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Magnesium in PDB 3ak8: Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis

Protein crystallography data

The structure of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis, PDB code: 3ak8 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) 36.99 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.699, 98.383, 208.915, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.2

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

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 (pdb code 3ak8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 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, PDB code: 3ak8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 3ak8

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Magnesium binding site 1 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg169

b:25.7
occ:1.00
 O I:HOH464 2.0 24.5 1.0
O I:HOH985 2.1 29.7 1.0
O E:HOH607 2.1 25.6 1.0
O A:HOH1102 2.2 26.9 1.0
O E:HOH520 2.2 24.7 1.0
O I:HOH1101 2.3 26.5 1.0
OD1 I:ASP146 3.5 18.4 1.0
OD1 E:ASP146 3.6 19.5 1.0
OD1 A:ASP146 3.6 20.2 1.0
O I:HOH281 4.1 20.8 1.0
O E:HOH499 4.1 19.2 1.0
O A:HOH468 4.2 18.5 1.0
O E:HOH287 4.3 19.3 1.0
O I:HOH462 4.3 18.8 1.0
O A:HOH347 4.5 19.5 1.0
CG E:ASP146 4.5 15.9 1.0
CG I:ASP146 4.5 15.6 1.0
CG A:ASP146 4.6 16.1 1.0
CB E:ASP146 4.7 14.2 1.0
CB I:ASP146 4.8 14.0 1.0
CB A:ASP146 4.9 14.1 1.0

Magnesium binding site 2 out of 15 in 3ak8

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Magnesium binding site 2 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg170

b:36.0
occ:1.00
 O A:HOH1554 2.0 0.1 1.0
O C:HOH1228 2.1 38.4 1.0
O A:HOH1390 2.1 37.5 1.0
O A:HOH1342 2.6 35.0 1.0
OD2 C:ASP67 4.0 26.9 1.0
O A:HOH1291 4.0 90.5 1.0
OD2 A:ASP78 4.1 21.8 1.0
OD1 C:ASP67 4.4 25.6 1.0
O A:HOH732 4.4 28.4 1.0
CG C:ASP67 4.5 21.3 1.0
OE2 A:GLU82 4.6 28.5 1.0
NZ C:LYS48 4.6 28.4 1.0
O A:HOH690 4.7 28.0 1.0
CB A:ASP78 4.8 15.0 1.0
OD1 A:ASP75 4.9 29.3 1.0
CG A:ASP78 4.9 18.5 1.0

Magnesium binding site 3 out of 15 in 3ak8

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Magnesium binding site 3 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg171

b:86.3
occ:1.00
 O A:HOH1618 1.8 90.8 1.0
O A:HOH1620 1.9 0.5 1.0
O C:HOH880 2.1 30.1 1.0
O C:HOH1621 2.3 0.3 1.0
OD2 A:ASP67 3.4 29.4 1.0
OD2 C:ASP78 4.1 23.8 1.0
O C:HOH1619 4.1 0.4 1.0
CG A:ASP67 4.5 21.6 1.0
O A:HOH1573 4.5 35.7 1.0
O A:HOH612 4.6 29.7 1.0
NZ A:LYS48 4.6 25.8 1.0
CB C:ASP78 4.8 15.7 1.0
O C:HOH708 4.9 30.2 1.0
CG C:ASP78 4.9 19.0 1.0
OD1 A:ASP67 4.9 26.7 1.0

Magnesium binding site 4 out of 15 in 3ak8

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Magnesium binding site 4 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg169

b:22.6
occ:1.00
 O L:HOH710 2.0 28.2 1.0
O B:HOH995 2.0 27.1 1.0
O L:HOH762 2.1 23.7 1.0
O G:HOH354 2.1 22.1 1.0
O L:HOH816 2.2 24.7 1.0
O L:HOH855 2.2 23.5 1.0
OD1 L:ASP146 3.5 20.0 1.0
OD1 G:ASP146 3.6 20.1 1.0
OD1 B:ASP146 3.6 19.8 1.0
O G:HOH323 4.2 22.5 1.0
O L:HOH364 4.2 22.1 1.0
O B:HOH562 4.2 22.3 1.0
O G:HOH175 4.4 19.2 1.0
O B:HOH322 4.4 21.5 1.0
CG G:ASP146 4.5 17.8 1.0
CG L:ASP146 4.5 15.6 1.0
O L:HOH489 4.5 23.6 1.0
CG B:ASP146 4.6 17.6 1.0
CB G:ASP146 4.8 15.9 1.0
CB L:ASP146 4.8 14.5 1.0
CB B:ASP146 4.8 15.2 1.0

Magnesium binding site 5 out of 15 in 3ak8

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Magnesium binding site 5 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg170

b:36.7
occ:1.00
 O D:HOH1285 1.8 0.2 1.0
O D:HOH1555 1.9 0.4 1.0
O D:HOH1478 2.1 51.3 1.0
O B:HOH533 2.1 34.3 1.0
O B:HOH1383 2.2 33.5 1.0
O B:HOH919 3.7 34.7 1.0
OD2 D:ASP67 4.0 27.2 1.0
O B:HOH404 4.3 26.1 1.0
OD2 B:ASP78 4.3 24.1 1.0
OE2 B:GLU82 4.3 25.7 1.0
OD1 D:ASP67 4.4 26.8 1.0
O B:HOH1119 4.5 30.4 1.0
CG D:ASP67 4.6 22.5 1.0
NZ D:LYS48 4.7 29.2 1.0
CB B:ASP78 4.7 15.9 1.0
CG B:ASP78 5.0 18.7 1.0

Magnesium binding site 6 out of 15 in 3ak8

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Magnesium binding site 6 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg171

b:46.6
occ:1.00
 O B:HOH1438 2.0 0.9 1.0
O B:HOH1500 2.2 42.0 1.0
O D:HOH1379 2.4 36.4 1.0
O D:HOH1399 2.8 66.6 1.0
OD2 B:ASP67 3.5 16.9 0.5
OD2 B:ASP67 3.9 19.9 0.5
O D:HOH1286 4.0 32.6 1.0
OD2 D:ASP78 4.3 23.4 1.0
OD1 B:ASP67 4.3 19.0 0.5
O B:HOH1622 4.3 32.8 1.0
OE2 D:GLU82 4.4 29.6 1.0
CG B:ASP67 4.5 17.4 0.5
O F:HOH1482 4.5 40.9 1.0
CG B:ASP67 4.7 16.5 0.5
O B:HOH1172 4.7 29.2 1.0
NZ B:LYS48 4.8 27.3 1.0
O D:HOH628 4.8 26.7 1.0
CB D:ASP78 4.8 14.6 1.0
O D:HOH693 5.0 36.4 1.0
CG D:ASP78 5.0 18.9 1.0

Magnesium binding site 7 out of 15 in 3ak8

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Magnesium binding site 7 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg168

b:27.5
occ:1.00
 O H:HOH1540 2.0 28.7 1.0
O H:HOH1541 2.0 30.0 1.0
O C:HOH1491 2.3 44.5 1.0
O C:HOH454 2.3 19.8 1.0
O C:HOH1235 2.5 36.9 1.0
OE2 C:GLU142 3.8 20.6 1.0
OE1 C:GLU142 3.9 23.0 1.0
O H:HOH1126 3.9 27.8 1.0
O C:HOH418 4.0 20.5 1.0
CD C:GLU142 4.3 19.4 1.0
O H:ARG133 4.4 13.8 1.0
O C:HOH649 4.4 21.8 1.0
O H:HOH186 4.6 18.9 1.0
CA H:LYS134 4.8 14.2 1.0
C H:ARG133 5.0 12.9 1.0

Magnesium binding site 8 out of 15 in 3ak8

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Magnesium binding site 8 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg168

b:29.4
occ:1.00
 O D:HOH946 1.9 27.5 1.0
O F:HOH941 2.0 31.2 1.0
O F:HOH1542 2.1 26.3 1.0
O F:HOH1143 2.1 25.7 1.0
O F:HOH1058 2.1 29.4 1.0
O D:HOH739 2.2 23.2 1.0
OD1 K:ASP146 3.5 20.7 1.0
OD1 F:ASP146 3.6 19.3 1.0
OD1 D:ASP146 3.6 20.9 1.0
O F:HOH1617 3.7 34.6 1.0
O D:HOH554 4.0 23.6 1.0
O K:HOH232 4.0 20.1 1.0
O F:HOH546 4.2 21.4 1.0
O F:HOH362 4.3 19.6 1.0
O K:HOH368 4.3 21.6 1.0
O D:HOH181 4.4 19.3 1.0
CG F:ASP146 4.5 15.7 1.0
CG K:ASP146 4.5 14.7 1.0
CG D:ASP146 4.6 17.0 1.0
CB F:ASP146 4.8 14.2 1.0
CB D:ASP146 4.9 14.1 1.0
CB K:ASP146 4.9 13.9 1.0

Magnesium binding site 9 out of 15 in 3ak8

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Magnesium binding site 9 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg169

b:90.9
occ:1.00
 O F:HOH1340 1.9 51.8 1.0
O H:HOH1625 1.9 1.0 1.0
O H:HOH1223 2.2 32.1 1.0
O H:HOH1418 2.2 54.4 1.0
O F:HOH1624 2.2 99.8 1.0
OD2 F:ASP67 3.7 18.0 0.5
O H:HOH1194 3.9 34.1 1.0
OD2 F:ASP67 4.1 17.9 0.5
OD1 F:ASP67 4.3 17.6 0.5
OD2 H:ASP78 4.3 22.5 1.0
O H:HOH197 4.3 20.9 1.0
O J:HOH1475 4.4 52.0 1.0
OE2 H:GLU82 4.4 26.2 1.0
CG F:ASP67 4.5 15.7 0.5
O F:HOH737 4.6 26.9 1.0
O F:HOH1211 4.7 34.9 1.0
CG F:ASP67 4.8 15.1 0.5
NZ F:LYS48 4.8 24.7 1.0
CB H:ASP78 4.8 14.4 1.0

Magnesium binding site 10 out of 15 in 3ak8

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Magnesium binding site 10 out of 15 in the Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the SEP22 Dodecamer, A Dps-Like Protein From Salmonella Enterica Subsp. Enterica Serovar Enteritidis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg168

b:0.3
occ:1.00
 O H:HOH1556 2.0 58.9 1.0
O F:HOH1570 2.0 0.2 1.0
O H:HOH987 2.1 40.9 1.0
O F:HOH923 2.6 31.6 1.0
O F:HOH1436 2.6 60.5 1.0
OD2 H:ASP67 3.3 26.0 1.0
O F:HOH1571 4.2 23.6 1.0
O H:HOH972 4.2 31.0 1.0
OD2 F:ASP78 4.3 23.5 1.0
O F:HOH1146 4.3 30.3 1.0
CG H:ASP67 4.4 20.9 1.0
O F:HOH679 4.4 26.0 1.0
NZ H:LYS48 4.6 23.8 1.0
OD1 H:ASP67 4.9 25.6 1.0
OE2 F:GLU82 5.0 28.0 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: Wed Aug 14 08:37:08 2024

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