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Iron in PDB 2jd7: Crystal Structure of the Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus

Protein crystallography data

The structure of Crystal Structure of the Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus, PDB code: 2jd7 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 (°) 254.301, 342.878, 266.221, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 108;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus (pdb code 2jd7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 108 binding sites of Iron where determined in the Crystal Structure of the Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus, PDB code: 2jd7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 108 in 2jd7

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Iron binding site 1 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe201

b:54.3
occ:1.00
 OE1 0:GLU17 2.2 41.2 1.0
OE1 0:GLU50 2.3 38.3 1.0
ND1 0:HIS53 2.3 33.4 1.0
FE 0:FE202 2.9 45.9 0.5
CD 0:GLU17 3.1 36.1 1.0
CE1 0:HIS53 3.2 34.1 1.0
OE2 0:GLU17 3.2 37.8 1.0
CD 0:GLU50 3.3 37.6 1.0
CG 0:HIS53 3.4 30.1 1.0
OE2 0:GLU50 3.6 42.7 1.0
OE1 0:GLN127 3.7 33.1 1.0
CB 0:HIS53 3.8 26.8 1.0
NE2 0:HIS53 4.3 35.2 1.0
CG2 0:ILE97 4.4 32.5 1.0
CD2 0:HIS53 4.5 32.5 1.0
CG 0:GLU17 4.5 30.5 1.0
CG 0:GLU50 4.7 30.0 1.0
CD 0:GLN127 4.8 31.7 1.0
OE1 0:GLU94 4.9 42.6 1.0
CA 0:GLU50 4.9 27.8 1.0
CB 0:GLU17 4.9 28.6 1.0

Iron binding site 2 out of 108 in 2jd7

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Iron binding site 2 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe202

b:45.9
occ:0.50
 OE2 0:GLU50 2.1 42.7 1.0
OE2 0:GLU94 2.5 39.4 1.0
OE1 0:GLU94 2.8 42.6 1.0
OE1 0:GLU130 2.8 52.5 1.0
FE 0:FE201 2.9 54.3 1.0
CD 0:GLU94 3.0 39.1 1.0
CD 0:GLU50 3.0 37.6 1.0
OE1 0:GLU50 3.1 38.3 1.0
CD 0:GLU130 3.6 47.8 1.0
CG 0:GLU130 3.7 42.2 1.0
OE1 0:GLN127 3.7 33.1 1.0
CE1 0:HIS53 4.0 34.1 1.0
ND1 0:HIS53 4.1 33.4 1.0
CB 0:GLU130 4.2 34.2 1.0
CG 0:GLU50 4.4 30.0 1.0
CG 0:GLU94 4.4 33.9 1.0
NE2 0:GLN46 4.5 38.6 1.0
CD 0:GLN127 4.6 31.7 1.0
OE2 0:GLU130 4.6 47.6 1.0
CE2 0:TYR24 4.7 39.3 1.0
NE2 0:GLN127 4.7 31.5 1.0
OE1 0:GLU17 4.8 41.2 1.0
OH 0:TYR24 4.9 47.5 1.0

Iron binding site 3 out of 108 in 2jd7

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Iron binding site 3 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe203

b:55.9
occ:1.00
 OE2 0:GLU130 1.9 47.6 1.0
OE1 0:GLU126 2.0 43.9 1.0
OE1 0:GLU49 2.2 50.9 1.0
OE1 0:GLU129 2.3 55.8 1.0
OE2 0:GLU129 2.9 54.0 1.0
CD 0:GLU129 3.0 51.1 1.0
CD 0:GLU49 3.0 42.8 1.0
CD 0:GLU130 3.1 47.8 1.0
CD 0:GLU126 3.1 41.0 1.0
OE2 0:GLU49 3.1 45.6 1.0
OE2 0:GLU126 3.6 39.5 1.0
CG 0:GLU130 3.7 42.2 1.0
OE1 0:GLU130 4.1 52.5 1.0
CG 0:GLU126 4.4 30.1 1.0
CG 0:GLU49 4.4 35.6 1.0
CG 0:GLU129 4.5 41.5 1.0
N 0:GLU130 4.7 33.8 1.0
CA 0:GLU130 4.7 34.0 1.0
O 0:GLU126 4.8 31.2 1.0
CB 0:GLU130 4.8 34.2 1.0
NE2 0:HIS53 4.9 35.2 1.0
NE2 0:GLN46 4.9 38.6 1.0
CE1 0:HIS53 4.9 34.1 1.0
CB 0:GLU129 5.0 33.9 1.0

Iron binding site 4 out of 108 in 2jd7

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Iron binding site 4 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe201

b:54.1
occ:1.00
 OE1 1:GLU17 2.2 41.3 1.0
ND1 1:HIS53 2.2 33.3 1.0
OE1 1:GLU50 2.3 38.3 1.0
FE 1:FE202 3.0 45.9 0.5
CD 1:GLU17 3.1 36.3 1.0
CE1 1:HIS53 3.1 34.2 1.0
OE2 1:GLU17 3.3 38.0 1.0
CD 1:GLU50 3.3 37.8 1.0
CG 1:HIS53 3.3 30.2 1.0
OE2 1:GLU50 3.6 42.9 1.0
CB 1:HIS53 3.7 26.8 1.0
OE1 1:GLN127 3.8 33.0 1.0
NE2 1:HIS53 4.3 35.2 1.0
CD2 1:HIS53 4.4 32.4 1.0
CG2 1:ILE97 4.5 35.0 1.0
CG 1:GLU17 4.5 30.7 1.0
CG 1:GLU50 4.6 30.4 1.0
CA 1:GLU50 4.8 27.7 1.0
CB 1:GLU50 4.9 27.8 1.0
CD 1:GLN127 4.9 31.7 1.0
CB 1:GLU17 5.0 28.6 1.0
OE1 1:GLU94 5.0 42.6 1.0

Iron binding site 5 out of 108 in 2jd7

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Iron binding site 5 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe202

b:45.9
occ:0.50
 OE2 1:GLU50 2.2 42.9 1.0
OE2 1:GLU94 2.4 39.5 1.0
OE1 1:GLU94 2.7 42.6 1.0
OE1 1:GLU130 2.9 52.7 1.0
CD 1:GLU94 2.9 39.2 1.0
FE 1:FE201 3.0 54.1 1.0
CD 1:GLU50 3.0 37.8 1.0
OE1 1:GLU50 3.1 38.3 1.0
CD 1:GLU130 3.6 47.8 1.0
CG 1:GLU130 3.7 42.0 1.0
OE1 1:GLN127 3.7 33.0 1.0
CE1 1:HIS53 4.1 34.2 1.0
ND1 1:HIS53 4.1 33.3 1.0
NE2 1:GLN46 4.1 33.8 1.0
CB 1:GLU130 4.2 34.4 1.0
CG 1:GLU94 4.4 34.1 1.0
CG 1:GLU50 4.4 30.4 1.0
CD 1:GLN127 4.6 31.7 1.0
NE2 1:GLN127 4.7 31.2 1.0
OE2 1:GLU130 4.7 47.6 1.0
OE1 1:GLU17 4.8 41.3 1.0
OH 1:TYR24 4.9 47.0 1.0

Iron binding site 6 out of 108 in 2jd7

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Iron binding site 6 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe203

b:56.8
occ:1.00
 OE2 1:GLU130 1.9 47.6 1.0
OE1 1:GLU126 2.1 43.7 1.0
OE1 1:GLU49 2.2 51.0 1.0
OE1 1:GLU129 2.4 56.0 1.0
CD 1:GLU49 3.0 42.9 1.0
OE2 1:GLU129 3.0 54.1 1.0
CD 1:GLU129 3.0 51.1 1.0
CD 1:GLU130 3.0 47.8 1.0
CD 1:GLU126 3.1 41.0 1.0
OE2 1:GLU49 3.2 45.6 1.0
OE2 1:GLU126 3.6 39.4 1.0
CG 1:GLU130 3.7 42.0 1.0
OE1 1:GLU130 4.1 52.7 1.0
CG 1:GLU49 4.4 35.6 1.0
CG 1:GLU126 4.4 30.2 1.0
CG 1:GLU129 4.5 41.5 1.0
N 1:GLU130 4.8 33.9 1.0
CA 1:GLU130 4.8 34.3 1.0
NE2 1:GLN46 4.8 33.8 1.0
CB 1:GLU130 4.8 34.4 1.0
NE2 1:HIS53 4.8 35.2 1.0
O 1:GLU126 4.9 31.1 1.0
CE1 1:HIS53 4.9 34.2 1.0

Iron binding site 7 out of 108 in 2jd7

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Iron binding site 7 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe201

b:53.3
occ:1.00
 OE1 2:GLU17 2.1 41.4 1.0
OE1 2:GLU50 2.2 38.0 1.0
ND1 2:HIS53 2.2 33.3 1.0
FE 2:FE202 3.1 46.2 0.5
CD 2:GLU17 3.1 36.2 1.0
CE1 2:HIS53 3.1 34.1 1.0
CD 2:GLU50 3.2 37.8 1.0
CG 2:HIS53 3.3 30.2 1.0
OE2 2:GLU17 3.3 38.2 1.0
OE2 2:GLU50 3.5 43.0 1.0
CB 2:HIS53 3.6 26.6 1.0
OE1 2:GLN127 3.8 33.0 1.0
NE2 2:HIS53 4.3 35.0 1.0
CD2 2:HIS53 4.4 32.4 1.0
CG 2:GLU17 4.5 30.7 1.0
CG 2:GLU50 4.6 30.4 1.0
CG2 2:ILE97 4.6 32.5 1.0
CA 2:GLU50 4.8 27.9 1.0
CB 2:GLU50 4.9 27.9 1.0
CB 2:GLU17 4.9 28.6 1.0
CD 2:GLN127 4.9 31.6 1.0

Iron binding site 8 out of 108 in 2jd7

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Iron binding site 8 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe202

b:46.2
occ:0.50
 OE2 2:GLU50 2.0 43.0 1.0
OE2 2:GLU94 2.4 39.6 1.0
OE1 2:GLU130 2.7 52.6 1.0
OE1 2:GLU94 2.8 42.7 1.0
CD 2:GLU94 2.9 39.2 1.0
CD 2:GLU50 2.9 37.8 1.0
FE 2:FE201 3.1 53.3 1.0
OE1 2:GLU50 3.1 38.0 1.0
CD 2:GLU130 3.5 47.9 1.0
CG 2:GLU130 3.6 42.1 1.0
OE1 2:GLN127 3.8 33.0 1.0
NE2 2:GLN46 3.8 35.9 1.0
CE1 2:HIS53 4.1 34.1 1.0
ND1 2:HIS53 4.1 33.3 1.0
CB 2:GLU130 4.1 34.5 1.0
CG 2:GLU50 4.3 30.4 1.0
CG 2:GLU94 4.4 34.1 1.0
OE2 2:GLU130 4.5 47.5 1.0
CD 2:GLN127 4.7 31.6 1.0
OH 2:TYR24 4.7 46.0 1.0
NE2 2:GLN127 4.7 31.3 1.0
CE2 2:TYR24 4.8 43.7 1.0
OE1 2:GLU17 4.9 41.4 1.0

Iron binding site 9 out of 108 in 2jd7

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Iron binding site 9 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe203

b:56.3
occ:1.00
 OE1 2:GLU126 2.0 43.7 1.0
OE2 2:GLU130 2.0 47.5 1.0
OE1 2:GLU49 2.1 51.0 1.0
OE1 2:GLU129 2.3 55.9 1.0
CD 2:GLU49 2.9 42.9 1.0
CD 2:GLU129 3.0 51.0 1.0
CD 2:GLU126 3.1 40.9 1.0
OE2 2:GLU129 3.1 54.0 1.0
OE2 2:GLU49 3.1 45.7 1.0
CD 2:GLU130 3.1 47.9 1.0
OE2 2:GLU126 3.5 39.3 1.0
CG 2:GLU130 3.7 42.1 1.0
OE1 2:GLU130 4.2 52.6 1.0
CG 2:GLU49 4.3 35.5 1.0
CG 2:GLU126 4.3 30.0 1.0
CG 2:GLU129 4.5 41.4 1.0
NE2 2:HIS53 4.8 35.0 1.0
CA 2:GLU130 4.8 34.1 1.0
N 2:GLU130 4.8 33.7 1.0
CE1 2:HIS53 4.9 34.1 1.0
CB 2:GLU130 4.9 34.5 1.0
O 2:GLU126 4.9 31.1 1.0

Iron binding site 10 out of 108 in 2jd7

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Iron binding site 10 out of 108 in the Crystal Structure of the Fe-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 Fe-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe201

b:53.8
occ:1.00
 OE1 3:GLU50 2.2 38.1 1.0
ND1 3:HIS53 2.2 33.2 1.0
OE1 3:GLU17 2.2 41.3 1.0
FE 3:FE202 3.0 45.7 0.5
CE1 3:HIS53 3.1 34.0 1.0
CD 3:GLU17 3.2 36.2 1.0
CD 3:GLU50 3.2 37.8 1.0
CG 3:HIS53 3.3 30.2 1.0
OE2 3:GLU17 3.4 38.0 1.0
OE2 3:GLU50 3.5 43.0 1.0
CB 3:HIS53 3.7 26.8 1.0
OE1 3:GLN127 3.8 33.0 1.0
NE2 3:HIS53 4.2 34.9 1.0
CD2 3:HIS53 4.4 32.2 1.0
CG2 3:ILE97 4.4 27.5 1.0
CG 3:GLU17 4.5 30.5 1.0
CG 3:GLU50 4.5 30.4 1.0
CA 3:GLU50 4.8 27.8 1.0
CB 3:GLU50 4.9 27.6 1.0
CB 3:GLU17 4.9 28.6 1.0
CD 3:GLN127 5.0 31.7 1.0

Reference:

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
Page generated: Sat Aug 3 23:39:14 2024

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