Magnesium in PDB 9fra: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna

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

Zinc

(Zn)

8 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 - 58;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna (pdb code 9fra). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 58 binding sites of Magnesium where determined in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna, PDB code: 9fra:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1501 b:95.6 occ:1.00 OP2 2:A532 1.8 73.8 1.0 O 2:HOH1636 1.9 74.0 1.0 O 2:HOH1687 1.9 74.5 1.0 O 2:HOH1649 1.9 78.2 1.0 OP2 2:A531 2.3 78.6 1.0 OP2 2:A533 2.3 71.9 1.0 P 2:A532 2.9 70.5 1.0 P 2:A531 3.0 74.4 1.0 OP1 2:A532 3.2 64.2 1.0 OP1 2:A531 3.2 79.3 1.0 O5' 2:A531 3.3 68.8 1.0 P 2:A533 3.6 66.8 1.0 C5' 2:A531 3.8 64.9 1.0 O5' 2:A532 4.0 71.0 1.0 O3' 2:A531 4.0 67.9 1.0 OP1 2:A533 4.1 63.4 1.0 OP1 2:U530 4.2 70.7 1.0 C3' 2:A531 4.3 57.7 1.0 C3' 2:A532 4.3 61.0 1.0 C5' 2:A532 4.4 66.1 1.0 O3' 2:A532 4.5 65.3 1.0 O3' 2:U530 4.5 62.0 1.0 N7 2:A533 4.5 61.7 1.0 C4' 2:A531 4.6 60.9 1.0 OP2 2:U530 4.7 69.6 1.0 O5' 2:A533 4.8 66.6 1.0 P 2:U530 4.8 73.7 1.0 C8 2:A533 4.8 58.7 1.0 MG 2:MG1531 4.9 108.6 1.0 O 2:HOH1741 4.9 98.8 1.0 O5' 2:U530 5.0 68.6 1.0 C4' 2:A532 5.0 63.9 1.0

Magnesium binding site 2 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1502 b:80.0 occ:1.00 O 2:HOH1635 1.9 72.7 1.0 O 2:HOH1712 1.9 77.3 1.0 O 2:HOH1654 1.9 68.2 1.0 O 2:HOH1632 1.9 78.4 1.0 OP2 2:A567 2.2 70.4 1.0 P 2:A567 3.4 76.7 1.0 N7 2:A568 3.7 66.4 1.0 O5' 2:A567 3.8 63.2 1.0 OP1 2:A567 4.0 68.9 1.0 N7 2:G569 4.0 67.4 1.0 N6 2:A568 4.2 61.9 1.0 N7 2:A567 4.4 62.7 1.0 C8 2:A567 4.4 61.1 1.0 OP2 2:A568 4.5 70.0 1.0 OP1 2:A566 4.6 67.4 1.0 O3' 2:A566 4.7 60.9 1.0 C5 2:A568 4.7 61.4 1.0 C8 2:G569 4.7 71.1 1.0 C8 2:A568 4.7 64.0 1.0 C6 2:A568 4.9 61.5 1.0 C5 2:G569 4.9 67.0 1.0

Magnesium binding site 3 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1503 b:69.8 occ:1.00 OP2 2:G719 2.0 80.8 1.0 OP1 2:A718 2.2 67.6 1.0 P 2:G719 3.4 83.5 1.0 P 2:A718 3.4 73.5 1.0 O5' 2:A718 3.9 71.6 1.0 OP2 2:A718 4.0 78.1 1.0 O6 2:G720 4.1 76.2 1.0 O5' 2:G719 4.2 77.8 1.0 N7 2:G720 4.2 73.7 1.0 OP1 2:G719 4.2 75.7 1.0 N3 2:C535 4.3 65.3 1.0 O3' 2:A718 4.4 67.9 1.0 C5' 2:A718 4.5 68.2 1.0 N4 2:C535 4.5 63.4 1.0 O3' 2:G717 4.7 65.1 1.0 C3' 2:A718 4.8 67.6 1.0 C6 2:G720 4.9 75.5 1.0 C5 2:G720 4.9 74.2 1.0 C4 2:C535 5.0 62.3 1.0

Magnesium binding site 4 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1504 b:82.5 occ:1.00 O1P 2:6MZ1457 1.8 70.5 1.0 O 2:HOH1617 1.9 73.8 1.0 O 2:HOH1672 1.9 82.3 1.0 O 2:HOH1631 1.9 78.6 1.0 OP1 2:G1462 2.0 81.0 1.0 OP1 2:G1465 2.1 76.4 1.0 N14 2:SPM1576 3.1 72.3 1.0 P 2:6MZ1457 3.2 69.8 1.0 P 2:G1465 3.2 76.9 1.0 O3' 2:A1464 3.3 76.6 1.0 P 2:G1462 3.4 74.4 1.0 O5' 2:6MZ1457 3.9 63.4 1.0 OP1 2:G1461 3.9 71.8 1.0 C5' 2:G1465 4.0 64.6 1.0 O2P 2:6MZ1457 4.0 79.3 1.0 OP2 2:G1462 4.0 72.1 1.0 O5' 2:G1465 4.1 70.0 1.0 C3' 2:G1461 4.2 62.9 1.0 OP2 2:C1458 4.2 68.4 1.0 O3' 2:G1461 4.2 66.7 1.0 O3' 2:A1456 4.3 68.9 1.0 C5' 2:6MZ1457 4.3 63.3 1.0 C13 2:SPM1576 4.4 67.9 1.0 O5' 2:G1462 4.4 69.4 1.0 O2' 2:G1461 4.4 72.0 1.0 OP2 2:G1465 4.4 72.0 1.0 C5' 2:G1462 4.5 71.5 1.0 O2' 2:U1463 4.5 74.5 1.0 C3' 2:A1464 4.7 72.8 1.0 C2' 2:G1461 4.8 64.5 1.0 P 2:G1461 4.8 74.8 1.0 OP2 2:G1461 4.9 71.4 1.0

Magnesium binding site 5 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1505 b:105.4 occ:1.00 O 2:HOH1763 1.9 91.0 1.0 O 2:HOH1677 1.9 91.6 1.0 O 2:HOH1746 1.9 84.9 1.0 O 2:HOH1733 1.9 92.4 1.0 O 2:HOH1685 1.9 91.9 1.0 O 2:HOH1686 1.9 91.8 1.0 OP2 2:G690 3.6 68.4 1.0 OP1 2:G690 4.0 74.8 1.0 P 2:G690 4.1 73.1 1.0 OP1 2:A689 4.2 66.3 1.0 O3' 2:A689 4.2 66.3 1.0 N1 2:A773 4.2 64.8 1.0 O3' 2:G1483 4.3 63.0 1.0 C5' 2:A689 4.5 61.7 1.0 O2' 2:G1483 4.6 62.6 1.0 C2 2:A773 4.6 67.0 1.0 OP2 2:A775 4.7 65.9 1.0 OP1 2:C1484 4.7 77.2 1.0 O5' 2:A689 4.9 65.9 1.0

Magnesium binding site 6 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1506 b:101.6 occ:1.00 O2P 2:6MZ1457 2.4 79.3 1.0 OP2 2:G1462 2.4 72.1 1.0 OP2 2:A1456 3.4 80.8 1.0 O3' 2:U1455 3.5 77.2 1.0 O2' 2:U1455 3.6 79.3 1.0 P 2:G1462 3.7 74.4 1.0 P 2:6MZ1457 3.9 69.8 1.0 O3' 2:G1461 3.9 66.7 1.0 P 2:A1456 4.1 82.4 1.0 O2' 2:G1461 4.4 72.0 1.0 C3' 2:U1455 4.5 78.2 1.0 C3' 2:A1456 4.5 63.2 1.0 N7 2:6MZ1457 4.5 64.8 1.0 C2' 2:U1455 4.6 79.3 1.0 O5' 2:6MZ1457 4.6 63.4 1.0 O5' 2:G1462 4.7 69.4 1.0 O3' 2:A1456 4.7 68.9 1.0 OP1 2:G1462 4.7 81.0 1.0 O1P 2:6MZ1457 4.8 70.5 1.0 O 2:HOH1739 4.8 74.6 1.0 C8 2:6MZ1457 4.9 67.3 1.0 O5' 2:A1456 4.9 72.0 1.0

Magnesium binding site 7 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1507 b:105.7 occ:1.00 OP2 2:A468 1.5 84.4 1.0 OP2 2:A467 1.8 78.3 1.0 O 2:HOH1634 1.9 81.1 1.0 O 2:HOH1717 1.9 91.3 1.0 O 2:HOH1621 1.9 91.5 1.0 O 2:HOH1643 1.9 90.9 1.0 P 2:A468 3.0 86.6 1.0 P 2:A467 3.3 73.1 1.0 C3' 2:A467 3.8 69.6 1.0 OP1 2:A468 3.8 77.3 1.0 O3' 2:A467 3.9 71.2 1.0 O3' 2:C466 3.9 77.3 1.0 O5' 2:A468 3.9 81.2 1.0 OP1 2:G464 4.0 71.3 1.0 O5' 2:A467 4.1 76.2 1.0 OP1 2:A467 4.3 60.0 1.0 N7 2:A468 4.4 71.4 1.0 C8 2:A468 4.4 71.6 1.0 C5' 2:A467 4.4 70.1 1.0 OP2 2:G465 4.6 77.2 1.0 C4' 2:A467 4.7 67.8 1.0 C2' 2:A467 4.9 69.8 1.0

Magnesium binding site 8 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1508 b:87.9 occ:1.00 O 2:HOH1628 1.9 81.7 1.0 OP2 2:A96 1.9 71.4 1.0 O 2:HOH1611 1.9 81.7 1.0 OP2 2:G294 2.1 75.8 1.0 OP2 2:G97 2.2 78.4 1.0 P 2:G294 3.3 81.2 1.0 P 2:A96 3.3 78.7 1.0 O5' 2:G294 3.5 65.9 1.0 P 2:G97 3.7 83.9 1.0 O3' 2:G95 3.8 69.4 1.0 O5' 2:A96 4.1 71.1 1.0 O4 2:U98 4.1 78.5 1.0 N7 2:G97 4.2 66.8 1.0 OP1 2:G294 4.3 73.2 1.0 C3' 2:A96 4.4 64.7 1.0 O3' 2:A293 4.4 73.9 1.0 O5' 2:G97 4.4 73.3 1.0 O3' 2:A96 4.5 69.4 1.0 OP1 2:A96 4.5 72.8 1.0 C3' 2:A293 4.5 70.5 1.0 C8 2:G97 4.5 69.1 1.0 C5' 2:A96 4.5 63.0 1.0 OP1 2:G97 4.6 78.1 1.0 C4 2:U98 4.8 69.7 1.0 C5 2:U98 4.9 66.8 1.0 O5' 2:A293 4.9 75.3 1.0 C5' 2:G294 4.9 57.1 1.0

Magnesium binding site 9 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1509 b:107.2 occ:1.00 O 2:HOH1759 2.2 103.6 1.0 O 2:HOH1646 2.3 103.7 1.0 O6 2:G469 3.9 93.5 1.0 O6 2:G498 4.5 98.5 1.0 N6 2:A497 4.5 97.4 1.0 N7 2:A497 4.6 92.7 1.0 OP2 2:C495 4.7 84.4 1.0 N4 2:C499 4.7 90.3 1.0 C6 2:G469 4.9 89.9 1.0

Magnesium binding site 10 out of 58 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1510 b:85.5 occ:1.00 O4 2:U945 2.0 90.7 1.0 OP2 2:C944 2.1 89.3 1.0 O6 2:G1185 2.1 88.2 1.0 OP1 2:U943 2.2 93.6 1.0 C4 2:U945 3.1 85.6 1.0 C6 2:G1185 3.3 87.0 1.0 P 2:U943 3.4 97.3 1.0 P 2:C944 3.4 92.9 1.0 C5 2:U945 3.8 87.5 1.0 N4 2:C1186 3.9 79.0 1.0 O5' 2:U943 3.9 90.5 1.0 O2 2:U946 4.0 93.1 1.0 OP1 2:C944 4.0 90.8 1.0 OP2 2:U943 4.1 97.9 1.0 C5' 2:U943 4.2 88.0 1.0 N1 2:G1185 4.2 85.1 1.0 N3 2:U945 4.3 82.3 1.0 O3' 2:U943 4.3 87.0 1.0 C5 2:G1185 4.4 85.8 1.0 O6 2:G1184 4.5 89.2 1.0 O5' 2:C944 4.5 90.8 1.0 C8 2:SPM1567 4.5 99.3 1.0 C4 2:C1186 4.6 76.6 1.0 C2 2:U946 4.6 87.8 1.0 O3' 2:A942 4.7 84.4 1.0 N7 2:G1185 4.7 87.1 1.0 C3' 2:U943 4.7 85.1 1.0 N3 2:U946 4.7 86.0 1.0 N3 2:C1186 4.8 78.1 1.0 C4' 2:U943 5.0 87.8 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