Magnesium in PDB 9fs8: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna

The structure of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna also contains other interesting chemical elements:

Zinc

(Zn)

9 atoms

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 - 57;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna (pdb code 9fs8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 57 binding sites of Magnesium where determined in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna, PDB code: 9fs8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1501 b:131.8 occ:1.00 OP2 2:A532 1.8 125.6 1.0 OP2 2:A531 2.3 128.0 1.0 OP2 2:A533 2.3 124.9 1.0 P 2:A532 2.9 125.6 1.0 P 2:A531 2.9 128.0 1.0 OP1 2:A532 3.1 125.6 1.0 OP1 2:A531 3.2 128.0 1.0 O5' 2:A531 3.3 128.0 1.0 P 2:A533 3.6 124.9 1.0 C5' 2:A531 3.7 128.0 1.0 O5' 2:A532 4.0 125.6 1.0 O3' 2:A531 4.0 128.0 1.0 OP1 2:A533 4.1 124.9 1.0 OP1 2:U530 4.2 126.7 1.0 C3' 2:A531 4.3 128.0 1.0 C3' 2:A532 4.3 125.6 1.0 C5' 2:A532 4.4 125.6 1.0 O3' 2:A532 4.5 125.6 1.0 O3' 2:U530 4.5 126.7 1.0 C4' 2:A531 4.5 128.0 1.0 N7 2:A533 4.6 124.9 1.0 OP2 2:U530 4.8 126.7 1.0 O5' 2:A533 4.8 124.9 1.0 P 2:U530 4.8 126.7 1.0 C8 2:A533 4.9 124.9 1.0 O5' 2:U530 5.0 126.7 1.0 C4' 2:A532 5.0 125.6 1.0

Magnesium binding site 2 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1502 b:134.2 occ:1.00 O 2:HOH1627 1.9 134.7 1.0 O 2:HOH1640 1.9 132.9 1.0 O 2:HOH1614 1.9 135.2 1.0 O 2:HOH1616 1.9 132.3 1.0 OP2 2:A567 2.2 130.8 1.0 P 2:A567 3.3 130.8 1.0 N7 2:A568 3.7 132.0 1.0 O5' 2:A567 3.7 130.8 1.0 OP1 2:A567 4.0 130.8 1.0 N7 2:G569 4.0 136.0 1.0 N6 2:A568 4.2 132.0 1.0 N7 2:A567 4.4 130.8 1.0 C8 2:A567 4.4 130.8 1.0 OP2 2:A568 4.5 132.0 1.0 OP1 2:A566 4.6 131.2 1.0 O3' 2:A566 4.6 131.2 1.0 C8 2:G569 4.7 136.0 1.0 C5 2:A568 4.7 132.0 1.0 C8 2:A568 4.7 132.0 1.0 C6 2:A568 4.9 132.0 1.0 C5 2:G569 4.9 136.0 1.0 C3' 2:A566 5.0 131.2 1.0

Magnesium binding site 3 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1503 b:126.7 occ:1.00 OP2 2:G719 2.0 129.4 1.0 OP1 2:A718 2.2 126.9 1.0 P 2:G719 3.4 129.4 1.0 P 2:A718 3.4 126.9 1.0 O5' 2:A718 3.9 126.9 1.0 OP2 2:A718 4.0 126.9 1.0 O6 2:G720 4.1 131.6 1.0 O5' 2:G719 4.2 129.4 1.0 OP1 2:G719 4.2 129.4 1.0 N7 2:G720 4.2 131.6 1.0 N3 2:C535 4.3 127.0 1.0 O3' 2:A718 4.4 126.9 1.0 C5' 2:A718 4.5 126.9 1.0 N4 2:C535 4.5 127.0 1.0 O3' 2:G717 4.6 123.3 1.0 C3' 2:A718 4.8 126.9 1.0 C6 2:G720 4.9 131.6 1.0 C5 2:G720 4.9 131.6 1.0 C4 2:C535 5.0 127.0 1.0

Magnesium binding site 4 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1504 b:113.4 occ:1.00 O1P 2:6MZ1457 1.8 107.9 1.0 OP1 2:G1462 2.0 110.2 1.0 OP1 2:G1465 2.1 112.1 1.0 N14 2:SPM1575 3.1 47.0 1.0 O3' 2:A1464 3.1 113.8 1.0 P 2:6MZ1457 3.2 107.9 1.0 P 2:G1465 3.2 112.1 1.0 P 2:G1462 3.4 110.2 1.0 O5' 2:6MZ1457 3.9 107.9 1.0 OP1 2:G1461 3.9 109.4 1.0 C5' 2:G1465 4.0 112.1 1.0 O2P 2:6MZ1457 4.0 107.9 1.0 OP2 2:G1462 4.0 110.2 1.0 O5' 2:G1465 4.1 112.1 1.0 O3' 2:A1456 4.2 93.1 1.0 C3' 2:G1461 4.2 109.4 1.0 OP2 2:C1458 4.3 107.8 1.0 O3' 2:G1461 4.3 109.4 1.0 C5' 2:6MZ1457 4.3 107.9 1.0 C13 2:SPM1575 4.4 47.0 1.0 O2' 2:G1461 4.4 109.4 1.0 O5' 2:G1462 4.4 110.2 1.0 C3' 2:A1464 4.4 113.8 1.0 OP2 2:G1465 4.5 112.1 1.0 C5' 2:G1462 4.5 110.2 1.0 O2' 2:U1463 4.5 112.9 1.0 C2' 2:G1461 4.8 109.4 1.0 P 2:G1461 4.9 109.4 1.0 OP2 2:G1461 4.9 109.4 1.0 O2' 2:A1464 5.0 113.8 1.0

Magnesium binding site 5 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1505 b:133.9 occ:1.00 OP2 2:G690 3.6 128.7 1.0 O b:GLY16 3.9 73.8 1.0 OP1 2:G690 4.0 128.7 1.0 P 2:G690 4.1 128.7 1.0 OP1 2:A689 4.2 127.6 1.0 O3' 2:A689 4.2 127.6 1.0 N1 2:A773 4.3 128.3 1.0 O3' 2:G1483 4.3 136.4 1.0 C5' 2:A689 4.4 127.6 1.0 O2' 2:G1483 4.6 136.4 1.0 C2 2:A773 4.6 128.3 1.0 OP1 2:C1484 4.7 139.3 1.0 OP2 2:A775 4.7 126.8 1.0 C b:GLY16 4.9 73.8 1.0 O5' 2:A689 4.9 127.6 1.0

Magnesium binding site 6 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1506 b:61.1 occ:1.00 OP2 2:G1462 1.9 110.2 1.0 O2P 2:6MZ1457 1.9 107.9 1.0 OP2 2:A1456 2.6 93.1 1.0 P 2:G1462 3.3 110.2 1.0 O3' 2:U1455 3.4 115.9 1.0 P 2:6MZ1457 3.4 107.9 1.0 P 2:A1456 3.5 93.1 1.0 O3' 2:G1461 3.8 109.4 1.0 C3' 2:A1456 4.0 93.1 1.0 O2' 2:U1455 4.0 115.9 1.0 O3' 2:A1456 4.1 93.1 1.0 O1P 2:6MZ1457 4.1 107.9 1.0 OP1 2:G1462 4.2 110.2 1.0 O5' 2:G1462 4.2 110.2 1.0 O5' 2:A1456 4.3 93.1 1.0 O5' 2:6MZ1457 4.4 107.9 1.0 O2' 2:G1461 4.5 109.4 1.0 C3' 2:U1455 4.5 115.9 1.0 C5' 2:A1456 4.5 93.1 1.0 OP1 2:A1456 4.8 93.1 1.0 C4' 2:A1456 4.8 93.1 1.0 C2' 2:U1455 4.9 115.9 1.0

Magnesium binding site 7 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1507 b:123.1 occ:1.00 OP2 2:A468 2.1 121.6 1.0 OP2 2:A467 2.3 120.1 1.0 OP1 2:G464 3.3 118.2 1.0 P 2:A468 3.5 121.6 1.0 P 2:A467 3.6 120.1 1.0 O3' 2:C466 4.0 118.1 1.0 O5' 2:A468 4.3 121.6 1.0 OP2 2:G465 4.3 117.7 1.0 OP1 2:A468 4.3 121.6 1.0 N7 2:A468 4.3 121.6 1.0 C3' 2:A467 4.4 120.1 1.0 O3' 2:A467 4.4 120.1 1.0 C8 2:A468 4.5 121.6 1.0 OP1 2:A467 4.6 120.1 1.0 P 2:G464 4.6 118.2 1.0 O5' 2:A467 4.6 120.1 1.0 OP2 2:G464 4.9 118.2 1.0 C5' 2:A467 5.0 120.1 1.0

Magnesium binding site 8 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1508 b:112.1 occ:1.00 OP2 2:A96 1.9 112.5 1.0 OP2 2:G294 2.1 110.5 1.0 OP2 2:G97 2.2 114.2 1.0 P 2:G294 3.3 110.5 1.0 P 2:A96 3.3 112.5 1.0 O5' 2:G294 3.5 110.5 1.0 P 2:G97 3.7 114.2 1.0 O3' 2:G95 3.8 112.7 1.0 O5' 2:A96 4.0 112.5 1.0 O4 2:U98 4.1 114.0 1.0 N7 2:G97 4.2 114.2 1.0 OP1 2:G294 4.2 110.5 1.0 C3' 2:A96 4.4 112.5 1.0 O3' 2:A293 4.4 114.2 1.0 O5' 2:G97 4.4 114.2 1.0 OP1 2:A96 4.5 112.5 1.0 O3' 2:A96 4.5 112.5 1.0 C5' 2:A96 4.5 112.5 1.0 C8 2:G97 4.5 114.2 1.0 C3' 2:A293 4.5 114.2 1.0 OP1 2:G97 4.6 114.2 1.0 C4 2:U98 4.8 114.0 1.0 O5' 2:A293 4.9 114.2 1.0 C5 2:U98 4.9 114.0 1.0 C5' 2:G294 4.9 110.5 1.0

Magnesium binding site 9 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1509 b:124.4 occ:1.00 OP2 2:C495 4.2 138.2 1.0 O6 2:G469 4.3 133.6 1.0 N6 2:A497 4.3 136.8 1.0 N7 2:A497 4.6 136.8 1.0 O6 2:G498 4.6 137.7 1.0 N4 2:C496 4.8 136.6 1.0

Magnesium binding site 10 out of 57 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1510 b:142.8 occ:1.00 OP2 2:G1160 1.9 136.2 1.0 OP2 2:C1011 2.2 141.1 1.0 P 2:G1160 3.1 136.2 1.0 O3' 2:A1159 3.4 140.1 1.0 P 2:C1011 3.4 141.1 1.0 O3' 2:G1010 3.7 138.6 1.0 OP1 2:G1160 4.0 136.2 1.0 O5' 2:G1160 4.3 136.2 1.0 OP1 2:C1011 4.3 141.1 1.0 O2' 2:G1010 4.3 138.6 1.0 OP2 2:G1161 4.3 135.8 1.0 O4 2:U1162 4.5 137.8 1.0 N7 2:G1160 4.5 136.2 1.0 N7 2:G1161 4.6 135.8 1.0 O5' 2:C1011 4.6 141.1 1.0 C8 2:G1160 4.6 136.2 1.0 C3' 2:A1159 4.8 140.1 1.0 O2' 2:A1159 4.8 140.1 1.0 N1 2:SPM1568 4.9 136.2 1.0 C5' 2:C1011 4.9 141.1 1.0 C3' 2:G1010 4.9 138.6 1.0

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