Magnesium in PDB 2fkz: Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin

The structure of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin, PDB code: 2fkz was solved by L.Swartz, M.Kunchinskas, H.Li, T.L.Poulos, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.55 / 2.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	123.676, 123.676, 284.279, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 24.7

The structure of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin also contains other interesting chemical elements:

Iron

(Fe)

22 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin (pdb code 2fkz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin, PDB code: 2fkz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1701 b:44.9 occ:1.00 O A:HOH1771 1.9 32.4 1.0 O A:HOH1754 2.3 34.4 1.0 OD1 A:ASP132 4.0 25.6 1.0 OE1 A:GLU135 4.1 29.6 1.0 O A:HOH1747 4.4 26.6 1.0 CB A:GLU135 4.7 26.1 1.0 OD2 A:ASP139 4.9 26.9 1.0 OG1 A:THR136 4.9 25.8 1.0 CD A:GLU135 4.9 29.0 1.0

Magnesium binding site 2 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1702 b:37.5 occ:1.00 OE1 A:GLU118 2.7 28.1 1.0 CD A:GLU118 3.2 27.0 1.0 OE2 A:GLU118 3.3 28.6 1.0 OE1 A:GLU121 4.5 29.2 1.0 CG A:GLU118 4.5 25.8 1.0 CG A:GLU121 4.9 27.0 1.0 O A:HOH1744 5.0 35.4 1.0

Magnesium binding site 3 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1702 b:37.9 occ:1.00 O C:HOH1823 2.0 37.8 1.0 O D:HOH3133 2.0 37.8 1.0 O B:HOH3079 2.0 37.6 1.0 O B:HOH3078 2.0 38.0 1.0 O D:HOH3134 2.0 37.9 1.0 O D:HOH3135 2.1 37.7 1.0 OD1 D:ASP34 3.7 23.0 1.0 O B:HOH3057 3.9 47.0 1.0 OD1 B:ASP132 4.0 26.1 1.0 OD2 D:ASP34 4.1 23.1 1.0 OE1 B:GLU135 4.1 29.1 1.0 CG D:ASP34 4.2 22.4 1.0 O D:ASP34 4.3 19.7 1.0 O B:HOH3045 4.3 23.2 1.0 O C:PHE64 4.6 20.0 1.0 O B:HOH3049 4.7 41.7 1.0 O C:LEU63 4.8 17.5 1.0 O C:HOH1756 4.8 29.9 1.0 N C:MET1 4.8 35.1 1.0 CB B:GLU135 4.8 26.4 1.0 O B:HOH3058 4.8 45.5 1.0 OG1 B:THR136 4.9 26.6 1.0 OD2 B:ASP139 5.0 28.9 1.0 CG C:GLU66 5.0 25.4 1.0 CA C:PHE64 5.0 19.6 1.0

Magnesium binding site 4 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1701 b:46.9 occ:1.00 OE1 F:GLU118 2.8 28.9 1.0 OE2 F:GLU118 2.9 28.4 1.0 OE1 C:GLU118 3.0 27.3 1.0 OE1 C:GLU121 3.0 26.2 1.0 OE2 C:GLU118 3.0 26.9 1.0 OE1 B:GLU118 3.0 28.9 1.0 CD F:GLU118 3.2 27.2 1.0 OE2 B:GLU118 3.3 28.9 1.0 CD C:GLU118 3.4 25.6 1.0 CD B:GLU118 3.4 27.7 1.0 OE1 F:GLU121 3.4 29.2 1.0 OE1 B:GLU121 3.5 28.3 1.0 CD C:GLU121 4.0 24.8 1.0 OE2 B:GLU121 4.1 27.3 1.0 OE2 C:GLU121 4.1 25.6 1.0 CD B:GLU121 4.2 27.2 1.0 O C:HOH1746 4.3 29.1 1.0 O F:HOH1775 4.5 41.8 1.0 CD F:GLU121 4.6 28.4 1.0 CG B:GLU118 4.7 26.3 1.0 CG F:GLU118 4.7 25.6 1.0 CG C:GLU118 4.8 24.1 1.0 O C:HOH1725 5.0 28.7 1.0

Magnesium binding site 5 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1703 b:26.5 occ:1.00 O E:HOH3081 2.0 26.7 1.0 O F:HOH1782 2.0 27.1 1.0 O E:HOH3082 2.0 26.7 1.0 O C:HOH1824 2.0 26.3 1.0 O C:HOH1825 2.0 26.6 1.0 O C:HOH1826 2.1 26.9 1.0 OD1 C:ASP132 3.8 21.1 1.0 OD2 E:ASP34 4.0 23.2 1.0 OD1 E:ASP34 4.1 23.4 1.0 O C:HOH1719 4.2 22.7 1.0 O E:HOH3064 4.2 43.8 1.0 OE1 C:GLU135 4.3 22.7 1.0 O E:ASP34 4.3 21.9 1.0 CG E:ASP34 4.4 23.0 1.0 OG1 C:THR136 4.4 18.3 1.0 OD2 C:ASP139 4.5 22.4 1.0 O F:PHE64 4.7 19.6 1.0 CB C:GLU135 4.7 20.5 1.0 O F:LEU63 4.9 17.5 1.0 CD1 F:PHE64 4.9 20.2 1.0 N F:MET1 4.9 33.4 1.0 O F:HOH1723 4.9 29.3 1.0

Magnesium binding site 6 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1701 b:54.8 occ:0.50 O D:HOH3120 2.5 45.5 1.0 OE1 D:GLU118 3.0 27.4 1.0 OE1 D:GLU121 3.1 27.1 1.0 OE2 D:GLU118 3.6 28.4 1.0 CD D:GLU118 3.7 26.7 1.0 CD D:GLU121 4.0 25.6 1.0 OE2 D:GLU121 4.1 26.6 1.0 O D:HOH3060 4.9 34.4 1.0

Magnesium binding site 7 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1704 b:24.1 occ:1.00 O C:HOH1827 2.0 24.2 1.0 O C:HOH1828 2.0 23.7 1.0 O C:HOH1829 2.0 24.1 1.0 O D:HOH3136 2.0 24.2 1.0 O D:HOH3138 2.0 23.3 1.0 O D:HOH3137 2.0 24.1 1.0 O C:HOH1771 3.9 35.3 1.0 OD2 C:ASP34 3.9 22.0 1.0 OD1 C:ASP34 4.0 21.9 1.0 CG C:ASP34 4.3 21.6 1.0 O C:ASP34 4.3 20.1 1.0 O C:HOH1796 4.4 44.9 1.0 O D:HOH3108 4.5 35.0 1.0 O D:PHE64 4.7 20.0 1.0 O D:LEU63 4.8 17.9 1.0 N D:MET1 4.9 32.2 1.0 CD1 D:PHE64 5.0 20.3 1.0 CA D:PHE64 5.0 19.1 1.0

Magnesium binding site 8 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1705 b:35.0 occ:1.00 O E:HOH3084 2.0 35.3 1.0 O E:HOH3083 2.0 35.0 1.0 O E:HOH3086 2.0 35.2 1.0 O E:HOH3085 2.0 35.3 1.0 O E:HOH3087 2.0 35.5 1.0 O E:HOH3088 2.1 35.5 1.0 O E:HOH3026 4.1 30.4 1.0 OD1 E:ASP132 4.1 24.3 1.0 O E:HOH3060 4.2 36.1 1.0 OE1 E:GLU135 4.3 27.4 1.0 OG1 E:THR136 4.6 25.1 1.0 OD1 E:ASP139 4.6 27.4 1.0 CB E:GLU135 4.6 25.5 1.0

Magnesium binding site 9 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1701 b:32.9 occ:1.00 O F:HOH1780 2.0 32.5 1.0 O B:HOH3077 2.0 33.3 1.0 O F:HOH1781 2.0 33.1 1.0 O A:HOH1777 2.0 33.1 1.0 O A:HOH1778 2.1 33.0 1.0 O A:HOH1779 2.1 32.8 1.0 OD1 F:ASP132 4.0 24.0 1.0 OD1 A:ASP34 4.0 23.8 1.0 OE1 F:GLU135 4.1 26.6 1.0 OD2 A:ASP34 4.1 23.1 1.0 O F:HOH1725 4.2 29.5 1.0 O A:ASP34 4.3 22.0 1.0 O B:HOH3050 4.4 35.5 1.0 CG A:ASP34 4.4 23.0 1.0 OG1 F:THR136 4.6 24.8 1.0 OD1 F:ASP139 4.6 27.3 1.0 CB F:GLU135 4.6 25.1 1.0 O B:PHE64 4.7 21.2 1.0 N B:MET1 4.9 32.9 1.0 CD1 B:PHE64 4.9 24.4 1.0 CA B:PHE64 5.0 21.6 1.0

Magnesium binding site 10 out of 13 in the Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Reduced (All Ferrous) Form of the Azotobacter Vinelandii Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1701 b:19.2 occ:1.00 O H:HOH3087 1.9 18.1 1.0 OE2 H:GLU85 2.0 18.5 1.0 O H:HOH3047 2.0 19.4 1.0 O H:HOH3044 2.1 23.5 1.0 CD H:GLU85 3.0 19.2 1.0 OE1 H:GLU85 3.2 19.8 1.0 O H:HOH3117 3.6 41.9 1.0 O H:HOH3088 3.9 33.4 1.0 OE1 H:GLU81 4.0 25.4 1.0 CG H:GLU85 4.3 18.7 1.0 CD H:GLU81 4.8 24.7 1.0

L.Swartz, M.Kuchinskas, H.Li, T.L.Poulos, W.N.Lanzilotta. Redox-Dependent Structural Changes in the Azotobacter Vinelandii Bacterioferritin: New Insights Into the Ferroxidase and Iron Transport Mechanism(,). Biochemistry V. 45 4421 2006.
ISSN: ISSN 0006-2960
PubMed: 16584178
DOI: 10.1021/BI060146W