Zinc 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:

Iron

(Fe)

36 atoms

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 - 72;

Binding sites:

The binding sites of Zinc 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 Zinc atom.
In total 72 binding sites of Zinc where determined in the Crystal Structure of the Zn-Soaked Ferritin From the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus, PDB code: 2jd8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 72 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 Zinc with other atoms in the Zn 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:Zn201 b:44.0 occ:0.90 OE1 0:GLU17 2.2 34.2 1.0 ND1 0:HIS53 2.2 28.9 1.0 OE1 0:GLU50 2.3 29.6 1.0 ZN 0:ZN202 2.7 34.8 0.5 CD 0:GLU17 3.0 30.3 1.0 CE1 0:HIS53 3.1 27.6 1.0 OE2 0:GLU17 3.2 31.4 1.0 CD 0:GLU50 3.3 31.5 1.0 CG 0:HIS53 3.3 25.3 1.0 OE2 0:GLU50 3.6 35.7 1.0 CB 0:HIS53 3.7 24.3 1.0 OE1 0:GLN127 3.7 29.8 1.0 NE2 0:HIS53 4.3 29.4 1.0 CD2 0:HIS53 4.4 26.0 1.0 CG2 0:ILE97 4.4 26.6 1.0 CG 0:GLU17 4.4 26.9 1.0 CG 0:GLU50 4.7 26.8 1.0 CD 0:GLN127 4.9 28.1 1.0 OE1 0:GLU94 4.9 35.5 1.0 OE2 0:GLU94 4.9 33.2 1.0 CA 0:GLU50 4.9 25.9 1.0 CB 0:GLU17 5.0 25.4 1.0

Zinc binding site 2 out of 72 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 Zinc with other atoms in the Zn 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 0:Zn202 b:34.8 occ:0.50 OE2 0:GLU50 2.1 35.7 1.0 OE2 0:GLU94 2.4 33.2 1.0 ZN 0:ZN201 2.7 44.0 0.9 OE1 0:GLU94 2.8 35.5 1.0 OE1 0:GLU130 2.9 42.8 1.0 CD 0:GLU50 2.9 31.5 1.0 CD 0:GLU94 2.9 32.8 1.0 OE1 0:GLU50 3.0 29.6 1.0 CD 0:GLU130 3.6 39.4 1.0 OE1 0:GLN127 3.8 29.8 1.0 CG 0:GLU130 3.8 35.0 1.0 ND1 0:HIS53 4.0 28.9 1.0 CE1 0:HIS53 4.0 27.6 1.0 CG 0:GLU50 4.3 26.8 1.0 CG 0:GLU94 4.4 29.5 1.0 CB 0:GLU130 4.4 28.1 1.0 NE2 0:GLN46 4.5 34.4 1.0 OE2 0:GLU130 4.6 39.5 1.0 CD 0:GLN127 4.6 28.1 1.0 OE1 0:GLU17 4.6 34.2 1.0 OH 0:TYR24 4.6 31.1 1.0 NE2 0:GLN127 4.6 28.5 1.0 CE2 0:TYR24 4.7 26.9 1.0 CG2 0:ILE97 5.0 26.6 1.0

Zinc binding site 3 out of 72 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 Zinc with other atoms in the Zn 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 1:Zn201 b:44.0 occ:0.90 OE1 1:GLU17 2.2 34.8 1.0 ND1 1:HIS53 2.2 29.7 1.0 OE1 1:GLU50 2.4 29.4 1.0 ZN 1:ZN202 2.9 32.4 0.5 CD 1:GLU17 3.0 31.2 1.0 OE2 1:GLU17 3.1 32.6 1.0 CE1 1:HIS53 3.1 27.0 1.0 CG 1:HIS53 3.2 26.3 1.0 CD 1:GLU50 3.4 32.1 1.0 CB 1:HIS53 3.5 23.9 1.0 OE2 1:GLU50 3.7 36.7 1.0 OE1 1:GLN127 3.8 30.7 1.0 NE2 1:HIS53 4.2 29.3 1.0 CD2 1:HIS53 4.2 26.2 1.0 CG 1:GLU17 4.4 27.0 1.0 CG2 1:ILE97 4.5 30.4 1.0 CG 1:GLU50 4.7 27.6 1.0 CA 1:GLU50 4.8 25.7 1.0 CB 1:GLU50 4.9 26.3 1.0 CB 1:GLU17 4.9 25.1 1.0 OE1 1:GLU94 5.0 35.8 1.0 CD 1:GLN127 5.0 28.5 1.0

Zinc binding site 4 out of 72 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 Zinc with other atoms in the Zn 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 1:Zn202 b:32.4 occ:0.50 OE2 1:GLU50 2.1 36.7 1.0 OE2 1:GLU94 2.5 32.9 1.0 OE1 1:GLU130 2.7 42.9 1.0 OE1 1:GLU94 2.9 35.8 1.0 CD 1:GLU50 2.9 32.1 1.0 ZN 1:ZN201 2.9 44.0 0.9 OE1 1:GLU50 3.0 29.4 1.0 CD 1:GLU94 3.0 33.0 1.0 CD 1:GLU130 3.4 39.1 1.0 CG 1:GLU130 3.6 34.6 1.0 OE1 1:GLN127 3.8 30.7 1.0 CE1 1:HIS53 3.8 27.0 1.0 ND1 1:HIS53 3.8 29.7 1.0 NE2 1:GLN46 4.1 31.6 1.0 CB 1:GLU130 4.3 28.5 1.0 CG 1:GLU50 4.3 27.6 1.0 OE2 1:GLU130 4.5 39.5 1.0 CG 1:GLU94 4.5 29.7 1.0 CD 1:GLN127 4.7 28.5 1.0 OE1 1:GLU17 4.7 34.8 1.0 NE2 1:GLN127 4.8 28.1 1.0 OH 1:TYR24 5.0 35.2 1.0 CE2 1:TYR24 5.0 34.2 1.0

Zinc binding site 5 out of 72 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 Zinc with other atoms in the Zn 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 2:Zn201 b:43.4 occ:0.90 ND1 2:HIS53 2.1 28.4 1.0 OE1 2:GLU50 2.2 28.3 1.0 OE1 2:GLU17 2.2 35.5 1.0 CE1 2:HIS53 3.0 26.6 1.0 CD 2:GLU17 3.0 31.4 1.0 ZN 2:ZN202 3.1 38.0 0.5 CG 2:HIS53 3.2 26.3 1.0 CD 2:GLU50 3.2 32.2 1.0 OE2 2:GLU17 3.2 33.0 1.0 OE2 2:GLU50 3.6 36.7 1.0 CB 2:HIS53 3.6 24.4 1.0 OE1 2:GLN127 3.6 29.6 1.0 NE2 2:HIS53 4.1 29.3 1.0 CD2 2:HIS53 4.2 26.2 1.0 CG 2:GLU17 4.4 27.3 1.0 CG2 2:ILE97 4.5 20.8 1.0 CG 2:GLU50 4.6 27.4 1.0 CA 2:GLU50 4.8 26.1 1.0 CD 2:GLN127 4.8 27.8 1.0 CB 2:GLU17 4.9 25.1 1.0 CB 2:GLU50 4.9 26.1 1.0

Zinc binding site 6 out of 72 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 Zinc with other atoms in the Zn 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 2:Zn202 b:38.0 occ:0.50 OE2 2:GLU50 2.0 36.7 1.0 OE2 2:GLU94 2.4 33.2 1.0 OE1 2:GLU130 2.6 42.9 1.0 CD 2:GLU50 2.9 32.2 1.0 OE1 2:GLU94 2.9 35.5 1.0 CD 2:GLU94 3.0 32.9 1.0 OE1 2:GLU50 3.1 28.3 1.0 ZN 2:ZN201 3.1 43.4 0.9 CD 2:GLU130 3.4 39.0 1.0 CG 2:GLU130 3.6 34.6 1.0 NE2 2:GLN46 3.8 23.8 1.0 OE1 2:GLN127 3.9 29.6 1.0 CE1 2:HIS53 3.9 26.6 1.0 ND1 2:HIS53 4.1 28.4 1.0 CB 2:GLU130 4.2 28.8 1.0 CG 2:GLU50 4.3 27.4 1.0 OE2 2:GLU130 4.3 39.0 1.0 CG 2:GLU94 4.4 29.5 1.0 CE2 2:TYR24 4.5 33.3 1.0 OH 2:TYR24 4.6 30.6 1.0 CD 2:GLN127 4.8 27.8 1.0 NE2 2:GLN127 4.9 28.0 1.0 OE1 2:GLU17 4.9 35.5 1.0

Zinc binding site 7 out of 72 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 Zinc with other atoms in the Zn 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 3:Zn201 b:41.2 occ:0.90 ND1 3:HIS53 2.1 29.1 1.0 OE1 3:GLU50 2.2 30.2 1.0 OE1 3:GLU17 2.2 33.8 1.0 CE1 3:HIS53 2.9 26.8 1.0 ZN 3:ZN202 3.0 31.5 0.5 CD 3:GLU17 3.1 31.0 1.0 CG 3:HIS53 3.2 26.3 1.0 CD 3:GLU50 3.2 31.9 1.0 OE2 3:GLU17 3.2 32.6 1.0 OE2 3:GLU50 3.6 36.1 1.0 CB 3:HIS53 3.6 23.9 1.0 OE1 3:GLN127 3.8 30.1 1.0 NE2 3:HIS53 4.1 28.7 1.0 CD2 3:HIS53 4.2 25.9 1.0 CG2 3:ILE97 4.4 16.1 1.0 CG 3:GLU17 4.5 27.2 1.0 CG 3:GLU50 4.6 27.2 1.0 CA 3:GLU50 4.7 25.8 1.0 CB 3:GLU50 4.9 25.8 1.0 CB 3:GLU17 4.9 24.7 1.0 OE1 3:GLU130 5.0 42.1 1.0 CD 3:GLN127 5.0 28.3 1.0 OE2 3:GLU94 5.0 33.1 1.0

Zinc binding site 8 out of 72 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 Zinc with other atoms in the Zn 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 3:Zn202 b:31.5 occ:0.50 OE2 3:GLU50 2.2 36.1 1.0 OE2 3:GLU94 2.4 33.1 1.0 OE1 3:GLU130 2.4 42.1 1.0 OE1 3:GLU94 2.7 35.9 1.0 CD 3:GLU94 2.9 32.9 1.0 ZN 3:ZN201 3.0 41.2 0.9 CD 3:GLU50 3.1 31.9 1.0 CD 3:GLU130 3.2 39.1 1.0 OE1 3:GLU50 3.2 30.2 1.0 CG 3:GLU130 3.4 34.4 1.0 OE1 3:GLN127 3.7 30.1 1.0 CE1 3:HIS53 3.9 26.8 1.0 NE2 3:GLN46 4.0 23.6 1.0 CB 3:GLU130 4.0 28.5 1.0 ND1 3:HIS53 4.0 29.1 1.0 OE2 3:GLU130 4.2 40.3 1.0 CG 3:GLU94 4.3 29.1 1.0 CG 3:GLU50 4.5 27.2 1.0 CD 3:GLN127 4.6 28.3 1.0 OH 3:TYR24 4.7 31.0 1.0 NE2 3:GLN127 4.7 28.1 1.0 CE1 3:TYR24 4.9 31.2 1.0 OE1 3:GLU17 5.0 33.8 1.0

Zinc binding site 9 out of 72 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 Zinc with other atoms in the Zn 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 4:Zn201 b:42.2 occ:0.90 ND1 4:HIS53 2.1 29.1 1.0 OE1 4:GLU17 2.2 34.8 1.0 OE1 4:GLU50 2.3 30.4 1.0 ZN 4:ZN202 2.8 30.9 0.5 CE1 4:HIS53 2.9 27.0 1.0 CD 4:GLU17 3.1 31.4 1.0 CG 4:HIS53 3.2 26.0 1.0 OE2 4:GLU17 3.2 32.8 1.0 CD 4:GLU50 3.4 32.0 1.0 OE1 4:GLN127 3.6 29.5 1.0 CB 4:HIS53 3.7 23.4 1.0 OE2 4:GLU50 3.7 36.9 1.0 NE2 4:HIS53 4.1 29.1 1.0 CD2 4:HIS53 4.2 26.4 1.0 CG2 4:ILE97 4.4 21.9 1.0 CG 4:GLU17 4.5 26.8 1.0 CG 4:GLU50 4.7 26.8 1.0 CD 4:GLN127 4.8 28.7 1.0 CA 4:GLU50 4.9 25.8 1.0 OE1 4:GLU130 5.0 43.0 1.0 OE2 4:GLU94 5.0 32.8 1.0 OE1 4:GLU94 5.0 35.4 1.0 CB 4:GLU50 5.0 25.6 1.0

Zinc binding site 10 out of 72 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 Zinc with other atoms in the Zn 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 4:Zn202 b:30.9 occ:0.50 OE2 4:GLU50 2.3 36.9 1.0 OE2 4:GLU94 2.4 32.8 1.0 OE1 4:GLU130 2.7 43.0 1.0 ZN 4:ZN201 2.8 42.2 0.9 OE1 4:GLU94 2.8 35.4 1.0 OE1 4:GLU50 2.9 30.4 1.0 CD 4:GLU94 2.9 33.0 1.0 CD 4:GLU50 3.0 32.0 1.0 OE1 4:GLN127 3.5 29.5 1.0 CD 4:GLU130 3.6 39.0 1.0 CG 4:GLU130 3.7 34.9 1.0 CE1 4:HIS53 3.8 27.0 1.0 ND1 4:HIS53 3.9 29.1 1.0 CB 4:GLU130 4.3 28.6 1.0 CG 4:GLU94 4.4 30.1 1.0 CD 4:GLN127 4.4 28.7 1.0 CG 4:GLU50 4.5 26.8 1.0 NE2 4:GLN46 4.6 31.1 1.0 OE1 4:GLU17 4.6 34.8 1.0 NE2 4:GLN127 4.6 29.3 1.0 OE2 4:GLU130 4.7 39.4 1.0 CG2 4:ILE97 4.9 21.9 1.0 CE1 4:TYR24 5.0 38.1 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