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Iron in PDB 4itt: Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries

Protein crystallography data

The structure of Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries, PDB code: 4itt 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) 42.55 / 2.10
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 175.283, 175.283, 175.283, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.5

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 4itt

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Iron binding site 1 out of 6 in the Crystal Structure of Iron Soaked (5 Min) 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 Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:34.7
occ:0.40
OE2 D:GLU48 2.1 41.6 1.0
OE2 D:GLU94 2.4 27.2 1.0
O D:HOH399 2.5 36.8 1.0
CD D:GLU48 2.9 32.1 1.0
OE1 D:GLU44 3.0 50.1 1.0
OE2 D:GLU130 3.1 46.7 1.0
CD D:GLU94 3.3 23.8 1.0
OE1 D:GLU94 3.5 22.4 1.0
CD D:GLU130 3.6 43.3 1.0
OE1 D:GLU48 3.6 45.8 1.0
CG D:GLU48 3.7 27.5 1.0
CG D:GLU130 3.9 37.0 1.0
OH D:TYR22 3.9 18.4 1.0
CD D:GLU44 4.0 47.7 1.0
CE1 D:TYR22 4.1 15.3 1.0
CZ D:TYR22 4.3 17.0 1.0
ND2 D:ASN97 4.4 27.7 1.0
OE1 D:GLU130 4.5 39.1 1.0
CG D:GLU94 4.6 21.1 1.0
OE2 D:GLU44 4.7 60.4 1.0
CB D:GLU130 4.8 27.8 1.0
CE1 D:HIS51 4.8 29.2 1.0
CG D:GLU44 4.9 39.4 1.0
OE1 D:GLN127 4.9 26.5 1.0

Iron binding site 2 out of 6 in 4itt

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Iron binding site 2 out of 6 in the Crystal Structure of Iron Soaked (5 Min) 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 Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:37.1
occ:0.45
OE2 B:GLU48 1.9 49.2 1.0
OE2 B:GLU94 2.4 24.5 1.0
O B:HOH386 2.8 50.9 1.0
OE1 B:GLU44 2.8 43.9 1.0
CD B:GLU48 3.0 32.1 1.0
OE1 B:GLU130 3.2 60.5 1.0
CD B:GLU94 3.2 29.4 1.0
OE1 B:GLU94 3.4 26.8 1.0
CD B:GLU130 3.6 44.1 1.0
OE1 B:GLU47 3.8 73.2 1.0
OE1 B:GLU48 3.8 39.0 1.0
CD B:GLU44 3.9 44.2 1.0
CG B:GLU130 3.9 37.4 1.0
CG B:GLU48 3.9 29.1 1.0
OH B:TYR22 4.0 22.1 1.0
O B:HOH398 4.1 60.2 1.0
CE1 B:TYR22 4.2 20.1 1.0
OE2 B:GLU44 4.4 54.3 1.0
CZ B:TYR22 4.4 21.8 1.0
OE2 B:GLU130 4.4 53.4 1.0
ND2 B:ASN97 4.5 28.2 1.0
CG B:GLU94 4.6 27.8 1.0
CB B:GLU130 4.7 27.2 1.0
OE1 B:GLN127 4.7 25.6 1.0
CD B:GLU47 4.8 59.3 1.0
CE1 B:HIS51 4.8 37.0 1.0

Iron binding site 3 out of 6 in 4itt

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Iron binding site 3 out of 6 in the Crystal Structure of Iron Soaked (5 Min) 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 (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:39.1
occ:0.50
OE2 C:GLU48 2.3 38.9 1.0
OE2 C:GLU94 2.4 26.0 1.0
OE1 C:GLU44 2.9 47.5 1.0
OE2 C:GLU130 2.9 47.1 1.0
CD C:GLU48 3.0 34.0 1.0
CD C:GLU94 3.3 25.7 1.0
OE1 C:GLU94 3.5 25.2 1.0
CD C:GLU130 3.6 41.3 1.0
OE1 C:GLU48 3.7 43.5 1.0
CG C:GLU48 3.9 28.8 1.0
OH C:TYR22 3.9 19.4 1.0
CD C:GLU44 4.0 43.2 1.0
CE1 C:TYR22 4.0 17.1 1.0
CG C:GLU130 4.0 38.8 1.0
O C:HOH311 4.2 45.8 1.0
CZ C:TYR22 4.3 18.7 1.0
O C:HOH395 4.5 42.5 1.0
OE1 C:GLU130 4.6 42.4 1.0
OE2 C:GLU44 4.6 45.5 1.0
CG C:GLU94 4.6 23.3 1.0
ND2 C:ASN97 4.7 35.1 1.0
CB C:GLU130 4.7 27.2 1.0
OE1 C:GLN127 4.8 23.9 1.0

Iron binding site 4 out of 6 in 4itt

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Iron binding site 4 out of 6 in the Crystal Structure of Iron Soaked (5 Min) 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 (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:41.7
occ:0.50
OE2 E:GLU48 2.0 41.3 1.0
O E:HOH387 2.3 30.0 1.0
OE2 E:GLU94 2.6 30.3 1.0
OE1 E:GLU44 2.8 45.9 1.0
CD E:GLU48 3.1 32.2 1.0
OE1 E:GLU130 3.4 57.3 1.0
CD E:GLU94 3.4 28.1 1.0
CG E:GLU130 3.4 43.7 1.0
CD E:GLU130 3.4 50.3 1.0
OE1 E:GLU94 3.5 26.0 1.0
CD E:GLU44 3.9 46.4 1.0
CG E:GLU48 3.9 28.9 1.0
OE1 E:GLU48 4.0 35.1 1.0
OH E:TYR22 4.2 21.9 1.0
OE2 E:GLU130 4.2 43.1 1.0
CE1 E:TYR22 4.3 18.1 1.0
OE2 E:GLU44 4.4 53.7 1.0
CZ E:TYR22 4.6 17.1 1.0
CE1 E:HIS51 4.6 30.5 1.0
CB E:GLU130 4.7 29.4 1.0
ND2 E:ASN97 4.7 26.0 1.0
OE1 E:GLN127 4.8 26.7 1.0
CG E:GLU94 4.8 26.2 1.0
ND1 E:HIS51 4.9 30.6 1.0

Iron binding site 5 out of 6 in 4itt

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Iron binding site 5 out of 6 in the Crystal Structure of Iron Soaked (5 Min) 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 (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:37.0
occ:0.45
OE2 G:GLU48 2.1 39.6 1.0
O G:HOH404 2.3 43.2 1.0
OE2 G:GLU94 2.4 25.8 1.0
O G:HOH411 2.7 44.8 1.0
OE1 G:GLU44 2.7 45.2 1.0
CD G:GLU48 3.1 31.1 1.0
CD G:GLU94 3.3 23.3 1.0
OE1 G:GLU130 3.4 47.1 1.0
OE1 G:GLU94 3.6 24.1 1.0
CD G:GLU130 3.7 40.2 1.0
OH G:TYR22 3.9 16.3 1.0
OE1 G:GLU48 3.9 34.6 1.0
CD G:GLU44 3.9 43.5 1.0
CG G:GLU130 3.9 33.8 1.0
OE2 G:GLU47 4.0 62.2 1.0
CG G:GLU48 4.0 28.6 1.0
CE1 G:TYR22 4.2 14.6 1.0
O G:HOH405 4.2 46.0 1.0
CZ G:TYR22 4.4 16.1 1.0
OE2 G:GLU130 4.5 54.2 1.0
CE1 G:HIS51 4.6 32.9 1.0
CB G:GLU130 4.6 25.9 1.0
CG G:GLU94 4.7 21.1 1.0
O G:HOH412 4.7 53.0 1.0
OE2 G:GLU44 4.8 48.2 1.0
ND2 G:ASN97 4.8 14.2 0.5
CG G:GLU44 4.8 32.4 1.0
OE1 G:GLN127 4.9 21.2 1.0
CD G:GLU47 4.9 53.8 1.0

Iron binding site 6 out of 6 in 4itt

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Iron binding site 6 out of 6 in the Crystal Structure of Iron Soaked (5 Min) 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 (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:46.6
occ:0.50
OE2 H:GLU94 2.5 26.9 1.0
OE1 H:GLU48 2.8 36.1 1.0
OE2 H:GLU48 2.9 46.0 1.0
CD H:GLU48 2.9 32.0 1.0
OE1 H:GLU44 3.1 47.5 1.0
CD H:GLU94 3.3 25.2 1.0
OE1 H:GLU94 3.5 23.4 1.0
OE1 H:GLU130 3.8 51.2 1.0
CG H:GLU48 3.9 31.4 1.0
CD H:GLU130 3.9 46.3 1.0
CD H:GLU44 4.0 46.9 1.0
OH H:TYR22 4.0 20.8 1.0
CE1 H:TYR22 4.1 19.8 1.0
CG H:GLU130 4.2 35.1 1.0
OE2 H:GLU44 4.2 57.8 1.0
CZ H:TYR22 4.4 21.9 1.0
ND2 H:ASN97 4.4 43.3 1.0
OE2 H:GLU130 4.5 57.6 1.0
O H:HOH313 4.5 38.6 1.0
OE1 H:GLN127 4.6 23.0 1.0
CG H:GLU94 4.7 21.7 1.0
CE1 H:HIS51 4.7 26.1 1.0
CB H:GLU130 4.8 25.7 1.0
ND1 H:HIS51 4.9 31.8 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 04:14:59 2024

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