Iron in PDB 4ixk: Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries

Protein crystallography data

The structure of Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries, PDB code: 4ixk 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) 48.40 / 2.10
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 174.323, 174.323, 174.323, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.7

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 4ixk

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Iron binding site 1 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (2 H) 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 1 of Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:47.2
occ:0.55
OE1 A:GLU48 2.2 47.6 1.0
O A:HOH301 2.2 40.2 1.0
OE1 A:GLU15 2.3 43.8 1.0
ND1 A:HIS51 2.4 34.2 1.0
CD A:GLU48 3.2 38.1 1.0
CE1 A:HIS51 3.2 30.7 1.0
CD A:GLU15 3.2 42.4 1.0
CG A:HIS51 3.4 30.6 1.0
OE2 A:GLU15 3.4 52.5 1.0
OE2 A:GLU48 3.5 48.2 1.0
CB A:HIS51 3.8 26.5 1.0
NE2 A:HIS51 4.3 32.3 1.0
OE1 A:GLN127 4.4 33.8 1.0
CD2 A:HIS51 4.5 28.3 1.0
CG A:GLU48 4.5 29.9 1.0
CA A:GLU48 4.6 24.3 1.0
CG A:GLU15 4.6 34.6 1.0
OD1 A:ASN97 4.7 42.7 1.0
CB A:GLU48 4.8 24.7 1.0
O A:GLU48 5.0 31.2 1.0
OE1 A:GLN126 5.0 76.7 1.0

Iron binding site 2 out of 8 in 4ixk

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Iron binding site 2 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (2 H) 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 2 of Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:43.6
occ:0.45
OE1 D:GLU15 2.2 34.5 1.0
OE1 D:GLU48 2.2 48.7 1.0
O D:HOH301 2.3 45.2 1.0
ND1 D:HIS51 2.5 33.8 1.0
CD D:GLU15 3.1 39.1 1.0
CD D:GLU48 3.3 38.1 1.0
OE2 D:GLU15 3.3 46.8 1.0
CE1 D:HIS51 3.5 30.0 1.0
CG D:HIS51 3.5 33.5 1.0
OE2 D:GLU48 3.6 49.0 1.0
CB D:HIS51 3.8 28.4 1.0
O D:HOH340 3.9 38.6 1.0
OE1 D:GLN127 4.3 35.4 1.0
ND2 D:ASN97 4.4 34.8 1.0
CG D:GLU15 4.5 31.2 1.0
CA D:GLU48 4.5 27.0 1.0
CG D:GLU48 4.6 34.1 1.0
NE2 D:HIS51 4.6 33.8 1.0
CD2 D:HIS51 4.7 30.8 1.0
CB D:GLU48 4.8 27.3 1.0
CG D:ASN97 4.9 41.0 1.0
O D:GLU48 4.9 28.3 1.0
CB D:GLU15 4.9 26.3 1.0

Iron binding site 3 out of 8 in 4ixk

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Iron binding site 3 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (2 H) 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 Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:43.1
occ:0.45
O B:HOH302 2.2 50.6 1.0
OE1 B:GLU15 2.3 42.9 1.0
OE1 B:GLU48 2.3 41.0 1.0
ND1 B:HIS51 2.7 41.1 1.0
CD B:GLU15 3.2 38.3 1.0
CD B:GLU48 3.3 34.4 1.0
OE2 B:GLU15 3.3 38.0 1.0
CE1 B:HIS51 3.5 39.8 1.0
OE2 B:GLU48 3.6 56.0 1.0
CG B:HIS51 3.6 33.3 1.0
CB B:HIS51 3.9 28.2 1.0
O B:HOH301 4.1 36.7 1.0
OE1 B:GLN127 4.2 35.1 1.0
ND2 B:ASN97 4.3 32.1 1.0
CA B:GLU48 4.5 24.9 1.0
CG B:GLU48 4.6 28.7 1.0
OE1 B:GLN126 4.6 63.1 1.0
CG B:GLU15 4.6 25.7 1.0
NE2 B:HIS51 4.7 37.5 1.0
CD2 B:HIS51 4.7 36.2 1.0
CB B:GLU48 4.8 23.9 1.0
CG B:ASN97 4.8 32.2 1.0
O B:GLU48 5.0 23.2 1.0

Iron binding site 4 out of 8 in 4ixk

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Iron binding site 4 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (2 H) 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 4 of Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:45.7
occ:0.55
OE1 C:GLU48 2.1 53.1 1.0
OE1 C:GLU15 2.2 42.5 1.0
ND1 C:HIS51 2.5 41.3 1.0
CD C:GLU15 3.0 41.8 1.0
OE2 C:GLU15 3.1 46.5 1.0
CD C:GLU48 3.1 37.5 1.0
CE1 C:HIS51 3.4 42.3 1.0
OE2 C:GLU48 3.5 51.2 1.0
CG C:HIS51 3.5 34.4 1.0
CB C:HIS51 3.8 27.7 1.0
O C:HOH346 4.1 36.5 1.0
OE1 C:GLN127 4.3 35.4 1.0
CG C:GLU48 4.4 32.6 1.0
CG C:GLU15 4.4 32.0 1.0
CA C:GLU48 4.5 24.6 1.0
NE2 C:HIS51 4.6 40.7 1.0
ND2 C:ASN97 4.6 37.2 1.0
CD2 C:HIS51 4.7 34.8 1.0
CB C:GLU48 4.7 24.0 1.0
CG C:ASN97 4.9 38.9 1.0
O C:GLU48 4.9 29.6 1.0

Iron binding site 5 out of 8 in 4ixk

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Iron binding site 5 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (2 H) 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 Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:44.6
occ:0.50
OE1 E:GLU15 2.2 50.3 1.0
OE1 E:GLU48 2.2 41.4 1.0
ND1 E:HIS51 2.8 37.8 1.0
CD E:GLU15 3.0 43.1 1.0
OE2 E:GLU15 3.1 54.1 1.0
CD E:GLU48 3.2 41.1 1.0
OE2 E:GLU48 3.5 51.0 1.0
CE1 E:HIS51 3.7 38.6 1.0
CG E:HIS51 3.8 40.3 1.0
CB E:HIS51 3.9 30.8 1.0
ND2 E:ASN97 4.3 27.4 1.0
OE1 E:GLN127 4.4 35.5 1.0
CG E:GLU15 4.5 29.0 1.0
CG E:GLU48 4.6 34.8 1.0
CA E:GLU48 4.6 25.8 1.0
CG E:ASN97 4.7 30.4 1.0
O E:HOH301 4.8 51.8 1.0
CB E:GLU48 4.9 27.0 1.0
NE2 E:HIS51 4.9 37.3 1.0
CD2 E:HIS51 4.9 32.9 1.0
CB E:ASN97 5.0 25.7 1.0
CB E:GLU15 5.0 26.2 1.0

Iron binding site 6 out of 8 in 4ixk

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Iron binding site 6 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (2 H) 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 Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:46.4
occ:0.50
OE1 F:GLU48 2.2 46.7 1.0
OE1 F:GLU15 2.3 48.2 1.0
O F:HOH302 2.5 45.3 1.0
ND1 F:HIS51 2.6 38.4 1.0
CD F:GLU48 3.2 36.7 1.0
CD F:GLU15 3.4 43.8 1.0
CE1 F:HIS51 3.5 38.0 1.0
OE2 F:GLU48 3.5 45.9 1.0
CG F:HIS51 3.6 38.0 1.0
OE2 F:GLU15 3.7 52.9 1.0
CB F:HIS51 3.8 30.3 1.0
O F:HOH301 4.0 37.3 1.0
OE1 F:GLN127 4.3 33.7 1.0
CA F:GLU48 4.4 26.6 1.0
ND2 F:ASN97 4.5 31.2 1.0
CG F:GLU48 4.5 34.9 1.0
NE2 F:HIS51 4.6 42.7 1.0
CD2 F:HIS51 4.7 36.8 1.0
CG F:GLU15 4.7 29.7 1.0
CB F:GLU48 4.7 27.4 1.0
O F:GLU48 4.9 26.4 1.0
CG F:ASN97 4.9 37.8 1.0
CB F:GLU15 4.9 24.2 1.0

Iron binding site 7 out of 8 in 4ixk

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Iron binding site 7 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (2 H) 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 Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:44.0
occ:0.50
OE1 G:GLU15 2.1 41.8 1.0
OE1 G:GLU48 2.1 39.9 1.0
ND1 G:HIS51 2.5 39.5 1.0
CD G:GLU15 3.1 38.9 1.0
CD G:GLU48 3.2 39.0 1.0
CE1 G:HIS51 3.3 39.1 1.0
OE2 G:GLU15 3.4 44.1 1.0
CG G:HIS51 3.5 35.9 1.0
OE2 G:GLU48 3.6 44.6 1.0
O G:HOH302 3.9 41.7 1.0
CB G:HIS51 3.9 28.9 1.0
OE1 G:GLN127 4.3 29.7 1.0
ND2 G:ASN97 4.4 35.0 1.0
CG G:GLU48 4.5 32.3 1.0
NE2 G:HIS51 4.5 37.3 1.0
CA G:GLU48 4.5 24.0 1.0
CG G:GLU15 4.5 29.1 1.0
CD2 G:HIS51 4.6 31.0 1.0
CG G:ASN97 4.6 33.4 1.0
CB G:GLU48 4.7 26.3 1.0
O G:HOH301 4.7 44.9 1.0
O G:GLU48 4.9 25.9 1.0
CB G:GLU15 4.9 26.9 1.0

Iron binding site 8 out of 8 in 4ixk

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Iron binding site 8 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (2 H) 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 Anaerobic Crystal Structure of Iron Soaked (2 H) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:43.9
occ:0.65
OE1 H:GLU15 2.1 43.3 1.0
OE1 H:GLU48 2.2 52.1 1.0
O H:HOH301 2.2 43.0 1.0
ND1 H:HIS51 2.6 38.3 1.0
CD H:GLU15 3.1 37.7 1.0
CD H:GLU48 3.2 36.7 1.0
OE2 H:GLU15 3.4 48.2 1.0
CE1 H:HIS51 3.4 36.2 1.0
OE2 H:GLU48 3.5 48.6 1.0
CG H:HIS51 3.7 35.1 1.0
CB H:HIS51 4.0 28.9 1.0
OE1 H:GLN127 4.3 29.6 1.0
CG H:GLU15 4.5 29.1 1.0
ND2 H:ASN97 4.5 45.2 1.0
CG H:GLU48 4.6 33.5 1.0
NE2 H:HIS51 4.6 37.3 1.0
CA H:GLU48 4.6 26.9 1.0
CD2 H:HIS51 4.7 36.5 1.0
CG H:ASN97 4.8 45.3 1.0
CB H:GLU48 4.8 26.9 1.0
CB H:GLU15 5.0 25.0 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: Sun Dec 13 15:38:00 2020

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