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Iron in PDB 4iwk: Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries

Protein crystallography data

The structure of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries, PDB code: 4iwk was solved by S.Pfaffen, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 1.65
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 126.251, 126.251, 170.299, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.5

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries (pdb code 4iwk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries, PDB code: 4iwk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 4iwk

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Iron binding site 1 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


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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 Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:24.5
occ:0.90
 OE1 A:GLU15 2.0 25.6 1.0
O A:HOH429 2.1 28.3 1.0
OE1 A:GLU48 2.1 22.9 1.0
O A:HOH423 2.1 28.0 1.0
ND1 A:HIS51 2.4 26.0 1.0
CD A:GLU15 3.0 22.9 1.0
CD A:GLU48 3.0 26.0 1.0
CE1 A:HIS51 3.3 26.8 1.0
OE2 A:GLU15 3.3 27.2 1.0
OE2 A:GLU48 3.4 26.3 1.0
ND2 A:ASN97 3.5 23.0 1.0
CG A:HIS51 3.5 21.7 1.0
FE A:FE203 3.6 24.0 0.8
CB A:HIS51 3.9 20.6 1.0
OE1 A:GLN127 4.1 22.6 1.0
O A:HOH430 4.1 28.2 1.0
CG A:ASN97 4.3 25.7 1.0
CG A:GLU15 4.3 19.4 1.0
CG A:GLU48 4.3 18.4 1.0
O A:HOH432 4.4 34.5 1.0
CA A:GLU48 4.5 17.7 1.0
NE2 A:HIS51 4.5 26.6 1.0
CB A:GLU48 4.6 16.9 1.0
CD2 A:HIS51 4.6 22.8 1.0
CB A:ASN97 4.7 22.1 1.0
CB A:GLU15 4.8 17.6 1.0
OE1 A:GLU94 4.8 23.5 1.0
CA A:GLU15 4.9 15.8 1.0
CD A:GLN127 4.9 20.9 1.0
OD1 A:ASN97 5.0 22.5 1.0
OE1 A:GLU130 5.0 27.6 1.0

Iron binding site 2 out of 24 in 4iwk

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Iron binding site 2 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:40.6
occ:0.35
 OE2 A:GLU44 2.1 47.5 1.0
O A:HOH424 2.2 39.1 1.0
O A:HOH433 2.2 45.6 1.0
CD A:GLU44 3.2 37.9 1.0
FE A:FE204 3.3 39.5 0.4
OH A:TYR40 3.4 49.4 1.0
O A:HOH431 3.6 43.9 1.0
OE1 A:GLU44 4.0 38.5 1.0
NZ A:LYS133 4.0 55.3 1.0
CZ A:TYR40 4.0 36.4 1.0
CG A:GLU44 4.1 29.8 1.0
OE1 A:GLU47 4.2 52.2 1.0
CE A:LYS133 4.3 56.7 1.0
CE2 A:TYR40 4.4 28.7 1.0
CD A:LYS133 4.6 51.8 1.0
OE2 A:GLU47 4.7 60.4 1.0
CE1 A:TYR40 4.8 31.6 1.0
CD A:GLU47 4.8 54.4 1.0

Iron binding site 3 out of 24 in 4iwk

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Iron binding site 3 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:24.0
occ:0.85
 O A:HOH432 1.8 34.5 1.0
O A:HOH423 1.9 28.0 1.0
OE2 A:GLU94 2.1 20.8 1.0
OE2 A:GLU48 2.1 26.3 1.0
OE1 A:GLU130 2.1 27.6 1.0
OE1 A:GLU94 2.6 23.5 1.0
CD A:GLU94 2.6 21.6 1.0
CD A:GLU48 2.9 26.0 1.0
CD A:GLU130 3.0 32.3 1.0
OE2 A:GLU130 3.3 30.9 1.0
OE1 A:GLU48 3.5 22.9 1.0
FE A:FE201 3.6 24.5 0.9
FE A:FE204 3.7 39.5 0.4
ND2 A:ASN97 3.7 23.0 1.0
OE1 A:GLU44 3.9 38.5 1.0
OE1 A:GLN127 4.0 22.6 1.0
CG A:GLU48 4.0 18.4 1.0
CG A:GLU94 4.1 20.1 1.0
O A:HOH431 4.1 43.9 1.0
OH A:TYR22 4.3 21.2 1.0
CE1 A:HIS51 4.3 26.8 1.0
OE2 A:GLU47 4.3 60.4 1.0
CE1 A:TYR22 4.4 19.6 1.0
CG A:GLU130 4.4 25.8 1.0
ND1 A:HIS51 4.6 26.0 1.0
NE2 A:GLN127 4.7 20.6 1.0
CB A:GLU130 4.7 22.7 1.0
CD A:GLN127 4.8 20.9 1.0
O A:HOH429 4.8 28.3 1.0
CZ A:TYR22 4.8 19.2 1.0
CG A:ASN97 5.0 25.7 1.0

Iron binding site 4 out of 24 in 4iwk

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Iron binding site 4 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:39.5
occ:0.40
 O A:HOH424 2.0 39.1 1.0
OE1 A:GLU44 2.1 38.5 1.0
OE2 A:GLU47 2.1 60.4 1.0
O A:HOH432 2.2 34.5 1.0
OE2 A:GLU130 2.4 30.9 1.0
OE2 A:GLU44 2.6 47.5 1.0
CD A:GLU44 2.6 37.9 1.0
CD A:GLU130 2.8 32.3 1.0
O A:HOH431 2.8 43.9 1.0
CD A:GLU47 3.0 54.4 1.0
OE1 A:GLU130 3.3 27.6 1.0
FE A:FE202 3.3 40.6 0.3
OE1 A:GLU47 3.4 52.2 1.0
FE A:FE203 3.7 24.0 0.8
CG A:GLU130 3.7 25.8 1.0
O A:HOH433 4.0 45.6 1.0
CG A:GLU44 4.1 29.8 1.0
OE1 A:GLN126 4.2 49.1 1.0
CG A:GLU47 4.3 38.1 1.0
OE2 A:GLU94 4.3 20.8 1.0
CB A:GLU47 4.6 26.2 1.0
CB A:GLU130 4.7 22.7 1.0
CB A:GLU44 4.7 21.1 1.0
OH A:TYR22 4.9 21.2 1.0
CA A:GLU44 5.0 20.2 1.0
OE2 A:GLU48 5.0 26.3 1.0
O A:HOH423 5.0 28.0 1.0

Iron binding site 5 out of 24 in 4iwk

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Iron binding site 5 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:38.7
occ:0.50
 OE1 B:GLU44 2.1 37.2 1.0
OE2 B:GLU130 2.3 28.9 1.0
O B:HOH434 2.5 25.9 1.0
CD B:GLU130 2.7 29.3 1.0
OE2 B:GLU47 2.8 62.1 1.0
CD B:GLU44 2.9 41.9 1.0
O B:HOH447 2.9 39.2 1.0
OE2 B:GLU44 3.1 46.8 1.0
CD B:GLU47 3.1 45.0 1.0
OE1 B:GLU130 3.1 28.2 1.0
O B:HOH450 3.3 35.1 1.0
OE1 B:GLU47 3.4 42.6 1.0
FE B:FE203 3.7 21.8 0.8
CG B:GLU130 3.7 21.0 1.0
CG B:GLU47 4.0 30.0 1.0
O B:HOH449 4.0 45.4 1.0
NE2 B:GLN126 4.2 33.2 0.5
OE2 B:GLU94 4.2 22.6 1.0
CG B:GLU44 4.3 28.1 1.0
CB B:GLU47 4.5 23.3 1.0
CB B:GLU130 4.7 20.3 1.0
CB B:GLU44 4.8 20.8 1.0
CE1 B:HIS51 4.8 30.0 1.0
OH B:TYR22 4.9 21.3 1.0
OE2 B:GLU48 4.9 25.8 1.0
O B:HOH444 5.0 24.2 1.0
CA B:GLU44 5.0 19.9 1.0

Iron binding site 6 out of 24 in 4iwk

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Iron binding site 6 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:22.6
occ:0.85
 OE1 B:GLU15 2.0 20.4 1.0
O B:HOH448 2.1 31.2 1.0
OE1 B:GLU48 2.1 23.8 1.0
O B:HOH444 2.2 24.2 1.0
ND1 B:HIS51 2.4 28.1 1.0
CD B:GLU15 3.0 26.0 1.0
CD B:GLU48 3.1 26.5 1.0
OE2 B:GLU15 3.3 26.0 1.0
CE1 B:HIS51 3.3 30.0 1.0
OE2 B:GLU48 3.4 25.8 1.0
ND2 B:ASN97 3.5 22.4 1.0
CG B:HIS51 3.5 24.4 1.0
FE B:FE203 3.6 21.8 0.8
CB B:HIS51 3.8 20.3 1.0
O B:HOH339 4.1 27.3 1.0
OE1 B:GLN127 4.2 20.9 1.0
CG B:ASN97 4.2 23.8 1.0
O B:HOH434 4.4 25.9 1.0
CG B:GLU48 4.4 18.6 1.0
CG B:GLU15 4.4 19.1 1.0
NE2 B:HIS51 4.5 26.3 1.0
CA B:GLU48 4.5 17.5 1.0
CB B:ASN97 4.6 20.5 1.0
CD2 B:HIS51 4.6 27.2 1.0
CB B:GLU48 4.6 16.5 1.0
OE1 B:GLU94 4.8 21.5 1.0
CB B:GLU15 4.8 16.5 1.0
CD B:GLN127 4.9 19.4 1.0
OD1 B:ASN97 4.9 22.1 1.0

Iron binding site 7 out of 24 in 4iwk

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Iron binding site 7 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe203

b:21.8
occ:0.80
 O B:HOH434 1.4 25.9 1.0
O B:HOH444 1.9 24.2 1.0
OE2 B:GLU94 2.1 22.6 1.0
OE2 B:GLU48 2.1 25.8 1.0
OE1 B:GLU130 2.2 28.2 1.0
OE1 B:GLU94 2.5 21.5 1.0
CD B:GLU94 2.6 20.3 1.0
CD B:GLU48 3.0 26.5 1.0
CD B:GLU130 3.1 29.3 1.0
OE2 B:GLU130 3.4 28.9 1.0
OE1 B:GLU48 3.4 23.8 1.0
FE B:FE202 3.6 22.6 0.8
FE B:FE201 3.7 38.7 0.5
ND2 B:ASN97 3.7 22.4 1.0
OE1 B:GLN127 4.0 20.9 1.0
CG B:GLU94 4.1 18.0 1.0
CG B:GLU48 4.1 18.6 1.0
CE1 B:HIS51 4.2 30.0 1.0
OE1 B:GLU44 4.3 37.2 1.0
OH B:TYR22 4.4 21.3 1.0
CE1 B:TYR22 4.4 19.9 1.0
CG B:GLU130 4.4 21.0 1.0
ND1 B:HIS51 4.5 28.1 1.0
NE2 B:GLN127 4.6 20.6 1.0
CB B:GLU130 4.7 20.3 1.0
CD B:GLN127 4.7 19.4 1.0
O B:HOH448 4.8 31.2 1.0
CZ B:TYR22 4.9 19.6 1.0
CG B:ASN97 4.9 23.8 1.0

Iron binding site 8 out of 24 in 4iwk

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Iron binding site 8 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:22.8
occ:0.85
 OE1 C:GLU15 2.0 22.4 1.0
OE1 C:GLU48 2.0 21.9 1.0
O C:HOH453 2.1 27.7 1.0
O C:HOH442 2.2 28.6 1.0
ND1 C:HIS51 2.4 25.8 1.0
CD C:GLU48 3.0 23.3 1.0
CD C:GLU15 3.0 22.0 1.0
OE2 C:GLU15 3.2 24.8 1.0
CE1 C:HIS51 3.3 25.7 1.0
OE2 C:GLU48 3.3 25.3 1.0
CG C:HIS51 3.5 23.3 1.0
ND2 C:ASN97 3.5 24.4 1.0
FE C:FE202 3.6 21.1 0.8
CB C:HIS51 3.9 19.0 1.0
O C:HOH355 4.1 27.9 1.0
OE1 C:GLN127 4.2 22.3 1.0
CG C:ASN97 4.2 22.8 1.0
CG C:GLU15 4.3 18.2 1.0
CG C:GLU48 4.3 18.5 1.0
O C:HOH454 4.4 26.7 1.0
NE2 C:HIS51 4.5 26.4 1.0
CA C:GLU48 4.5 16.9 1.0
CB C:ASN97 4.6 18.1 1.0
CD2 C:HIS51 4.6 24.9 1.0
CB C:GLU48 4.7 16.4 1.0
CB C:GLU15 4.8 16.1 1.0
OE1 C:GLU94 4.8 21.4 1.0
OD1 C:ASN97 4.9 22.9 1.0
CD C:GLN127 5.0 21.2 1.0
CA C:GLU15 5.0 15.4 1.0

Iron binding site 9 out of 24 in 4iwk

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Iron binding site 9 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:21.1
occ:0.80
 O C:HOH454 1.4 26.7 1.0
O C:HOH442 1.8 28.6 1.0
OE2 C:GLU48 2.0 25.3 1.0
OE2 C:GLU94 2.1 22.8 1.0
OE2 C:GLU130 2.1 27.3 1.0
OE1 C:GLU94 2.5 21.4 1.0
CD C:GLU94 2.6 18.1 1.0
CD C:GLU48 2.9 23.3 1.0
CD C:GLU130 3.1 28.4 1.0
OE1 C:GLU48 3.4 21.9 1.0
OE1 C:GLU130 3.4 28.6 1.0
FE C:FE201 3.6 22.8 0.8
FE C:FE203 3.6 38.7 0.5
ND2 C:ASN97 3.7 24.4 1.0
OE1 C:GLN127 4.0 22.3 1.0
OE1 C:GLU44 4.0 39.7 1.0
CG C:GLU94 4.1 17.9 1.0
CG C:GLU48 4.1 18.5 1.0
CE1 C:HIS51 4.2 25.7 1.0
OE2 C:GLU47 4.2 60.4 1.0
OH C:TYR22 4.3 20.5 1.0
CE2 C:TYR22 4.4 17.6 1.0
CG C:GLU130 4.5 20.4 1.0
ND1 C:HIS51 4.5 25.8 1.0
NE2 C:GLN127 4.6 20.9 1.0
CB C:GLU130 4.6 18.6 1.0
CD C:GLN127 4.8 21.2 1.0
O C:HOH453 4.8 27.7 1.0
CZ C:TYR22 4.9 17.9 1.0
CG C:ASN97 4.9 22.8 1.0

Iron binding site 10 out of 24 in 4iwk

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Iron binding site 10 out of 24 in the Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Iron Soaked (Overnight) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe203

b:38.7
occ:0.50
 OE2 C:GLU47 1.9 60.4 1.0
OE1 C:GLU44 2.0 39.7 1.0
O C:HOH443 2.3 37.0 1.0
O C:HOH454 2.4 26.7 1.0
OE1 C:GLU130 2.4 28.6 1.0
CD C:GLU44 2.7 35.4 1.0
CD C:GLU130 2.8 28.4 1.0
OE2 C:GLU44 2.8 47.8 1.0
CD C:GLU47 2.9 50.2 1.0
OE2 C:GLU130 3.2 27.3 1.0
OE1 C:GLU47 3.3 52.8 1.0
FE C:FE204 3.3 36.6 0.3
FE C:FE202 3.6 21.1 0.8
CG C:GLU130 3.7 20.4 1.0
CG C:GLU47 4.1 31.8 1.0
CG C:GLU44 4.2 29.3 1.0
OE2 C:GLU94 4.2 22.8 1.0
O C:HOH447 4.3 40.1 1.0
CB C:GLU47 4.4 21.8 1.0
CB C:GLU130 4.6 18.6 1.0
CB C:GLU44 4.7 19.5 1.0
OE2 C:GLU48 4.8 25.3 1.0
CE1 C:HIS51 4.8 25.7 1.0
CA C:GLU44 4.9 18.9 1.0
OH C:TYR22 4.9 20.5 1.0
O C:HOH442 4.9 28.6 1.0

Reference:

S.Pfaffen, R.Abdulqadir, N.E.Le Brun, M.E.Murphy. Mechanism of Ferrous Iron Binding and Oxidation By Ferritin From A Pennate Diatom. J.Biol.Chem. V. 288 14917 2013.
ISSN: ISSN 0021-9258
PubMed: 23548912
DOI: 10.1074/JBC.M113.454496
Page generated: Mon Aug 5 04:16:43 2024

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