Magnesium in PDB 9fhl: High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna

Other elements in 9fhl:

The structure of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 59;

Binding sites:

The binding sites of Magnesium atom in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna (pdb code 9fhl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 59 binding sites of Magnesium where determined in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna, PDB code: 9fhl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 59 in 9fhl

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Magnesium binding site 1 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1501

b:19.7
occ:1.00
 O 2:HOH1842 1.8 14.7 1.0
O 2:HOH1971 1.8 18.2 1.0
O 2:HOH1834 1.9 17.7 1.0
OP2 2:A532 2.0 25.3 1.0
OP2 2:A531 2.2 23.3 1.0
OP2 2:A533 2.2 15.0 1.0
P 2:A532 3.2 8.3 1.0
P 2:A531 3.3 11.3 1.0
OP1 2:A532 3.6 10.9 1.0
P 2:A533 3.6 10.6 1.0
OP1 2:A531 3.7 22.7 1.0
O5' 2:A531 3.9 25.8 1.0
OP1 2:U530 4.1 15.6 1.0
C5' 2:A531 4.1 19.9 1.0
OP1 2:A533 4.2 21.5 1.0
O5' 2:A532 4.3 21.8 1.0
O3' 2:A531 4.3 13.5 1.0
N7 2:A533 4.4 14.3 1.0
C3' 2:A532 4.5 17.4 1.0
OP2 2:U530 4.5 22.5 1.0
O3' 2:A532 4.5 29.3 1.0
C3' 2:A531 4.5 8.9 1.0
O5' 2:A533 4.6 21.3 1.0
C8 2:A533 4.6 15.6 1.0
P 2:U530 4.6 12.5 1.0
O3' 2:U530 4.7 15.8 1.0
C5' 2:A532 4.7 15.1 1.0
O 2:HOH1883 4.7 20.8 1.0
O5' 2:U530 4.9 23.1 1.0
C4' 2:A531 4.9 17.5 1.0

Magnesium binding site 2 out of 59 in 9fhl

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Magnesium binding site 2 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1502

b:26.3
occ:1.00
 O 2:HOH1902 1.8 23.0 1.0
O 2:HOH1881 1.9 20.4 1.0
O 2:HOH1767 2.0 16.1 1.0
OP2 2:A567 2.1 22.8 1.0
O 2:HOH1774 2.4 13.1 1.0
P 2:A567 3.4 19.1 1.0
O5' 2:A567 3.7 18.8 1.0
N7 2:A568 3.9 14.1 1.0
O 2:HOH1730 4.1 15.2 1.0
OP1 2:A567 4.1 28.0 1.0
N6 2:A568 4.3 9.5 1.0
N7 2:A567 4.3 10.3 1.0
O 2:HOH1929 4.3 13.0 1.0
C8 2:A567 4.3 13.5 1.0
OP1 2:A566 4.4 14.2 1.0
N7 2:G569 4.6 16.9 1.0
O3' 2:A566 4.6 21.2 1.0
OP2 2:A568 4.8 22.1 1.0
C5 2:A568 4.8 11.8 1.0
C8 2:A568 4.8 9.5 1.0
C3' 2:A566 4.8 20.1 1.0
C6 2:A568 5.0 10.8 1.0

Magnesium binding site 3 out of 59 in 9fhl

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Magnesium binding site 3 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1503

b:26.4
occ:1.00
 OP2 2:G719 1.9 20.4 1.0
OP1 2:A718 1.9 10.6 1.0
P 2:A718 3.1 13.5 1.0
P 2:G719 3.3 20.3 1.0
OP2 2:A718 3.6 20.6 1.0
O5' 2:A718 3.7 14.2 1.0
O5' 2:G719 4.1 17.8 1.0
O6 2:G720 4.1 13.9 1.0
N7 2:G720 4.2 12.7 1.0
OP1 2:G719 4.2 13.5 1.0
O3' 2:A718 4.2 10.9 1.0
C5' 2:A718 4.3 6.3 1.0
O3' 2:G717 4.4 10.6 1.0
N4 2:C535 4.4 20.4 1.0
N3 2:C535 4.5 20.1 1.0
C3' 2:A718 4.6 9.6 1.0
C6 2:G720 4.9 10.4 1.0
C5 2:G720 4.9 10.6 1.0

Magnesium binding site 4 out of 59 in 9fhl

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Magnesium binding site 4 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1504

b:16.5
occ:1.00
 O 2:HOH1832 1.8 14.0 1.0
OP1 2:G1462 1.9 16.0 1.0
O1P 2:6MZ1457 2.0 10.8 1.0
O 2:HOH1854 2.0 14.0 1.0
OP1 2:G1465 2.2 23.3 1.0
O 2:HOH1736 2.2 6.3 1.0
P 2:G1462 3.3 14.8 1.0
P 2:6MZ1457 3.3 7.5 1.0
P 2:G1465 3.4 14.8 1.0
O3' 2:A1464 3.4 24.6 1.0
OP1 2:G1461 3.7 18.4 1.0
O 2:HOH1957 3.8 11.5 1.0
O2P 2:6MZ1457 3.9 10.4 1.0
C3' 2:G1461 4.1 9.0 1.0
N14 2:SPM1579 4.1 10.3 1.0
OP2 2:G1462 4.1 2.8 1.0
O3' 2:G1461 4.1 15.0 1.0
C5' 2:G1465 4.2 13.4 1.0
O5' 2:6MZ1457 4.2 9.8 1.0
OP2 2:C1458 4.2 15.1 1.0
C5' 2:G1462 4.2 7.9 1.0
O2' 2:U1463 4.2 19.8 1.0
O5' 2:G1462 4.2 11.9 1.0
O5' 2:G1465 4.3 18.4 1.0
O2' 2:G1461 4.4 11.7 1.0
O3' 2:A1456 4.4 22.4 1.0
OP2 2:G1465 4.5 16.6 1.0
P 2:G1461 4.6 14.4 1.0
C2' 2:G1461 4.6 11.5 1.0
C5' 2:6MZ1457 4.7 4.7 1.0
OP2 2:G1461 4.7 21.7 1.0
C3' 2:A1464 4.8 18.2 1.0
C13 2:SPM1579 4.8 8.1 1.0
C2' 2:U1463 4.9 6.3 1.0
O5' 2:G1461 4.9 16.2 1.0

Magnesium binding site 5 out of 59 in 9fhl

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Magnesium binding site 5 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1505

b:25.5
occ:1.00
 O 2:HOH1913 1.9 16.4 1.0
O 2:HOH2114 2.0 22.7 1.0
O 2:HOH1866 2.0 21.4 1.0
O 2:HOH1851 2.0 15.7 1.0
O 2:HOH1824 2.4 3.7 1.0
O 2:HOH1920 2.5 13.3 1.0
O3' 2:G1483 4.0 17.5 1.0
OP2 2:G690 4.0 12.4 1.0
OP1 2:G690 4.3 18.8 1.0
OP1 2:C1484 4.3 24.9 1.0
OP2 2:A775 4.4 17.7 1.0
O2' 2:G1483 4.4 13.5 1.0
OP1 2:A689 4.4 24.2 1.0
N1 2:A773 4.4 20.1 1.0
P 2:G690 4.5 8.8 1.0
C2 2:A773 4.7 13.6 1.0
O3' 2:A689 4.7 20.4 1.0
P 2:C1484 4.8 1.0 1.0
C5' 2:A689 4.8 4.3 1.0
C5' 2:C1484 4.9 6.3 1.0
C3' 2:G1483 4.9 17.4 1.0
C4' 2:G1483 4.9 15.5 1.0

Magnesium binding site 6 out of 59 in 9fhl

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Magnesium binding site 6 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1506

b:24.4
occ:1.00
 O 2:HOH1796 1.8 17.5 1.0
OP2 2:G1462 2.0 2.8 1.0
O2P 2:6MZ1457 2.1 10.4 1.0
O 2:HOH1998 2.1 14.5 1.0
O 2:HOH1990 2.3 9.2 1.0
OP2 2:A1456 2.8 17.1 1.0
O3' 2:U1455 3.3 77.2 1.0
P 2:G1462 3.4 14.8 1.0
P 2:6MZ1457 3.6 7.5 1.0
P 2:A1456 3.6 16.8 1.0
O3' 2:G1461 3.8 15.0 1.0
O 2:HOH2027 3.8 18.9 1.0
O2' 2:U1455 4.0 79.3 1.0
C3' 2:A1456 4.0 7.1 1.0
OP1 2:G1462 4.2 16.0 1.0
O3' 2:A1456 4.2 22.4 1.0
O 2:HOH1957 4.2 11.5 1.0
O1P 2:6MZ1457 4.4 10.8 1.0
O5' 2:A1456 4.5 12.8 1.0
C3' 2:U1455 4.5 78.2 1.0
O2' 2:G1461 4.5 11.7 1.0
O5' 2:G1462 4.5 11.9 1.0
O5' 2:6MZ1457 4.5 9.8 1.0
O 2:HOH1985 4.5 18.7 1.0
N7 2:6MZ1457 4.6 7.8 1.0
C5' 2:A1456 4.8 7.5 1.0
C2' 2:U1455 4.8 79.3 1.0
O 2:HOH1891 4.8 14.9 1.0
OP1 2:A1456 4.8 17.4 1.0
C8 2:6MZ1457 4.8 9.6 1.0
C4' 2:A1456 5.0 5.7 1.0

Magnesium binding site 7 out of 59 in 9fhl

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Magnesium binding site 7 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1507

b:35.4
occ:1.00
 O 2:HOH1785 1.8 10.2 1.0
O 2:HOH1835 1.8 18.9 1.0
O 2:HOH1868 1.9 24.6 1.0
O 2:HOH1993 2.3 10.7 1.0
OP2 2:A467 2.4 19.8 1.0
OP2 2:A468 2.5 13.3 1.0
OP1 2:G464 3.2 24.4 1.0
P 2:A467 3.7 13.1 1.0
O3' 2:C466 3.7 24.8 1.0
P 2:A468 3.9 17.7 1.0
OP2 2:G465 4.1 23.0 1.0
N7 2:A468 4.2 11.3 1.0
P 2:G464 4.4 17.4 1.0
C8 2:A468 4.4 10.7 1.0
O 2:HOH1810 4.5 13.1 1.0
O5' 2:A468 4.6 19.9 1.0
O5' 2:A467 4.6 22.8 1.0
O2' 2:C466 4.6 22.6 1.0
OP2 2:G464 4.6 20.7 1.0
C3' 2:A467 4.7 20.3 1.0
OP1 2:A467 4.7 20.0 1.0
OP1 2:A468 4.8 25.9 1.0
O3' 2:A467 4.8 23.3 1.0
C3' 2:C466 4.9 15.4 1.0

Magnesium binding site 8 out of 59 in 9fhl

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Magnesium binding site 8 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1508

b:18.7
occ:1.00
 OP2 2:G97 1.8 20.2 1.0
OP2 2:A96 1.9 23.0 1.0
O 2:HOH2005 2.1 14.8 1.0
O 2:HOH2034 2.5 16.2 1.0
OP2 2:G294 2.6 17.2 1.0
P 2:G97 3.3 25.9 1.0
P 2:A96 3.3 10.5 1.0
O3' 2:A96 4.0 24.5 1.0
P 2:G294 4.0 13.7 1.0
O5' 2:A96 4.0 23.6 1.0
C3' 2:A96 4.0 18.2 1.0
C5' 2:A96 4.1 13.9 1.0
OP1 2:G97 4.1 25.8 1.0
O3' 2:G95 4.2 18.0 1.0
O 2:HOH1828 4.2 23.5 1.0
O5' 2:G97 4.2 19.6 1.0
OP1 2:A96 4.3 20.6 1.0
O5' 2:G294 4.3 16.2 1.0
N7 2:G97 4.5 4.3 1.0
O4 2:U98 4.7 16.1 1.0
C4' 2:A96 4.7 18.9 1.0
C8 2:G97 4.7 9.4 1.0
O5' 2:A293 4.8 17.6 1.0
OP2 2:A293 4.9 26.8 1.0
OP1 2:G294 4.9 25.2 1.0
C3' 2:A293 5.0 17.7 1.0
O3' 2:A293 5.0 22.1 1.0

Magnesium binding site 9 out of 59 in 9fhl

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Magnesium binding site 9 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1509

b:32.1
occ:1.00
 O 2:HOH1821 1.8 22.9 1.0
O 2:HOH2106 1.9 24.6 1.0
O 2:HOH2055 1.9 30.1 1.0
O 2:HOH2101 2.4 23.7 1.0
O6 2:G469 4.0 15.4 1.0
O 2:HOH2094 4.0 21.7 1.0
O 2:HOH2025 4.4 25.9 1.0
OP2 2:C495 4.6 20.5 1.0
O 2:HOH2059 4.7 27.5 1.0
O6 2:G498 4.9 36.9 1.0
N7 2:G462 4.9 8.5 1.0
N4 2:C499 4.9 22.3 1.0
O6 2:G462 4.9 19.7 1.0

Magnesium binding site 10 out of 59 in 9fhl

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Magnesium binding site 10 out of 59 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1510

b:24.0
occ:1.00
 O 2:HOH1884 1.8 19.1 1.0
OP2 2:G1160 1.8 21.8 1.0
O 2:HOH1839 1.8 25.8 1.0
OP2 2:C1011 2.2 29.8 1.0
O 2:HOH1959 2.2 22.3 1.0
O 2:HOH1943 2.7 24.3 1.0
P 2:G1160 3.1 25.8 1.0
P 2:C1011 3.3 32.8 1.0
O3' 2:G1010 3.6 35.2 1.0
O3' 2:A1159 3.6 27.0 1.0
OP1 2:C1011 3.9 35.6 1.0
OP1 2:G1160 3.9 31.8 1.0
OP2 2:G1161 4.0 14.9 1.0
N7 2:G1161 4.0 16.7 1.0
O2' 2:G1010 4.1 30.8 1.0
O4 2:U1162 4.3 22.0 1.0
O5' 2:G1160 4.3 21.5 1.0
C8 2:G1161 4.5 17.4 1.0
O5' 2:C1011 4.6 31.9 1.0
N1 2:SPM1571 4.6 28.7 1.0
N7 2:G1160 4.7 16.2 1.0
C8 2:G1160 4.7 11.2 1.0
O 2:HOH1701 4.7 30.0 1.0
C3' 2:G1010 4.8 31.9 1.0
C2' 2:G1010 4.9 28.6 1.0
C3' 2:G1160 4.9 20.8 1.0

Reference:

G.Bourgeois, P.D.Coureux, C.Lazennec-Schurdevin, C.Madru, T.Gaillard, M.Duchateau, J.Chamot-Rooke, S.Bourcier, Y.Mechulam, E.Schmitt. Structures of Saccharolobus Solfataricus Initiation Complexes with Leaderless Mrnas Highlight Archaeal Features and Eukaryotic Proximity. Nat Commun V. 16 348 2025.
ISSN: ESSN 2041-1723
PubMed: 39753558
DOI: 10.1038/S41467-024-55718-5
Page generated: Sat Feb 8 22:09:39 2025

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