1.0
CB E:GLN127 4.8 11.8 1.0
NE2 E:GLN127 4.8 12.8 1.0
CB E:HIS53 4.8 11.2 1.0
CG E:GLU50 4.9 15.1 1.0
CB E:ILE97 4.9 11.7 1.0
CD1 E:TYR123 4.9 12.0 1.0
NE2 E:HIS53 5.0 15.8 1.0

Reference:

K.H.Kim, K.J.Cho, J.H.Lee, H.J.Shin, I.S.Yang. Structural Basis For the Iron Uptake Mechanism of Helicobacter Pylori Ferritin To Be Published.
Page generated: Tue Aug 5 00:01:02 2025

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