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

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

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 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 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 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 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 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 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 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 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 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

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