Magnesium 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:

Iron

(Fe)

8 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg1001 b:38.3 occ:1.00 O A:HOH2077 2.0 34.3 1.0 O A:HOH2033 2.1 32.5 1.0 OD2 A:ASP152 2.1 37.4 1.0 NE2 A:HIS58 2.3 31.5 1.0 O A:HOH2081 2.3 35.0 1.0 OE1 A:GLU54 2.5 37.8 1.0 CD2 A:HIS58 3.1 32.3 1.0 CG A:ASP152 3.1 38.2 1.0 CE1 A:HIS58 3.4 32.7 1.0 CD A:GLU54 3.6 39.2 1.0 CB A:ASP152 3.9 38.7 1.0 O A:HOH2035 4.0 45.0 1.0 OD1 A:ASP152 4.0 36.5 1.0 OE1 A:GLU148 4.2 42.4 1.0 OE1 A:GLU57 4.2 38.1 1.0 OE2 A:GLU54 4.2 43.9 1.0 CG A:HIS58 4.3 32.1 1.0 O A:HOH2080 4.3 32.4 1.0 ND1 A:HIS58 4.4 32.5 1.0 CD2 A:HIS149 4.6 35.9 1.0 O A:HOH2027 4.6 39.6 1.0 OE1 A:GLU61 4.6 37.3 1.0 CG A:GLU54 4.8 38.9 1.0 CB A:GLU54 4.9 35.7 1.0 O A:HOH2076 5.0 49.2 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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 B:Mg1001 b:38.5 occ:1.00 OD2 B:ASP152 2.0 37.9 1.0 O B:HOH2072 2.2 39.3 1.0 O B:HOH2028 2.3 34.5 1.0 NE2 B:HIS58 2.3 31.4 1.0 O B:HOH2071 2.3 36.0 1.0 OE1 B:GLU54 2.4 37.8 1.0 CG B:ASP152 3.1 38.4 1.0 CD2 B:HIS58 3.1 32.4 1.0 CE1 B:HIS58 3.4 32.4 1.0 CD B:GLU54 3.6 39.2 1.0 CB B:ASP152 3.8 38.5 1.0 OD1 B:ASP152 4.0 36.6 1.0 OE2 B:GLU54 4.2 44.1 1.0 OE1 B:GLU148 4.2 42.3 1.0 O B:HOH2032 4.2 45.0 1.0 OE1 B:GLU57 4.2 37.7 1.0 CG B:HIS58 4.4 32.5 1.0 ND1 B:HIS58 4.5 32.5 1.0 CD2 B:HIS149 4.7 36.1 1.0 O B:HOH2030 4.7 42.4 1.0 OE1 B:GLU61 4.7 37.1 1.0 O B:HOH2021 4.8 45.1 1.0 CG B:GLU54 4.8 39.1 1.0 CB B:GLU54 4.9 35.8 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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 C:Mg1001 b:38.1 occ:1.00 OD2 C:ASP152 2.0 38.1 1.0 O C:HOH2072 2.1 30.4 1.0 O C:HOH2028 2.2 38.2 1.0 O C:HOH2074 2.2 29.5 1.0 NE2 C:HIS58 2.3 31.5 1.0 OE1 C:GLU54 2.5 37.2 1.0 CG C:ASP152 3.1 38.2 1.0 CD2 C:HIS58 3.1 32.5 1.0 CE1 C:HIS58 3.4 32.5 1.0 CD C:GLU54 3.7 39.1 1.0 CB C:ASP152 3.8 38.6 1.0 OD1 C:ASP152 3.9 36.3 1.0 OE1 C:GLU148 4.2 42.4 1.0 OE1 C:GLU57 4.3 38.0 1.0 OE2 C:GLU54 4.3 43.9 1.0 CG C:HIS58 4.3 32.5 1.0 ND1 C:HIS58 4.5 32.3 1.0 CD2 C:HIS149 4.6 36.3 1.0 OE1 C:GLU61 4.7 37.6 1.0 O C:HOH2030 4.8 43.9 1.0 CG C:GLU54 4.9 39.0 1.0 O C:HOH2024 4.9 45.5 1.0 CB C:GLU54 4.9 35.7 1.0 CG C:GLU148 5.0 38.1 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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 D:Mg1001 b:38.0 occ:1.00 OD2 D:ASP152 2.0 37.6 1.0 O D:HOH2024 2.2 39.5 1.0 O D:HOH2083 2.3 24.8 1.0 NE2 D:HIS58 2.3 31.5 1.0 O D:HOH2084 2.3 34.2 1.0 OE1 D:GLU54 2.4 37.5 1.0 CG D:ASP152 3.1 38.2 1.0 CD2 D:HIS58 3.1 32.4 1.0 CE1 D:HIS58 3.4 32.4 1.0 CD D:GLU54 3.6 39.2 1.0 CB D:ASP152 3.8 38.4 1.0 OD1 D:ASP152 3.9 36.3 1.0 O D:HOH2028 4.1 38.9 1.0 OE1 D:GLU148 4.2 42.6 1.0 O D:HOH2086 4.2 41.7 1.0 OE2 D:GLU54 4.2 44.3 1.0 CG D:HIS58 4.3 32.3 1.0 OE1 D:GLU57 4.3 37.6 1.0 ND1 D:HIS58 4.4 32.8 1.0 CD2 D:HIS149 4.6 36.0 1.0 OE1 D:GLU61 4.7 37.4 1.0 CG D:GLU54 4.8 39.0 1.0 CB D:GLU54 4.9 35.8 1.0 O D:HOH2019 4.9 36.8 1.0 CG D:GLU148 5.0 37.9 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