Magnesium in PDB 3ak9: Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form

The structure of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form, PDB code: 3ak9 was solved by T.Miyamoto, Y.Asahina, S.Miyazaki, H.Shimizu, U.Ohto, S.Noguchi, Y.Satow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.471, 98.003, 208.414, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.2

The structure of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form also contains other interesting chemical elements:

Iron

(Fe)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form (pdb code 3ak9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form, PDB code: 3ak9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg170 b:36.0 occ:1.00 O F:HOH1028 2.0 39.9 1.0 O F:HOH1033 2.2 37.3 1.0 O K:HOH1030 2.2 39.6 1.0 O D:HOH1031 2.2 43.8 1.0 O F:HOH1029 2.2 35.0 1.0 O D:HOH1032 2.3 35.9 1.0 OD1 D:ASP146 3.5 27.6 1.0 OD1 K:ASP146 3.6 27.5 1.0 OD1 F:ASP146 3.6 26.0 1.0 O F:HOH1034 4.0 41.2 1.0 O D:HOH553 4.1 32.4 1.0 O F:HOH436 4.1 27.8 1.0 O K:HOH209 4.1 29.1 1.0 O D:HOH292 4.2 26.7 1.0 O F:HOH409 4.3 27.5 1.0 O K:HOH578 4.3 30.4 1.0 CG D:ASP146 4.5 23.2 1.0 CG K:ASP146 4.6 23.6 1.0 CG F:ASP146 4.6 21.8 1.0 CB D:ASP146 4.8 21.6 1.0 CB K:ASP146 4.9 22.3 1.0 CB F:ASP146 4.9 20.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg169 b:36.7 occ:1.00 O G:HOH1016 2.0 37.1 1.0 O G:HOH824 2.0 49.0 1.0 O B:HOH821 2.2 44.0 1.0 O L:HOH1015 2.2 41.3 1.0 O L:HOH822 2.3 48.8 1.0 O B:HOH823 2.3 43.5 1.0 OD1 G:ASP146 3.5 28.1 1.0 OD1 L:ASP146 3.5 27.4 1.0 OD1 B:ASP146 3.5 27.3 1.0 O L:HOH1017 3.8 36.5 1.0 O G:HOH766 4.0 31.9 1.0 O L:HOH880 4.1 32.8 1.0 O B:HOH495 4.1 31.5 1.0 O G:HOH372 4.2 28.7 1.0 O B:HOH188 4.3 28.7 1.0 O L:HOH433 4.3 28.6 1.0 CG G:ASP146 4.5 24.0 1.0 CG L:ASP146 4.5 23.6 1.0 CG B:ASP146 4.5 24.1 1.0 CB L:ASP146 4.8 22.3 1.0 CB G:ASP146 4.8 22.7 1.0 CB B:ASP146 4.8 22.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg169 b:56.0 occ:1.00 O H:HOH1319 2.1 45.2 1.0 O H:HOH1069 2.2 46.9 1.0 O H:HOH1320 2.2 45.0 1.0 O C:HOH1318 2.3 58.4 1.0 O C:HOH1316 2.3 41.4 1.0 O J:HOH1317 2.4 46.1 1.0 OD1 H:ASP146 3.4 26.9 1.0 OD1 J:ASP146 3.5 27.0 1.0 OD1 C:ASP146 3.7 26.5 1.0 O C:HOH592 3.9 34.5 1.0 O J:HOH514 3.9 31.2 1.0 O H:HOH1124 3.9 35.0 1.0 O H:HOH695 4.1 29.7 1.0 O C:HOH188 4.2 30.4 1.0 O J:HOH971 4.2 29.6 1.0 O H:HOH450 4.2 30.1 1.0 CG H:ASP146 4.5 23.0 1.0 CG J:ASP146 4.5 22.8 1.0 CB H:ASP146 4.7 21.4 1.0 CG C:ASP146 4.7 22.6 1.0 CB J:ASP146 4.8 21.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, Fe-Soaked Form within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg169 b:52.8 occ:1.00 O I:HOH1006 1.9 50.0 1.0 O E:HOH1020 2.1 44.4 1.0 O A:HOH1019 2.2 46.6 1.0 O A:HOH1018 2.4 42.3 1.0 O E:HOH945 2.4 42.8 1.0 O A:HOH1021 2.5 47.7 1.0 OD1 I:ASP146 3.4 28.0 1.0 OD1 E:ASP146 3.6 28.0 1.0 OD1 A:ASP146 3.7 26.9 1.0 O I:HOH660 3.8 35.9 1.0 O E:HOH1315 3.9 38.1 1.0 O I:HOH941 4.0 30.9 1.0 O A:HOH1025 4.0 31.9 1.0 O E:HOH905 4.2 36.0 1.0 O E:HOH618 4.3 33.9 1.0 O A:HOH773 4.4 31.5 1.0 CG I:ASP146 4.4 23.4 1.0 CB I:ASP146 4.6 22.9 1.0 CG E:ASP146 4.6 23.0 1.0 CG A:ASP146 4.7 23.7 1.0 CA I:ASP146 4.9 21.9 1.0 CB E:ASP146 4.9 22.9 1.0

T.Miyamoto, Y.Asahina, S.Miyazaki, H.Shimizu, U.Ohto, S.Noguchi, Y.Satow. Structures of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis Acta Crystallogr.,Sect.F V. 67 17 2011.
ISSN: ESSN 1744-3091
PubMed: 21206015
DOI: 10.1107/S1744309110043113