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Iron in PDB 4itw: Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries

Protein crystallography data

The structure of Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries, PDB code: 4itw 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) 48.52 / 2.00
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 174.767, 174.767, 174.767, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.5

Iron Binding Sites:

The binding sites of Iron atom in the Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries (pdb code 4itw). 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 (75 Min) Ferritin From Pseudo-Nitzschia Multiseries, PDB code: 4itw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4itw

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Iron binding site 1 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (75 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 Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:41.6
occ:0.50
 O A:HOH394 2.0 37.7 1.0
OE1 A:GLU48 2.2 39.6 1.0
OE1 A:GLU15 2.3 33.5 1.0
O A:HOH388 2.5 54.4 1.0
ND1 A:HIS51 2.6 37.2 1.0
CD A:GLU15 3.2 35.8 1.0
CD A:GLU48 3.2 38.2 1.0
OE2 A:GLU15 3.3 42.8 1.0
CE1 A:HIS51 3.4 33.0 1.0
CG A:HIS51 3.5 33.5 1.0
OE2 A:GLU48 3.6 43.4 1.0
O A:HOH380 3.7 32.8 1.0
CB A:HIS51 3.8 26.5 1.0
OE1 A:GLN127 4.2 37.1 1.0
OD1 A:ASN97 4.3 49.6 1.0
CG A:GLU48 4.5 30.4 1.0
NE2 A:HIS51 4.6 37.5 1.0
CG A:GLU15 4.6 29.3 1.0
CD2 A:HIS51 4.6 30.4 1.0
CA A:GLU48 4.7 24.9 1.0
CG A:ASN97 4.7 44.9 1.0
O A:HOH352 4.7 51.6 1.0
CB A:GLU48 4.8 27.5 1.0
CB A:GLU15 5.0 26.5 1.0
O A:GLU48 5.0 26.6 1.0

Iron binding site 2 out of 8 in 4itw

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Iron binding site 2 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (75 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 Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:42.3
occ:0.50
 OE1 D:GLU48 2.1 50.0 1.0
OE1 D:GLU15 2.2 29.6 1.0
O D:HOH409 2.2 32.7 1.0
O D:HOH414 2.6 37.2 1.0
ND1 D:HIS51 2.8 32.9 1.0
CD D:GLU48 3.1 38.5 1.0
CD D:GLU15 3.2 33.2 1.0
OE2 D:GLU15 3.4 39.8 1.0
OE2 D:GLU48 3.5 41.6 1.0
CE1 D:HIS51 3.8 30.6 1.0
CG D:HIS51 3.8 27.8 1.0
O D:HOH380 3.9 29.9 1.0
CB D:HIS51 4.0 23.9 1.0
ND2 D:ASN97 4.1 37.5 1.0
OE1 D:GLN127 4.2 29.8 1.0
CG D:GLU48 4.5 29.3 1.0
CA D:GLU48 4.6 22.3 1.0
CG D:ASN97 4.6 38.9 1.0
CG D:GLU15 4.6 22.7 1.0
O D:HOH331 4.7 41.6 1.0
CB D:GLU48 4.7 25.5 1.0
NE2 D:HIS51 4.9 35.1 1.0
CB D:ASN97 4.9 32.1 1.0
CD2 D:HIS51 4.9 28.1 1.0
CB D:GLU15 5.0 20.7 1.0
O D:GLU48 5.0 22.6 1.0

Iron binding site 3 out of 8 in 4itw

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Iron binding site 3 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (75 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 Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:42.6
occ:0.50
 O B:HOH410 2.1 44.8 1.0
OE1 B:GLU48 2.3 38.1 1.0
OE1 B:GLU15 2.3 34.7 1.0
ND1 B:HIS51 2.8 40.3 1.0
CD B:GLU48 3.2 33.6 1.0
CD B:GLU15 3.2 34.4 1.0
OE2 B:GLU15 3.4 40.9 1.0
OE2 B:GLU48 3.5 45.8 1.0
CE1 B:HIS51 3.6 39.7 1.0
CG B:HIS51 3.8 30.1 1.0
CB B:HIS51 4.0 25.5 1.0
O B:HOH335 4.1 38.3 1.0
OE1 B:GLN127 4.2 32.7 1.0
ND2 B:ASN97 4.3 34.4 1.0
O B:HOH357 4.5 38.7 1.0
CG B:GLU48 4.5 28.4 1.0
CA B:GLU48 4.6 23.4 1.0
CG B:ASN97 4.6 32.0 1.0
CG B:GLU15 4.7 24.9 1.0
CB B:GLU48 4.7 23.6 1.0
NE2 B:HIS51 4.8 36.4 1.0
CB B:ASN97 4.8 29.3 1.0
CD2 B:HIS51 4.9 33.8 1.0

Iron binding site 4 out of 8 in 4itw

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Iron binding site 4 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (75 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 Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:44.7
occ:0.50
 OE1 C:GLU48 2.0 44.2 1.0
O C:HOH395 2.1 42.3 1.0
OE1 C:GLU15 2.2 37.3 1.0
ND1 C:HIS51 2.6 41.6 1.0
CD C:GLU15 3.1 37.6 1.0
CD C:GLU48 3.2 40.4 1.0
OE2 C:GLU15 3.3 45.5 1.0
CG C:HIS51 3.5 32.4 1.0
CE1 C:HIS51 3.6 40.0 1.0
OE2 C:GLU48 3.7 45.2 1.0
CB C:HIS51 3.7 25.6 1.0
O C:HOH380 4.0 35.4 1.0
OE1 C:GLN127 4.4 31.5 1.0
CG C:GLU48 4.4 31.8 1.0
CA C:GLU48 4.5 25.1 1.0
CG C:GLU15 4.5 30.0 1.0
ND2 C:ASN97 4.6 43.6 1.0
CB C:GLU48 4.6 26.3 1.0
NE2 C:HIS51 4.7 43.1 1.0
CD2 C:HIS51 4.7 33.7 1.0
O C:HOH347 4.8 38.5 1.0
CG C:ASN97 4.9 47.1 1.0
O C:GLU48 4.9 25.4 1.0
CB C:GLU15 5.0 26.4 1.0

Iron binding site 5 out of 8 in 4itw

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Iron binding site 5 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (75 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 Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:40.1
occ:0.45
 OE1 E:GLU15 2.1 37.4 1.0
OE1 E:GLU48 2.3 38.4 1.0
ND1 E:HIS51 2.9 35.9 1.0
O E:HOH400 3.0 39.1 1.0
CD E:GLU15 3.0 40.9 1.0
OE2 E:GLU15 3.2 46.7 1.0
CD E:GLU48 3.2 35.8 1.0
OE2 E:GLU48 3.4 44.7 1.0
CG E:HIS51 3.8 37.1 1.0
CE1 E:HIS51 3.9 34.5 1.0
CB E:HIS51 4.0 28.1 1.0
O E:HOH365 4.1 27.2 1.0
ND2 E:ASN97 4.1 35.1 1.0
OE1 E:GLN127 4.3 31.7 1.0
CG E:ASN97 4.5 33.4 1.0
CG E:GLU15 4.5 30.2 1.0
O E:HOH416 4.5 40.0 1.0
CG E:GLU48 4.6 28.0 1.0
CA E:GLU48 4.7 24.7 1.0
CB E:ASN97 4.7 29.8 1.0
CB E:GLU48 4.9 26.8 1.0
CB E:GLU15 5.0 27.5 1.0
NE2 E:HIS51 5.0 35.5 1.0
CD2 E:HIS51 5.0 33.4 1.0

Iron binding site 6 out of 8 in 4itw

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Iron binding site 6 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (75 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 Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:45.8
occ:0.40
 O F:HOH398 2.1 43.0 1.0
OE1 F:GLU15 2.2 37.8 1.0
OE1 F:GLU48 2.2 44.0 1.0
ND1 F:HIS51 2.5 40.4 1.0
O F:HOH375 2.6 44.5 1.0
CD F:GLU48 3.1 36.0 1.0
CD F:GLU15 3.1 38.8 1.0
OE2 F:GLU48 3.3 39.0 1.0
OE2 F:GLU15 3.3 48.3 1.0
CE1 F:HIS51 3.3 36.7 1.0
CG F:HIS51 3.6 34.0 1.0
O F:HOH387 3.9 46.8 1.0
CB F:HIS51 3.9 27.9 1.0
O F:HOH324 4.0 36.1 1.0
ND2 F:ASN97 4.2 34.9 1.0
OE1 F:GLN127 4.3 31.8 1.0
CG F:GLU48 4.4 29.9 1.0
CA F:GLU48 4.5 23.6 1.0
NE2 F:HIS51 4.5 40.2 1.0
CG F:GLU15 4.5 27.5 1.0
O F:HOH376 4.6 38.8 1.0
CG F:ASN97 4.7 38.0 1.0
CD2 F:HIS51 4.7 35.2 1.0
CB F:GLU48 4.7 25.9 1.0
CB F:ASN97 4.9 31.6 1.0
CB F:GLU15 4.9 23.9 1.0

Iron binding site 7 out of 8 in 4itw

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Iron binding site 7 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (75 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 7 of Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:38.4
occ:0.50
 O G:HOH338 2.1 40.1 1.0
OE1 G:GLU15 2.2 30.3 1.0
OE1 G:GLU48 2.2 33.3 1.0
ND1 G:HIS51 2.6 27.7 1.0
CD G:GLU48 3.2 34.3 1.0
CD G:GLU15 3.2 34.4 1.0
CE1 G:HIS51 3.4 27.9 1.0
OE2 G:GLU15 3.5 41.6 1.0
OE2 G:GLU48 3.6 42.1 1.0
CG G:HIS51 3.6 24.8 1.0
O G:HOH320 3.9 31.2 1.0
CB G:HIS51 4.0 20.3 1.0
OE1 G:GLN127 4.2 26.4 1.0
ND2 G:ASN97 4.2 36.6 1.0
CG G:GLU48 4.5 28.0 1.0
CG G:ASN97 4.5 35.1 1.0
NE2 G:HIS51 4.5 29.4 1.0
CA G:GLU48 4.6 21.1 1.0
CG G:GLU15 4.6 25.4 1.0
O G:HOH382 4.6 36.2 1.0
CD2 G:HIS51 4.7 24.3 1.0
CB G:GLU48 4.7 22.6 1.0
CB G:ASN97 4.9 31.0 1.0
CB G:GLU15 5.0 21.0 1.0
OD1 G:ASN97 5.0 35.8 1.0
O G:GLU48 5.0 20.1 1.0
CD G:GLN127 5.0 26.1 1.0

Iron binding site 8 out of 8 in 4itw

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Iron binding site 8 out of 8 in the Anaerobic Crystal Structure of Iron Soaked (75 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 8 of Anaerobic Crystal Structure of Iron Soaked (75 Min) Ferritin From Pseudo-Nitzschia Multiseries within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:35.4
occ:0.50
 O H:HOH389 2.0 39.1 1.0
OE1 H:GLU48 2.2 45.8 1.0
OE1 H:GLU15 2.2 33.3 1.0
ND1 H:HIS51 2.7 35.2 1.0
ND2 H:ASN97 3.1 31.2 0.5
CD H:GLU48 3.2 32.3 1.0
CD H:GLU15 3.2 34.1 1.0
OE2 H:GLU48 3.5 39.0 1.0
OE2 H:GLU15 3.5 39.0 1.0
CE1 H:HIS51 3.5 30.2 1.0
O H:HOH337 3.6 29.3 1.0
CG H:HIS51 3.6 31.0 1.0
CB H:HIS51 3.9 23.7 1.0
OE1 H:GLN127 4.2 28.7 1.0
ND2 H:ASN97 4.3 31.8 0.5
CG H:ASN97 4.4 31.3 0.5
CG H:GLU48 4.5 29.8 1.0
CG H:GLU15 4.6 24.3 1.0
NE2 H:HIS51 4.7 36.5 1.0
CA H:GLU48 4.7 24.8 1.0
O H:HOH366 4.7 50.8 1.0
CD2 H:HIS51 4.7 27.6 1.0
CG H:ASN97 4.8 33.2 0.5
CB H:GLU48 4.9 27.3 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 04:15:01 2024

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