Iron in PDB 2jd8: Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus

The structure of Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus, PDB code: 2jd8 was solved by J.Tatur, W.R.Hagen, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	204.12 / 2.80
Space group	C 2 2 21 2
Cell size a, b, c (Å), α, β, γ (°)	255.371, 342.055, 265.986, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.1

The structure of Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus also contains other interesting chemical elements:

Zinc

(Zn)

72 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus (pdb code 2jd8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus, PDB code: 2jd8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe203 b:30.4 occ:0.50 OE1 0:GLU129 2.0 50.5 1.0 OE2 0:GLU130 2.1 39.5 1.0 OE1 0:GLU49 2.3 41.9 1.0 OE1 0:GLU126 2.3 41.0 1.0 CD 0:GLU129 3.0 48.0 1.0 CD 0:GLU49 3.0 38.3 1.0 OE2 0:GLU49 3.1 35.4 1.0 OE2 0:GLU129 3.2 46.6 1.0 CD 0:GLU130 3.3 39.4 1.0 CD 0:GLU126 3.4 38.3 1.0 OE2 0:GLU126 3.8 36.8 1.0 CG 0:GLU130 3.9 35.0 1.0 OE1 0:GLU130 4.3 42.8 1.0 CG 0:GLU129 4.4 38.2 1.0 CG 0:GLU49 4.5 32.5 1.0 N 0:GLU130 4.6 28.1 1.0 CG 0:GLU126 4.7 27.7 1.0 CA 0:GLU130 4.7 27.8 1.0 CB 0:GLU129 4.9 29.7 1.0 O 0:GLU126 4.9 27.9 1.0 CB 0:GLU130 4.9 28.1 1.0 NE2 0:HIS53 5.0 29.4 1.0

Iron binding site 2 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 1:Fe203 b:44.0 occ:0.50 OE2 1:GLU130 1.9 39.5 1.0 OE1 1:GLU129 2.0 50.6 1.0 OE1 1:GLU49 2.4 42.4 1.0 OE1 1:GLU126 2.5 39.8 1.0 CD 1:GLU129 3.0 48.3 1.0 CD 1:GLU49 3.1 38.1 1.0 OE2 1:GLU49 3.1 35.3 1.0 CD 1:GLU130 3.2 39.1 1.0 OE2 1:GLU129 3.3 47.1 1.0 CD 1:GLU126 3.6 38.2 1.0 CG 1:GLU130 4.1 34.6 1.0 OE2 1:GLU126 4.1 36.4 1.0 OE1 1:GLU130 4.1 42.9 1.0 CG 1:GLU129 4.4 38.2 1.0 CG 1:GLU49 4.6 32.5 1.0 N 1:GLU130 4.7 28.5 1.0 CA 1:GLU130 4.7 28.4 1.0 NE2 1:GLN46 4.8 31.6 1.0 CG 1:GLU126 4.8 28.6 1.0 CB 1:GLU129 4.9 28.9 1.0 CB 1:GLU130 5.0 28.5 1.0

Iron binding site 3 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 2:Fe203 b:46.1 occ:0.50 OE1 2:GLU129 1.9 50.1 1.0 OE2 2:GLU130 2.0 39.0 1.0 OE1 2:GLU126 2.3 40.6 1.0 OE1 2:GLU49 2.3 42.1 1.0 CD 2:GLU129 2.9 48.1 1.0 CD 2:GLU49 3.1 37.7 1.0 OE2 2:GLU49 3.2 35.6 1.0 CD 2:GLU130 3.2 39.0 1.0 OE2 2:GLU129 3.3 47.0 1.0 CD 2:GLU126 3.4 38.1 1.0 CG 2:GLU130 3.9 34.6 1.0 OE2 2:GLU126 3.9 35.7 1.0 OE1 2:GLU130 4.2 42.9 1.0 CG 2:GLU129 4.3 38.1 1.0 CG 2:GLU49 4.5 32.4 1.0 CG 2:GLU126 4.6 27.7 1.0 CA 2:GLU130 4.7 28.0 1.0 N 2:GLU130 4.7 27.8 1.0 O 2:GLU126 4.8 26.8 1.0 CB 2:GLU130 4.9 28.8 1.0 CB 2:GLU129 4.9 29.1 1.0

Iron binding site 4 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 3:Fe203 b:31.0 occ:0.50 OE2 3:GLU130 1.9 40.3 1.0 OE1 3:GLU129 2.1 50.3 1.0 OE1 3:GLU49 2.2 42.0 1.0 OE1 3:GLU126 2.3 40.0 1.0 OE2 3:GLU49 2.8 35.7 1.0 CD 3:GLU49 2.9 38.0 1.0 CD 3:GLU129 3.1 48.3 1.0 CD 3:GLU130 3.1 39.1 1.0 OE2 3:GLU129 3.4 47.1 1.0 CD 3:GLU126 3.4 38.1 1.0 CG 3:GLU130 3.8 34.4 1.0 OE2 3:GLU126 4.0 35.8 1.0 OE1 3:GLU130 4.2 42.1 1.0 CG 3:GLU49 4.4 32.2 1.0 CG 3:GLU129 4.5 38.6 1.0 N 3:GLU130 4.6 28.0 1.0 CA 3:GLU130 4.6 27.7 1.0 CG 3:GLU126 4.6 28.9 1.0 CB 3:GLU130 4.8 28.5 1.0 O 3:GLU126 4.8 27.5 1.0 NE2 3:HIS53 4.9 28.7 1.0 CB 3:GLU129 5.0 29.3 1.0 CE1 3:HIS53 5.0 26.8 1.0

Iron binding site 5 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 4:Fe203 b:39.9 occ:0.50 OE2 4:GLU130 2.0 39.4 1.0 OE1 4:GLU129 2.0 50.5 1.0 OE1 4:GLU49 2.2 41.7 1.0 OE1 4:GLU126 2.4 40.2 1.0 CD 4:GLU49 2.8 38.2 1.0 OE2 4:GLU49 2.9 35.5 1.0 CD 4:GLU129 3.0 48.4 1.0 CD 4:GLU130 3.2 39.0 1.0 OE2 4:GLU129 3.2 46.4 1.0 CD 4:GLU126 3.6 38.0 1.0 CG 4:GLU130 3.9 34.9 1.0 OE2 4:GLU126 4.2 36.2 1.0 OE1 4:GLU130 4.2 43.0 1.0 CG 4:GLU49 4.3 32.6 1.0 CG 4:GLU129 4.4 37.7 1.0 N 4:GLU130 4.7 28.3 1.0 CG 4:GLU126 4.8 27.9 1.0 CA 4:GLU130 4.8 28.0 1.0 NE2 4:GLN46 4.9 31.1 1.0 CB 4:GLU129 4.9 29.6 1.0 CB 4:GLU130 5.0 28.6 1.0

Iron binding site 6 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 5:Fe203 b:47.5 occ:0.50 OE2 5:GLU130 1.9 39.8 1.0 OE1 5:GLU129 2.0 50.3 1.0 OE1 5:GLU126 2.5 40.2 1.0 OE1 5:GLU49 2.5 42.3 1.0 CD 5:GLU129 3.0 47.8 1.0 OE2 5:GLU49 3.0 36.0 1.0 CD 5:GLU130 3.1 39.3 1.0 CD 5:GLU49 3.1 38.5 1.0 OE2 5:GLU129 3.2 47.0 1.0 CD 5:GLU126 3.7 38.2 1.0 CG 5:GLU130 3.8 35.1 1.0 OE1 5:GLU130 4.1 42.5 1.0 OE2 5:GLU126 4.3 35.9 1.0 CG 5:GLU129 4.4 38.3 1.0 CA 5:GLU130 4.5 28.3 1.0 CG 5:GLU49 4.6 32.3 1.0 N 5:GLU130 4.6 28.2 1.0 CB 5:GLU130 4.8 29.2 1.0 CG 5:GLU126 4.9 27.6 1.0 CB 5:GLU129 5.0 29.5 1.0

Iron binding site 7 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 6:Fe203 b:44.3 occ:0.50 OE2 6:GLU130 2.0 40.0 1.0 OE1 6:GLU129 2.0 50.1 1.0 OE1 6:GLU49 2.3 42.0 1.0 OE1 6:GLU126 2.4 41.0 1.0 CD 6:GLU129 2.9 48.0 1.0 CD 6:GLU49 2.9 38.1 1.0 OE2 6:GLU49 3.0 36.1 1.0 OE2 6:GLU129 3.1 46.6 1.0 CD 6:GLU130 3.2 39.4 1.0 CD 6:GLU126 3.6 38.6 1.0 CG 6:GLU130 4.0 35.2 1.0 OE1 6:GLU130 4.1 42.9 1.0 OE2 6:GLU126 4.2 35.6 1.0 CG 6:GLU49 4.3 32.0 1.0 CG 6:GLU129 4.4 38.5 1.0 CG 6:GLU126 4.8 28.2 1.0 CA 6:GLU130 4.8 28.4 1.0 N 6:GLU130 4.9 28.1 1.0 CB 6:GLU130 5.0 28.7 1.0

Iron binding site 8 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 7:Fe203 b:33.4 occ:0.50 OE1 7:GLU129 1.9 50.0 1.0 OE2 7:GLU130 2.0 40.1 1.0 OE1 7:GLU126 2.0 39.3 1.0 OE1 7:GLU49 2.2 41.7 1.0 CD 7:GLU129 3.0 48.3 1.0 CD 7:GLU49 3.1 38.0 1.0 CD 7:GLU126 3.1 37.8 1.0 CD 7:GLU130 3.1 39.2 1.0 OE2 7:GLU49 3.3 35.6 1.0 OE2 7:GLU129 3.4 47.3 1.0 OE2 7:GLU126 3.6 36.5 1.0 CG 7:GLU130 3.8 34.5 1.0 OE1 7:GLU130 4.2 42.6 1.0 CG 7:GLU129 4.3 38.3 1.0 CG 7:GLU126 4.4 28.0 1.0 CG 7:GLU49 4.5 32.7 1.0 N 7:GLU130 4.5 28.8 1.0 CA 7:GLU130 4.6 27.9 1.0 O 7:GLU126 4.8 27.3 1.0 NE2 7:HIS53 4.8 29.4 1.0 CB 7:GLU130 4.8 28.2 1.0 CB 7:GLU129 4.8 29.0 1.0 CE1 7:HIS53 4.9 26.6 1.0

Iron binding site 9 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 8:Fe203 b:34.9 occ:0.50 OE2 8:GLU130 1.8 39.3 1.0 OE1 8:GLU129 2.0 50.0 1.0 OE1 8:GLU126 2.1 40.6 1.0 OE1 8:GLU49 2.4 41.2 1.0 CD 8:GLU130 2.9 38.6 1.0 CD 8:GLU129 3.0 48.2 1.0 CD 8:GLU49 3.2 37.5 1.0 OE2 8:GLU49 3.2 35.2 1.0 CD 8:GLU126 3.3 38.1 1.0 OE2 8:GLU129 3.4 47.1 1.0 CG 8:GLU130 3.5 34.8 1.0 OE2 8:GLU126 3.9 35.9 1.0 OE1 8:GLU130 4.0 41.9 1.0 CA 8:GLU130 4.4 27.9 1.0 N 8:GLU130 4.4 28.0 1.0 CG 8:GLU126 4.4 28.2 1.0 CG 8:GLU129 4.4 38.6 1.0 CB 8:GLU130 4.5 28.6 1.0 CG 8:GLU49 4.6 32.3 1.0 O 8:GLU126 4.6 25.8 1.0 CB 8:GLU129 4.8 29.1 1.0 NE2 8:HIS53 4.9 28.5 1.0 C 8:GLU129 4.9 28.3 1.0 CE1 8:HIS53 4.9 26.8 1.0

Iron binding site 10 out of 36 in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus


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 the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe203 b:43.6 occ:0.50 OE1 9:GLU129 1.9 50.2 1.0 OE2 9:GLU130 2.0 39.9 1.0 OE1 9:GLU49 2.3 41.2 1.0 OE1 9:GLU126 2.4 40.8 1.0 CD 9:GLU129 2.9 48.3 1.0 OE2 9:GLU49 3.0 35.5 1.0 CD 9:GLU49 3.0 37.5 1.0 CD 9:GLU130 3.2 39.2 1.0 OE2 9:GLU129 3.2 46.8 1.0 CD 9:GLU126 3.5 38.0 1.0 CG 9:GLU130 3.8 34.6 1.0 OE1 9:GLU130 4.2 42.8 1.0 OE2 9:GLU126 4.2 35.6 1.0 CG 9:GLU129 4.3 38.3 1.0 CG 9:GLU49 4.5 32.3 1.0 N 9:GLU130 4.5 28.0 1.0 CA 9:GLU130 4.5 27.9 1.0 CG 9:GLU126 4.6 27.8 1.0 CB 9:GLU130 4.8 28.2 1.0 CB 9:GLU129 4.9 29.2 1.0 O 9:GLU126 4.9 27.4 1.0 C 9:GLU129 4.9 28.7 1.0

J.Tatur, W.R.Hagen, P.M.Matias. Crystal Structure of the Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus J.Biol.Inorg.Chem. V. 12 615 2007.
ISSN: ISSN 0949-8257
PubMed: 17541801
DOI: 10.1007/S00775-007-0212-3