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Iron in PDB 4ztt: Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates

Enzymatic activity of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates

All present enzymatic activity of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates:
1.16.3.2;

Protein crystallography data

The structure of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates, PDB code: 4ztt was solved by S.Kim, Y.H.Park, S.W.Jung, J.H.Seok, Y.B.Chung, D.B.Lee, G.Gowda, J.H.Lee, H.R.Han, A.E.Cho, C.Lee, M.S.Chung, K.H.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.66 / 1.83
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 128.816, 128.816, 172.247, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.2

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates (pdb code 4ztt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates, PDB code: 4ztt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in 4ztt

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Iron binding site 1 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:18.6
occ:1.00
 FE1 A:FEO201 0.0 18.6 1.0
O A:FEO201 1.9 17.7 1.0
OE1 A:GLU130 2.0 25.7 1.0
OE2 A:GLU50 2.0 22.3 1.0
OE2 A:GLU94 2.0 20.1 1.0
O A:HOH301 2.0 19.8 0.3
CD A:GLU94 2.7 20.4 1.0
OE1 A:GLU94 2.7 20.6 1.0
CD A:GLU50 2.9 20.0 1.0
CD A:GLU130 3.1 20.7 1.0
OE1 A:GLU50 3.3 22.4 1.0
FE2 A:FEO201 3.4 17.2 1.0
O A:OH203 3.4 19.9 0.3
CG A:GLU130 3.5 16.9 1.0
NE2 A:HIS46 3.9 23.5 1.0
OE1 A:GLN127 4.1 18.8 1.0
CG A:GLU94 4.1 19.5 1.0
CE1 A:HIS53 4.2 20.5 1.0
CD1 A:ILE97 4.2 24.4 1.0
OE2 A:GLU130 4.2 24.2 1.0
CG A:GLU50 4.3 20.0 1.0
CB A:GLU130 4.3 20.5 1.0
ND1 A:HIS53 4.3 20.3 1.0
OH A:TYR24 4.3 27.8 1.0
CE2 A:TYR24 4.4 26.6 1.0
CD2 A:HIS46 4.4 23.8 1.0
NE2 A:GLN127 4.6 19.7 1.0
O A:OH202 4.7 16.5 1.0
CD A:GLN127 4.8 20.9 1.0
CZ A:TYR24 4.9 26.1 1.0
OE1 A:GLU17 4.9 19.7 1.0
CE2 A:PHE134 5.0 24.7 1.0

Iron binding site 2 out of 13 in 4ztt

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Iron binding site 2 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:17.2
occ:1.00
 FE2 A:FEO201 0.0 17.2 1.0
O A:FEO201 1.8 17.7 1.0
O A:OH203 1.9 19.9 0.3
OE1 A:GLU17 1.9 19.7 1.0
ND1 A:HIS53 2.0 20.3 1.0
OE1 A:GLU50 2.1 22.4 1.0
O A:OH202 2.2 16.5 1.0
CE1 A:HIS53 2.9 20.5 1.0
CD A:GLU17 3.1 18.1 1.0
CG A:HIS53 3.1 16.6 1.0
CD A:GLU50 3.1 20.0 1.0
FE1 A:FEO201 3.4 18.6 1.0
OE2 A:GLU17 3.4 20.3 1.0
O A:HOH301 3.4 19.8 0.3
CB A:HIS53 3.5 19.8 1.0
OE2 A:GLU50 3.5 22.3 1.0
OE1 A:GLN127 3.9 18.8 1.0
NE2 A:HIS53 4.1 20.3 1.0
CD2 A:HIS53 4.2 18.6 1.0
CG A:GLU17 4.3 21.4 1.0
CG A:GLU50 4.4 20.0 1.0
CG2 A:ILE97 4.6 17.7 1.0
OE1 A:GLU130 4.6 25.7 1.0
CD1 A:ILE97 4.6 24.4 1.0
CA A:GLU50 4.6 20.5 1.0
CB A:GLU50 4.7 20.1 1.0
CB A:GLU17 4.7 20.1 1.0
CD A:GLN127 4.9 20.9 1.0
CA A:HIS53 5.0 23.5 1.0

Iron binding site 3 out of 13 in 4ztt

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Iron binding site 3 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:15.8
occ:1.00
 FE1 B:FEO201 0.0 15.8 1.0
O B:FEO201 1.9 17.2 1.0
OE1 B:GLU17 1.9 20.0 1.0
ND1 B:HIS53 2.0 17.8 1.0
O B:OH203 2.0 26.5 0.3
OE1 B:GLU50 2.1 19.9 1.0
O B:OH202 2.3 17.2 1.0
CE1 B:HIS53 2.9 21.8 1.0
CD B:GLU17 3.0 18.8 1.0
CG B:HIS53 3.0 19.4 1.0
CD B:GLU50 3.1 21.3 1.0
FE2 B:FEO201 3.4 17.3 1.0
OE2 B:GLU17 3.4 21.7 1.0
CB B:HIS53 3.5 20.0 1.0
OE2 B:GLU50 3.6 19.9 1.0
OE1 B:GLN127 3.9 21.1 1.0
NE2 B:HIS53 4.0 22.2 1.0
CD2 B:HIS53 4.1 20.8 1.0
CG B:GLU17 4.3 19.8 1.0
CG B:GLU50 4.5 20.5 1.0
O B:HOH301 4.5 22.5 0.3
OE1 B:GLU130 4.5 22.6 1.0
CG2 B:ILE97 4.6 15.6 1.0
CD1 B:ILE97 4.6 20.5 1.0
CA B:GLU50 4.7 21.6 1.0
CB B:GLU50 4.8 20.0 1.0
CB B:GLU17 4.8 18.2 1.0
CD B:GLN127 4.9 20.7 1.0

Iron binding site 4 out of 13 in 4ztt

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Iron binding site 4 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:17.3
occ:1.00
 FE2 B:FEO201 0.0 17.3 1.0
O B:FEO201 1.9 17.2 1.0
OE1 B:GLU130 1.9 22.6 1.0
OE2 B:GLU94 2.0 19.7 1.0
OE2 B:GLU50 2.0 19.9 1.0
O B:HOH301 2.0 22.5 0.3
CD B:GLU94 2.7 21.3 1.0
OE1 B:GLU94 2.7 21.1 1.0
CD B:GLU50 2.9 21.3 1.0
CD B:GLU130 3.1 19.1 1.0
OE1 B:GLU50 3.2 19.9 1.0
FE1 B:FEO201 3.4 15.8 1.0
CG B:GLU130 3.5 18.4 1.0
NE2 B:HIS46 3.9 22.0 1.0
O B:OH203 4.0 26.5 0.3
CG B:GLU94 4.1 20.7 1.0
OE1 B:GLN127 4.1 21.1 1.0
CE1 B:HIS53 4.1 21.8 1.0
CD1 B:ILE97 4.2 20.5 1.0
OE2 B:GLU130 4.2 26.1 1.0
CB B:GLU130 4.3 20.0 1.0
ND1 B:HIS53 4.3 17.8 1.0
OH B:TYR24 4.3 23.6 1.0
CG B:GLU50 4.3 20.5 1.0
CD2 B:HIS46 4.4 22.8 1.0
CE2 B:TYR24 4.4 20.1 1.0
NE2 B:GLN127 4.6 18.1 1.0
O B:OH202 4.7 17.2 1.0
CD B:GLN127 4.8 20.7 1.0
CZ B:TYR24 4.9 22.5 1.0
CE2 B:PHE134 4.9 24.4 1.0
OE1 B:GLU17 5.0 20.0 1.0

Iron binding site 5 out of 13 in 4ztt

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Iron binding site 5 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:17.8
occ:1.00
 ND1 C:HIS53 1.9 20.3 1.0
O1 C:OXY203 1.9 18.2 0.5
OE1 C:GLU17 2.0 20.3 1.0
OE1 C:GLU50 2.1 23.7 1.0
O2 C:OXY203 2.1 10.7 0.5
O C:OH204 2.2 22.4 1.0
CE1 C:HIS53 2.8 17.5 1.0
O C:HOH301 2.9 24.2 0.3
CD C:GLU17 3.0 22.9 1.0
CG C:HIS53 3.1 18.7 1.0
CD C:GLU50 3.1 22.2 1.0
FE C:FE2202 3.3 18.8 1.0
OE2 C:GLU17 3.3 22.3 1.0
OE2 C:GLU50 3.5 24.4 1.0
CB C:HIS53 3.5 19.8 1.0
OE1 C:GLN127 3.8 17.3 1.0
NE2 C:HIS53 4.0 21.6 1.0
CD2 C:HIS53 4.1 19.6 1.0
CG C:GLU17 4.3 21.3 1.0
CD1 C:ILE97 4.5 22.2 1.0
CG C:GLU50 4.6 24.8 1.0
CG2 C:ILE97 4.6 22.3 1.0
OE1 C:GLU130 4.6 20.9 1.0
CB C:GLU17 4.7 20.9 1.0
CA C:GLU50 4.7 24.9 1.0
CB C:GLU50 4.9 21.9 1.0
CD C:GLN127 4.9 18.0 1.0

Iron binding site 6 out of 13 in 4ztt

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Iron binding site 6 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:18.8
occ:1.00
 O C:HOH301 1.2 24.2 0.3
O2 C:OXY203 1.8 10.7 0.5
OE1 C:GLU130 2.0 20.9 1.0
OE2 C:GLU94 2.0 19.9 1.0
OE2 C:GLU50 2.0 24.4 1.0
O1 C:OXY203 2.1 18.2 0.5
OE1 C:GLU94 2.6 19.8 1.0
CD C:GLU94 2.6 21.2 1.0
CD C:GLU50 3.0 22.2 1.0
CD C:GLU130 3.1 23.8 1.0
OE1 C:GLU50 3.2 23.7 1.0
FE C:FE201 3.3 17.8 1.0
CG C:GLU130 3.6 22.7 1.0
NE2 C:HIS46 3.9 26.8 1.0
OE1 C:GLN127 4.0 17.3 1.0
CE1 C:HIS53 4.1 17.5 1.0
CG C:GLU94 4.1 17.9 1.0
CD1 C:ILE97 4.1 22.2 1.0
OH C:TYR24 4.2 26.3 1.0
OE2 C:GLU130 4.3 24.2 1.0
ND1 C:HIS53 4.3 20.3 1.0
CB C:GLU130 4.3 22.6 1.0
CG C:GLU50 4.4 24.8 1.0
CD2 C:HIS46 4.4 25.5 1.0
CE2 C:TYR24 4.4 23.6 1.0
NE2 C:GLN127 4.7 21.4 1.0
O C:OH204 4.8 22.4 1.0
CD C:GLN127 4.8 18.0 1.0
CZ C:TYR24 4.9 25.1 1.0
CE1 C:PHE134 5.0 21.9 1.0
OE1 C:GLU17 5.0 20.3 1.0

Iron binding site 7 out of 13 in 4ztt

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Iron binding site 7 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:17.6
occ:1.00
 O D:HOH301 1.4 20.0 0.3
ND1 D:HIS53 1.9 20.8 1.0
OE1 D:GLU17 2.0 19.0 1.0
O1 D:PER203 2.0 17.1 0.5
O2 D:PER203 2.0 10.9 0.5
OE1 D:GLU50 2.1 22.4 1.0
O D:OH204 2.4 22.9 1.0
CE1 D:HIS53 2.8 21.2 1.0
CD D:GLU17 3.0 20.5 1.0
CG D:HIS53 3.1 20.9 1.0
CD D:GLU50 3.1 19.7 1.0
FE D:FE202 3.3 20.4 1.0
OE2 D:GLU17 3.4 20.2 1.0
OE2 D:GLU50 3.5 23.5 1.0
CB D:HIS53 3.6 21.6 1.0
OE1 D:GLN127 3.9 22.5 1.0
NE2 D:HIS53 4.0 22.1 1.0
CD2 D:HIS53 4.1 21.1 1.0
CG D:GLU17 4.3 18.3 1.0
CD1 D:ILE97 4.4 23.6 1.0
OE1 D:GLU130 4.5 21.7 1.0
CG D:GLU50 4.5 19.7 1.0
CG2 D:ILE97 4.6 21.4 1.0
CA D:GLU50 4.7 21.4 1.0
CB D:GLU17 4.7 18.7 1.0
CB D:GLU50 4.8 18.8 1.0
CD D:GLN127 5.0 18.4 1.0

Iron binding site 8 out of 13 in 4ztt

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Iron binding site 8 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:20.4
occ:1.00
 OE1 D:GLU130 1.9 21.7 1.0
O1 D:PER203 2.0 17.1 0.5
O2 D:PER203 2.0 10.9 0.5
OE2 D:GLU94 2.0 21.5 1.0
OE2 D:GLU50 2.0 23.5 1.0
OE1 D:GLU94 2.6 20.7 1.0
CD D:GLU94 2.6 21.1 1.0
CD D:GLU50 3.0 19.7 1.0
CD D:GLU130 3.1 25.8 1.0
OE1 D:GLU50 3.2 22.4 1.0
FE D:FE201 3.3 17.6 1.0
CG D:GLU130 3.6 22.7 1.0
NE2 D:HIS46 4.0 25.7 1.0
OE1 D:GLN127 4.0 22.5 1.0
CE1 D:HIS53 4.1 21.2 1.0
CG D:GLU94 4.1 20.5 1.0
CD1 D:ILE97 4.1 23.6 1.0
OE2 D:GLU130 4.2 24.3 1.0
ND1 D:HIS53 4.3 20.8 1.0
OH D:TYR24 4.3 26.6 1.0
CG D:GLU50 4.3 19.7 1.0
CB D:GLU130 4.3 21.8 1.0
CE2 D:TYR24 4.3 24.1 1.0
O D:HOH301 4.4 20.0 0.3
CD2 D:HIS46 4.4 25.6 1.0
NE2 D:GLN127 4.7 18.9 1.0
CD D:GLN127 4.8 18.4 1.0
CZ D:TYR24 4.8 25.5 1.0
CE2 D:PHE134 4.9 26.8 1.0
O D:OH204 4.9 22.9 1.0
OE1 D:GLU17 5.0 19.0 1.0

Iron binding site 9 out of 13 in 4ztt

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Iron binding site 9 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:16.2
occ:1.00
 FE1 E:FEO201 0.0 16.2 1.0
O E:HOH301 1.4 20.8 0.3
O E:FEO201 1.8 18.1 1.0
ND1 E:HIS53 1.9 18.8 1.0
OE1 E:GLU17 2.0 18.5 1.0
OE1 E:GLU50 2.1 19.6 1.0
O E:OH202 2.3 16.9 1.0
CE1 E:HIS53 2.8 18.0 1.0
O E:HOH303 2.8 8.1 0.3
CD E:GLU17 3.0 23.0 1.0
CG E:HIS53 3.0 16.0 1.0
CD E:GLU50 3.2 21.9 1.0
OE2 E:GLU17 3.3 21.7 1.0
FE2 E:FEO201 3.4 18.4 1.0
CB E:HIS53 3.4 17.9 1.0
OE2 E:GLU50 3.6 18.7 1.0
OE1 E:GLN127 3.9 18.2 1.0
NE2 E:HIS53 4.0 17.9 1.0
CD2 E:HIS53 4.1 21.6 1.0
CG E:GLU17 4.3 20.4 1.0
CD1 E:ILE97 4.5 22.2 1.0
CG2 E:ILE97 4.5 18.7 1.0
OE2 E:GLU130 4.5 19.3 1.0
CG E:GLU50 4.5 19.5 1.0
CA E:GLU50 4.7 20.5 1.0
CB E:GLU17 4.7 19.4 1.0
CB E:GLU50 4.7 20.8 1.0
CD E:GLN127 5.0 16.9 1.0
CA E:HIS53 5.0 19.4 1.0

Iron binding site 10 out of 13 in 4ztt

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Iron binding site 10 out of 13 in the Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structures of Ferritin Mutants Reveal Diferric-Peroxo Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:18.4
occ:1.00
 FE2 E:FEO201 0.0 18.4 1.0
O E:HOH303 1.1 8.1 0.3
OE2 E:GLU94 2.0 18.7 1.0
O E:FEO201 2.0 18.1 1.0
OE2 E:GLU130 2.0 19.3 1.0
OE2 E:GLU50 2.0 18.7 1.0
OE1 E:GLU94 2.6 18.7 1.0
CD E:GLU94 2.7 21.5 1.0
CD E:GLU50 2.9 21.9 1.0
CD E:GLU130 3.1 26.8 1.0
OE1 E:GLU50 3.3 19.6 1.0
FE1 E:FEO201 3.4 16.2 1.0
CG E:GLU130 3.6 19.6 1.0
NE2 E:HIS46 3.9 25.1 1.0
CE1 E:HIS53 4.0 18.0 1.0
OE1 E:GLN127 4.1 18.2 1.0
CG E:GLU94 4.1 19.6 1.0
CD1 E:ILE97 4.1 22.2 1.0
OE1 E:GLU130 4.2 25.1 1.0
ND1 E:HIS53 4.2 18.8 1.0
CB E:GLU130 4.2 20.6 1.0
CG E:GLU50 4.3 19.5 1.0
OH E:TYR24 4.4 23.9 1.0
CD2 E:HIS46 4.4 25.8 1.0
CE2 E:TYR24 4.4 23.1 1.0
NE2 E:GLN127 4.8 19.0 1.0
O E:OH202 4.8 16.9 1.0
O E:HOH301 4.8 20.8 0.3
CD E:GLN127 4.9 16.9 1.0
CE2 E:PHE134 4.9 24.5 1.0
CZ E:TYR24 4.9 27.5 1.0

Reference:

S.Kim, J.H.Lee, J.H.Seok, Y.H.Park, S.W.Jung, A.E.Cho, C.Lee, M.S.Chung, K.H.Kim. Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins From Gram-Negative Bacteria. J. Mol. Biol. V. 428 5007 2016.
ISSN: ESSN 1089-8638
PubMed: 27777002
DOI: 10.1016/J.JMB.2016.10.022
Page generated: Sun Dec 13 15:55:05 2020

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