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

Protein crystallography data

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

Other elements in 3ak9:

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:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 12 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 3ak9

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Iron binding site 1 out of 12 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 Iron with other atoms in the Fe 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
A:Fe168

b:25.9
occ:1.00
 O C:HOH463 1.9 26.8 1.0
OE2 A:GLU82 2.0 24.3 1.0
NE2 C:HIS51 2.2 23.0 1.0
O C:HOH297 2.2 30.9 1.0
OD2 A:ASP78 2.3 23.9 1.0
OD1 A:ASP78 2.3 23.9 1.0
CG A:ASP78 2.7 23.6 1.0
CD A:GLU82 2.9 24.3 1.0
CE1 C:HIS51 3.1 23.4 1.0
CD2 C:HIS51 3.2 23.6 1.0
NZ C:LYS48 3.2 30.1 1.0
OE1 A:GLU82 3.3 26.2 1.0
NE2 C:HIS63 3.9 24.7 1.0
CE1 C:HIS63 4.0 25.2 1.0
OD2 C:ASP67 4.1 28.0 1.0
CG A:GLU82 4.1 22.8 1.0
CB A:ASP78 4.2 22.4 1.0
ND1 C:HIS51 4.3 23.3 1.0
NE1 C:TRP52 4.3 22.4 1.0
CG C:HIS51 4.3 22.6 1.0
CD1 C:TRP52 4.4 21.8 1.0
OD1 C:ASP67 4.5 25.7 1.0
CE C:LYS48 4.7 29.7 1.0
CG C:ASP67 4.7 24.2 1.0
O C:HOH1118 4.7 51.6 1.0
O A:HOH1229 4.8 38.1 1.0
O A:ASP78 4.9 21.2 1.0

Iron binding site 2 out of 12 in 3ak9

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Iron binding site 2 out of 12 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 Iron with other atoms in the Fe 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
B:Fe168

b:24.5
occ:1.00
 OE2 B:GLU82 1.9 23.2 1.0
O D:HOH299 2.0 25.5 1.0
NE2 D:HIS51 2.2 23.0 1.0
O D:HOH238 2.2 28.2 1.0
OD1 B:ASP78 2.3 23.3 1.0
OD2 B:ASP78 2.3 22.7 1.0
CG B:ASP78 2.6 21.7 1.0
CD B:GLU82 2.9 24.6 1.0
CD2 D:HIS51 3.2 24.3 1.0
CE1 D:HIS51 3.2 22.3 1.0
OE1 B:GLU82 3.3 24.8 1.0
NE2 D:HIS63 4.0 23.8 1.0
CE1 D:HIS63 4.0 24.0 1.0
NZ D:LYS48 4.0 27.9 1.0
OD2 D:ASP67 4.1 27.0 1.0
CG B:GLU82 4.1 22.3 1.0
CB B:ASP78 4.2 21.4 1.0
ND1 D:HIS51 4.3 22.2 1.0
CG D:HIS51 4.3 21.7 1.0
NE1 D:TRP52 4.3 21.4 1.0
OD1 D:ASP67 4.4 24.7 1.0
CD1 D:TRP52 4.5 21.0 1.0
CG D:ASP67 4.7 23.8 1.0
O B:HOH741 4.8 33.6 1.0
O D:HOH1011 4.9 39.7 1.0
O B:ASP78 4.9 20.6 1.0
CA B:ASP78 5.0 20.9 1.0

Iron binding site 3 out of 12 in 3ak9

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Iron binding site 3 out of 12 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 Iron with other atoms in the Fe 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
C:Fe168

b:24.9
occ:1.00
 O A:HOH308 1.8 29.9 1.0
OE2 C:GLU82 2.0 24.5 1.0
NE2 A:HIS51 2.2 23.0 1.0
O A:HOH177 2.2 29.4 1.0
OD2 C:ASP78 2.3 23.1 1.0
OD1 C:ASP78 2.3 23.3 1.0
CG C:ASP78 2.7 22.1 1.0
CD C:GLU82 2.9 24.0 1.0
CE1 A:HIS51 3.1 21.9 1.0
CD2 A:HIS51 3.2 23.3 1.0
NZ A:LYS48 3.3 30.5 1.0
OE1 C:GLU82 3.4 24.7 1.0
NE2 A:HIS63 3.9 23.4 1.0
CE1 A:HIS63 4.0 21.9 1.0
OD2 A:ASP67 4.1 27.0 1.0
CG C:GLU82 4.2 21.4 1.0
CB C:ASP78 4.2 21.4 1.0
ND1 A:HIS51 4.3 22.6 1.0
CG A:HIS51 4.3 22.0 1.0
NE1 A:TRP52 4.4 22.0 1.0
OD1 A:ASP67 4.4 25.4 1.0
CD1 A:TRP52 4.5 21.9 1.0
CG A:ASP67 4.7 23.3 1.0
CE A:LYS48 4.7 30.9 1.0
O C:HOH914 4.8 32.9 1.0
O C:ASP78 4.9 20.8 1.0
O A:HOH1001 4.9 45.3 1.0

Iron binding site 4 out of 12 in 3ak9

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Iron binding site 4 out of 12 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 Iron with other atoms in the Fe 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
D:Fe168

b:24.1
occ:1.00
 O B:HOH279 2.0 26.1 1.0
OE2 D:GLU82 2.0 23.5 1.0
O B:HOH169 2.2 31.8 1.0
NE2 B:HIS51 2.2 21.5 1.0
OD2 D:ASP78 2.3 22.6 1.0
OD1 D:ASP78 2.3 23.1 1.0
CG D:ASP78 2.7 21.8 1.0
CD D:GLU82 2.9 22.2 1.0
CE1 B:HIS51 3.1 22.0 1.0
CD2 B:HIS51 3.2 22.4 1.0
OE1 D:GLU82 3.3 24.4 1.0
NZ B:LYS48 3.9 28.2 1.0
NE2 B:HIS63 4.0 23.5 1.0
CE1 B:HIS63 4.0 23.2 1.0
OD2 B:ASP67 4.1 26.8 1.0
CG D:GLU82 4.1 20.0 1.0
CB D:ASP78 4.2 20.8 1.0
ND1 B:HIS51 4.3 21.3 1.0
CG B:HIS51 4.3 20.6 1.0
NE1 B:TRP52 4.4 20.6 1.0
OD1 B:ASP67 4.4 23.9 1.0
CD1 B:TRP52 4.5 20.6 1.0
CG B:ASP67 4.7 23.5 1.0
O D:HOH554 4.7 32.6 1.0
O B:HOH1212 4.7 43.7 1.0
O B:HOH1198 4.9 41.4 1.0
O D:ASP78 5.0 20.1 1.0

Iron binding site 5 out of 12 in 3ak9

Go back to Iron Binding Sites List in 3ak9
Iron binding site 5 out of 12 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 Iron with other atoms in the Fe binding site number 5 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
E:Fe168

b:24.7
occ:1.00
 O G:HOH359 2.0 27.5 1.0
OE2 E:GLU82 2.0 23.4 1.0
NE2 G:HIS51 2.2 21.3 1.0
O E:HOH187 2.2 29.1 1.0
OD1 E:ASP78 2.3 23.6 1.0
OD2 E:ASP78 2.3 23.8 1.0
CG E:ASP78 2.7 22.7 1.0
CD E:GLU82 2.9 21.9 1.0
CE1 G:HIS51 3.2 21.4 1.0
CD2 G:HIS51 3.2 23.9 1.0
OE1 E:GLU82 3.4 24.6 1.0
NZ G:LYS48 3.9 28.8 1.0
NE2 G:HIS63 4.0 22.6 1.0
CE1 G:HIS63 4.0 23.1 1.0
OD2 G:ASP67 4.1 28.7 1.0
CG E:GLU82 4.1 21.8 1.0
CB E:ASP78 4.2 21.5 1.0
ND1 G:HIS51 4.3 21.7 1.0
O I:HOH1270 4.3 53.6 1.0
NE1 G:TRP52 4.3 21.3 1.0
CG G:HIS51 4.3 20.7 1.0
CD1 G:TRP52 4.4 20.5 1.0
OD1 G:ASP67 4.5 25.2 1.0
CG G:ASP67 4.7 24.0 1.0
O E:HOH1071 4.7 34.5 1.0
O E:ASP78 5.0 20.8 1.0

Iron binding site 6 out of 12 in 3ak9

Go back to Iron Binding Sites List in 3ak9
Iron binding site 6 out of 12 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 Iron with other atoms in the Fe binding site number 6 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
F:Fe168

b:24.0
occ:1.00
 O H:HOH288 1.9 25.2 1.0
OE2 F:GLU82 1.9 22.9 1.0
NE2 H:HIS51 2.2 22.1 1.0
O F:HOH419 2.2 31.4 1.0
OD1 F:ASP78 2.3 23.1 1.0
OD2 F:ASP78 2.3 23.6 1.0
CG F:ASP78 2.7 22.4 1.0
CD F:GLU82 2.9 21.5 1.0
CE1 H:HIS51 3.2 22.3 1.0
CD2 H:HIS51 3.2 23.4 1.0
OE1 F:GLU82 3.4 23.9 1.0
NZ H:LYS48 3.5 31.2 1.0
NE2 H:HIS63 4.0 23.9 1.0
CE1 H:HIS63 4.0 23.7 1.0
CG F:GLU82 4.1 20.3 1.0
OD2 H:ASP67 4.1 27.8 1.0
CB F:ASP78 4.2 20.7 1.0
ND1 H:HIS51 4.3 21.5 1.0
NE1 H:TRP52 4.3 20.3 1.0
CG H:HIS51 4.3 22.1 1.0
CD1 H:TRP52 4.4 20.9 1.0
OD1 H:ASP67 4.5 24.8 1.0
O F:HOH804 4.7 32.8 1.0
CG H:ASP67 4.7 23.9 1.0
O F:ASP78 4.9 19.4 1.0
CE H:LYS48 4.9 31.3 1.0
O H:HOH802 5.0 46.9 1.0

Iron binding site 7 out of 12 in 3ak9

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Iron binding site 7 out of 12 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 Iron with other atoms in the Fe binding site number 7 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:Fe168

b:25.5
occ:1.00
 O E:HOH794 1.9 28.9 1.0
OE2 G:GLU82 2.0 23.6 1.0
NE2 E:HIS51 2.2 22.4 1.0
O G:HOH368 2.2 30.6 1.0
OD2 G:ASP78 2.3 22.5 1.0
OD1 G:ASP78 2.3 24.2 1.0
CG G:ASP78 2.7 22.1 1.0
CD G:GLU82 3.0 22.1 1.0
CE1 E:HIS51 3.1 23.2 1.0
CD2 E:HIS51 3.2 23.9 1.0
OE1 G:GLU82 3.4 25.8 1.0
NE2 E:HIS63 4.0 25.3 1.0
NZ E:LYS48 4.0 30.1 1.0
CE1 E:HIS63 4.0 25.0 1.0
OD2 E:ASP67 4.1 28.9 1.0
CG G:GLU82 4.1 21.2 1.0
CB G:ASP78 4.2 21.0 1.0
ND1 E:HIS51 4.3 23.5 1.0
CG E:HIS51 4.3 22.3 1.0
NE1 E:TRP52 4.3 22.2 1.0
OD1 E:ASP67 4.5 26.7 1.0
CD1 E:TRP52 4.5 21.4 1.0
CG E:ASP67 4.7 25.2 1.0
O G:ASP78 5.0 20.7 1.0
O E:HOH1058 5.0 45.1 1.0

Iron binding site 8 out of 12 in 3ak9

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Iron binding site 8 out of 12 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 Iron with other atoms in the Fe binding site number 8 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:Fe168

b:23.3
occ:1.00
 O F:HOH354 1.9 26.0 1.0
OE2 H:GLU82 2.0 22.3 1.0
NE2 F:HIS51 2.1 21.2 1.0
O F:HOH380 2.3 28.4 1.0
OD2 H:ASP78 2.3 21.7 1.0
OD1 H:ASP78 2.3 21.4 1.0
CG H:ASP78 2.7 21.4 1.0
CD H:GLU82 2.9 21.9 1.0
CE1 F:HIS51 3.1 20.9 1.0
CD2 F:HIS51 3.2 22.5 1.0
OE1 H:GLU82 3.4 23.3 1.0
NZ F:LYS48 3.9 29.4 1.0
NE2 F:HIS63 4.0 22.1 1.0
CE1 F:HIS63 4.0 21.4 1.0
OD2 F:ASP67 4.1 26.8 1.0
CG H:GLU82 4.1 20.5 1.0
CB H:ASP78 4.2 20.8 1.0
ND1 F:HIS51 4.2 20.4 1.0
CG F:HIS51 4.3 20.6 1.0
NE1 F:TRP52 4.3 19.4 1.0
CD1 F:TRP52 4.4 19.2 1.0
OD1 F:ASP67 4.5 24.4 1.0
O H:HOH722 4.7 30.9 1.0
CG F:ASP67 4.7 23.0 1.0
O H:ASP78 5.0 19.5 1.0

Iron binding site 9 out of 12 in 3ak9

Go back to Iron Binding Sites List in 3ak9
Iron binding site 9 out of 12 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 Iron with other atoms in the Fe binding site number 9 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:Fe168

b:25.9
occ:1.00
 O K:HOH742 1.8 28.2 1.0
OE2 I:GLU82 2.0 24.2 1.0
O K:HOH460 2.2 30.8 1.0
NE2 K:HIS51 2.2 22.4 1.0
OD1 I:ASP78 2.3 23.4 1.0
OD2 I:ASP78 2.4 23.6 1.0
CG I:ASP78 2.7 22.2 1.0
CD I:GLU82 2.9 23.4 1.0
CE1 K:HIS51 3.2 22.8 1.0
CD2 K:HIS51 3.2 24.0 1.0
OE1 I:GLU82 3.4 26.2 1.0
NE2 K:HIS63 3.9 25.2 1.0
NZ K:LYS48 4.0 29.9 1.0
CE1 K:HIS63 4.0 23.1 1.0
O K:HOH1119 4.0 86.2 1.0
OD2 K:ASP67 4.0 29.3 1.0
CG I:GLU82 4.2 21.9 1.0
CB I:ASP78 4.2 21.5 1.0
ND1 K:HIS51 4.3 23.4 1.0
CG K:HIS51 4.3 21.6 1.0
NE1 K:TRP52 4.4 21.3 1.0
OD1 K:ASP67 4.4 26.5 1.0
CD1 K:TRP52 4.5 20.4 1.0
CG K:ASP67 4.7 24.2 1.0
O I:HOH819 4.8 35.5 1.0
O I:ASP78 5.0 20.9 1.0

Iron binding site 10 out of 12 in 3ak9

Go back to Iron Binding Sites List in 3ak9
Iron binding site 10 out of 12 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 Iron with other atoms in the Fe binding site number 10 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
J:Fe168

b:24.7
occ:1.00
 O L:HOH179 1.9 25.3 1.0
OE2 J:GLU82 2.0 23.5 1.0
O J:HOH616 2.1 30.1 1.0
NE2 L:HIS51 2.2 21.8 1.0
OD1 J:ASP78 2.3 22.9 1.0
OD2 J:ASP78 2.3 23.8 1.0
CG J:ASP78 2.6 22.6 1.0
CD J:GLU82 2.9 23.4 1.0
CD2 L:HIS51 3.2 22.1 1.0
CE1 L:HIS51 3.2 21.6 1.0
OE1 J:GLU82 3.3 24.4 1.0
NZ L:LYS48 3.9 28.7 1.0
NE2 L:HIS63 4.0 23.8 1.0
CE1 L:HIS63 4.0 22.8 1.0
OD2 L:ASP67 4.1 27.3 1.0
CB J:ASP78 4.2 21.7 1.0
CG J:GLU82 4.2 22.6 1.0
ND1 L:HIS51 4.3 22.6 1.0
NE1 L:TRP52 4.3 21.1 1.0
CG L:HIS51 4.3 21.7 1.0
OD1 L:ASP67 4.4 26.0 1.0
CD1 L:TRP52 4.4 21.1 1.0
O J:HOH954 4.7 31.9 1.0
CG L:ASP67 4.7 24.3 1.0
O L:HOH907 4.7 39.2 1.0
O L:HOH1074 5.0 43.3 1.0
O J:ASP78 5.0 20.5 1.0

Reference:

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
Page generated: Sun Aug 4 07:16:28 2024

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