Iron in PDB 2vzb: A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis

The structure of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis, PDB code: 2vzb was solved by G.H.Gauss, M.J.Young, T.Douglas, C.M.Lawrence, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.00 / 2.30
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	129.695, 129.695, 129.695, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.4

The structure of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Iron atom in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis (pdb code 2vzb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis, PDB code: 2vzb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe6204 b:49.4 occ:1.00 OE1 A:GLU62 2.0 33.8 1.0 OE2 A:GLU146 2.1 34.2 1.0 OE1 A:GLU29 2.2 35.8 1.0 OE2 A:GLU29 2.2 35.6 1.0 ND1 A:HIS65 2.3 32.5 1.0 O A:HOH2016 2.5 37.3 1.0 CD A:GLU29 2.5 36.1 1.0 CD A:GLU146 3.1 33.6 1.0 CE1 A:HIS65 3.1 34.0 1.0 CD A:GLU62 3.1 33.6 1.0 OE1 A:GLU146 3.4 35.2 1.0 CG A:HIS65 3.4 32.9 1.0 CB A:HIS65 3.7 33.4 1.0 OE2 A:GLU62 3.8 35.5 1.0 CG A:GLU29 4.0 35.3 1.0 CA A:GLU62 4.1 33.7 1.0 FE A:FE6205 4.1 54.3 1.0 O A:HOH2061 4.1 44.6 1.0 CB A:GLU62 4.1 33.5 1.0 CG A:GLU62 4.2 33.5 1.0 CG2 A:ILE142 4.2 32.3 1.0 O A:HOH2013 4.3 46.3 1.0 NE2 A:HIS65 4.3 33.1 1.0 CD2 A:HIS65 4.4 33.5 1.0 CG A:GLU146 4.4 33.9 1.0 OH A:TYR121 4.6 36.9 1.0 CE2 A:TYR121 4.6 36.3 1.0 CB A:GLU29 4.8 36.0 1.0 O A:GLU62 4.9 33.5 1.0 CA A:GLU29 5.0 35.9 1.0 N A:GLU62 5.0 33.6 1.0 C A:GLU62 5.0 33.5 1.0

Iron binding site 2 out of 8 in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe6205 b:54.3 occ:1.00 OE1 A:GLU146 2.1 35.2 1.0 OE2 A:GLU62 2.1 35.5 1.0 OE1 A:GLU114 2.2 31.6 1.0 ND1 A:HIS149 2.3 36.3 1.0 O A:HOH2061 2.3 44.6 1.0 OE2 A:GLU114 2.5 34.1 1.0 CD A:GLU114 2.7 35.4 1.0 CD A:GLU62 3.0 33.6 1.0 CE1 A:HIS149 3.1 36.2 1.0 CD A:GLU146 3.2 33.6 1.0 OE1 A:GLU62 3.3 33.8 1.0 CG A:HIS149 3.4 37.0 1.0 CB A:HIS149 3.8 36.9 1.0 OE2 A:GLU146 3.9 34.2 1.0 O A:HOH2016 4.0 37.3 1.0 FE A:FE6204 4.1 49.4 1.0 O A:HOH2060 4.1 38.6 1.0 CA A:GLU146 4.2 34.7 1.0 CG A:GLU114 4.2 38.9 1.0 NE2 A:HIS149 4.3 35.6 1.0 CB A:GLU146 4.3 34.7 1.0 CG A:GLU146 4.3 33.9 1.0 CG A:GLU62 4.4 33.5 1.0 CE2 A:TYR36 4.4 33.1 1.0 CD2 A:HIS149 4.4 35.9 1.0 OH A:TYR36 4.5 32.4 1.0 CE1 A:HIS65 4.8 34.0 1.0 O A:GLU146 4.9 34.7 1.0 CB A:GLU114 4.9 39.3 1.0 CA A:GLU114 4.9 40.2 1.0 CB A:ALA117 5.0 40.3 1.0 N A:GLU146 5.0 34.4 1.0

Iron binding site 3 out of 8 in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe6204 b:48.7 occ:1.00 OE1 B:GLU62 2.0 34.2 1.0 OE2 B:GLU146 2.1 34.3 1.0 OE1 B:GLU29 2.3 36.0 1.0 O B:HOH2033 2.3 41.9 1.0 OE2 B:GLU29 2.3 35.5 1.0 ND1 B:HIS65 2.3 32.4 1.0 CD B:GLU29 2.6 36.0 1.0 CD B:GLU146 3.0 33.5 1.0 CD B:GLU62 3.1 33.8 1.0 CE1 B:HIS65 3.1 34.1 1.0 OE1 B:GLU146 3.3 35.1 1.0 CG B:HIS65 3.5 32.9 1.0 OE2 B:GLU62 3.8 35.5 1.0 CB B:HIS65 3.9 33.1 1.0 FE B:FE6205 4.0 55.8 1.0 CA B:GLU62 4.1 33.6 1.0 CB B:GLU62 4.1 33.5 1.0 CG B:GLU62 4.1 33.5 1.0 CG B:GLU29 4.1 35.5 1.0 O B:HOH2055 4.1 38.7 1.0 CG2 B:ILE142 4.2 32.4 1.0 NE2 B:HIS65 4.3 33.0 1.0 CG B:GLU146 4.4 34.2 1.0 O B:HOH2007 4.4 38.5 1.0 CD2 B:HIS65 4.5 33.4 1.0 CE2 B:TYR121 4.6 36.4 1.0 OH B:TYR121 4.6 36.8 1.0 CB B:GLU29 4.9 35.9 1.0 O B:GLU62 4.9 33.5 1.0 CB B:ALA117 4.9 43.2 1.0 N B:GLU62 5.0 33.8 1.0

Iron binding site 4 out of 8 in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe6205 b:55.8 occ:1.00 OE2 B:GLU62 2.1 35.5 1.0 OE1 B:GLU146 2.1 35.1 1.0 OE1 B:GLU114 2.2 40.6 1.0 ND1 B:HIS149 2.3 36.5 1.0 OE2 B:GLU114 2.4 41.1 1.0 O B:HOH2055 2.6 38.7 1.0 CD B:GLU114 2.6 41.4 1.0 CD B:GLU62 3.0 33.8 1.0 CE1 B:HIS149 3.1 36.4 1.0 OE1 B:GLU62 3.2 34.2 1.0 CD B:GLU146 3.3 33.5 1.0 CG B:HIS149 3.4 36.5 1.0 O B:HOH2033 3.7 41.9 1.0 CB B:HIS149 3.8 36.8 1.0 OE2 B:GLU146 3.8 34.3 1.0 FE B:FE6204 4.0 48.7 1.0 CG B:GLU114 4.1 42.7 1.0 O B:HOH2054 4.2 42.7 1.0 CA B:GLU146 4.3 34.8 1.0 NE2 B:HIS149 4.3 35.6 1.0 CG B:GLU62 4.3 33.5 1.0 CE2 B:TYR36 4.3 33.1 1.0 CG B:GLU146 4.4 34.2 1.0 CB B:GLU146 4.4 34.7 1.0 OH B:TYR36 4.5 32.0 1.0 CD2 B:HIS149 4.5 36.1 1.0 CE1 B:HIS65 4.9 34.1 1.0 CB B:GLU114 4.9 44.0 1.0 CA B:GLU114 4.9 44.2 1.0 CZ B:TYR36 4.9 32.5 1.0 CB B:ALA117 4.9 43.2 1.0

Iron binding site 5 out of 8 in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe6204 b:46.4 occ:1.00 OE1 C:GLU62 2.0 33.5 1.0 OE2 C:GLU146 2.2 34.2 1.0 OE1 C:GLU29 2.2 35.8 1.0 OE2 C:GLU29 2.2 35.2 1.0 O C:HOH2008 2.3 38.5 1.0 ND1 C:HIS65 2.3 32.3 1.0 CD C:GLU29 2.5 36.1 1.0 CD C:GLU146 3.1 33.6 1.0 CE1 C:HIS65 3.1 34.2 1.0 CD C:GLU62 3.1 33.5 1.0 OE1 C:GLU146 3.3 34.9 1.0 CG C:HIS65 3.4 32.7 1.0 CB C:HIS65 3.8 33.1 1.0 OE2 C:GLU62 3.9 35.2 1.0 O C:HOH2033 3.9 33.6 1.0 CG C:GLU29 4.0 35.6 1.0 CA C:GLU62 4.0 33.6 1.0 CB C:GLU62 4.1 33.4 1.0 CG C:GLU62 4.1 33.6 1.0 FE C:FE6205 4.2 50.9 1.0 CG2 C:ILE142 4.2 32.3 1.0 O C:HOH2007 4.2 28.3 1.0 NE2 C:HIS65 4.3 33.2 1.0 CG C:GLU146 4.5 34.1 1.0 CD2 C:HIS65 4.5 33.3 1.0 OH C:TYR121 4.6 37.1 1.0 CE2 C:TYR121 4.6 36.1 1.0 CB C:GLU29 4.8 36.1 1.0 O C:GLU62 4.8 33.1 1.0 CA C:GLU29 5.0 36.1 1.0 C C:GLU62 5.0 33.3 1.0 N C:GLU62 5.0 33.6 1.0

Iron binding site 6 out of 8 in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe6205 b:50.9 occ:1.00 OE1 C:GLU146 2.1 34.9 1.0 OE2 C:GLU62 2.2 35.2 1.0 OE1 C:GLU114 2.2 38.5 1.0 ND1 C:HIS149 2.2 36.5 1.0 OE2 C:GLU114 2.4 38.4 1.0 O C:HOH2033 2.5 33.6 1.0 CD C:GLU114 2.6 37.9 1.0 CD C:GLU62 3.1 33.5 1.0 CE1 C:HIS149 3.1 36.4 1.0 OE1 C:GLU62 3.2 33.5 1.0 CD C:GLU146 3.3 33.6 1.0 CG C:HIS149 3.3 36.8 1.0 CB C:HIS149 3.7 36.6 1.0 O C:HOH2054 3.9 36.0 1.0 OE2 C:GLU146 3.9 34.2 1.0 O C:HOH2008 4.0 38.5 1.0 CG C:GLU114 4.2 39.5 1.0 FE C:FE6204 4.2 46.4 1.0 CA C:GLU146 4.2 34.7 1.0 NE2 C:HIS149 4.3 35.6 1.0 CG C:GLU146 4.4 34.1 1.0 CB C:GLU146 4.4 34.7 1.0 CE2 C:TYR36 4.4 33.3 1.0 OH C:TYR36 4.4 32.1 1.0 CD2 C:HIS149 4.4 36.3 1.0 CG C:GLU62 4.5 33.6 1.0 CB C:GLU114 4.9 39.7 1.0 CB C:ALA117 4.9 39.9 1.0 CA C:GLU114 4.9 40.2 1.0 CE1 C:HIS65 4.9 34.2 1.0 CZ C:TYR36 4.9 32.3 1.0 O C:GLU146 5.0 34.8 1.0 N C:GLU146 5.0 34.3 1.0

Iron binding site 7 out of 8 in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe6204 b:43.7 occ:1.00 OE2 D:GLU146 2.0 34.0 1.0 OE1 D:GLU62 2.1 34.2 1.0 O D:HOH2029 2.2 39.1 1.0 ND1 D:HIS65 2.2 32.5 1.0 OE2 D:GLU29 2.2 35.1 1.0 OE1 D:GLU29 2.3 35.5 1.0 CD D:GLU29 2.6 35.8 1.0 CD D:GLU146 3.0 33.5 1.0 CE1 D:HIS65 3.0 33.8 1.0 CD D:GLU62 3.2 33.5 1.0 OE1 D:GLU146 3.2 35.2 1.0 CG D:HIS65 3.3 32.4 1.0 CB D:HIS65 3.7 32.9 1.0 OE2 D:GLU62 3.8 35.2 1.0 FE D:FE6205 4.0 51.6 1.0 CA D:GLU62 4.1 33.7 1.0 CG2 D:ILE142 4.1 32.2 1.0 CG D:GLU29 4.1 35.3 1.0 O D:HOH2062 4.2 40.6 1.0 CB D:GLU62 4.2 33.5 1.0 CG D:GLU62 4.2 33.2 1.0 NE2 D:HIS65 4.2 32.9 1.0 O D:HOH2009 4.3 38.7 1.0 CG D:GLU146 4.3 34.0 1.0 CD2 D:HIS65 4.4 33.1 1.0 OH D:TYR121 4.6 36.4 1.0 CE2 D:TYR121 4.6 36.1 1.0 O D:GLU62 4.9 33.2 1.0 CB D:ALA117 4.9 40.0 1.0 CB D:GLU29 4.9 36.0 1.0 N D:GLU62 5.0 33.6 1.0 CZ D:TYR121 5.0 35.6 1.0 C D:GLU62 5.0 33.5 1.0

Iron binding site 8 out of 8 in the A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe6205 b:51.6 occ:1.00 OE2 D:GLU62 2.1 35.2 1.0 OE1 D:GLU146 2.1 35.2 1.0 OE1 D:GLU114 2.2 36.7 1.0 ND1 D:HIS149 2.3 36.4 1.0 O D:HOH2062 2.4 40.6 1.0 OE2 D:GLU114 2.5 33.5 1.0 CD D:GLU114 2.7 35.0 1.0 CD D:GLU62 3.0 33.5 1.0 CE1 D:HIS149 3.1 36.4 1.0 OE1 D:GLU62 3.2 34.2 1.0 CD D:GLU146 3.3 33.5 1.0 CG D:HIS149 3.4 36.7 1.0 O D:HOH2029 3.8 39.1 1.0 CB D:HIS149 3.8 36.6 1.0 OE2 D:GLU146 3.9 34.0 1.0 O D:HOH2061 4.0 31.9 1.0 FE D:FE6204 4.0 43.7 1.0 CG D:GLU114 4.1 36.7 1.0 CA D:GLU146 4.2 34.5 1.0 NE2 D:HIS149 4.3 35.8 1.0 CE2 D:TYR36 4.3 33.2 1.0 CG D:GLU62 4.4 33.2 1.0 CB D:GLU146 4.4 34.7 1.0 CG D:GLU146 4.4 34.0 1.0 CD2 D:HIS149 4.5 36.0 1.0 OH D:TYR36 4.5 32.2 1.0 CE1 D:HIS65 4.9 33.8 1.0 CB D:ALA117 4.9 40.0 1.0 CA D:GLU114 4.9 38.5 1.0 CB D:GLU114 4.9 37.5 1.0 CZ D:TYR36 5.0 32.1 1.0

G.H.Gauss, M.A.Reott, E.R.Rocha, M.J.Young, T.Douglas, C.J.Smith, C.M.Lawrence. Characterization of the Bacteroides Fragilis Bfr Gene Product Identifies A Bacterial Dps-Like Protein and Suggests Evolutionary Links in the Ferritin Superfamily. J.Bacteriol. V. 194 15 2012.
ISSN: ISSN 0021-9193
PubMed: 22020642
DOI: 10.1128/JB.05260-11