Magnesium in PDB 9fy0: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna

The structure of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless 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 - 47;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna (pdb code 9fy0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 47 binding sites of Magnesium where determined in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna, PDB code: 9fy0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1543 b:47.2 occ:1.00 O 2:HOH1666 1.8 25.9 1.0 O 2:HOH1668 1.8 37.2 1.0 O 2:HOH1721 1.8 43.8 1.0 OP2 2:A532 1.9 29.2 1.0 OP2 2:A533 2.2 33.6 1.0 OP2 2:A531 2.3 38.5 1.0 P 2:A531 2.8 28.3 1.0 OP1 2:A531 3.0 33.6 1.0 P 2:A532 3.0 32.6 1.0 O5' 2:A531 3.2 27.7 1.0 OP1 2:A532 3.3 25.7 1.0 P 2:A533 3.5 33.5 1.0 C5' 2:A531 3.8 27.1 1.0 OP1 2:A533 4.0 25.4 1.0 O3' 2:A531 4.1 32.1 1.0 O5' 2:A532 4.2 34.1 1.0 OP1 2:U530 4.3 26.4 1.0 C3' 2:A531 4.4 16.2 1.0 O3' 2:U530 4.4 18.4 1.0 C3' 2:A532 4.4 23.1 1.0 O3' 2:A532 4.5 31.7 1.0 C5' 2:A532 4.6 27.4 1.0 C4' 2:A531 4.6 28.6 1.0 O5' 2:A533 4.6 33.6 1.0 N7 2:A533 4.8 29.1 1.0 O 2:HOH1773 4.8 40.3 1.0 OP2 2:U530 4.8 33.2 1.0 P 2:U530 4.9 34.7 1.0 MG 2:MG1585 4.9 48.6 1.0 O5' 2:U530 4.9 26.0 1.0 C8 2:A533 5.0 23.5 1.0

Magnesium binding site 2 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1544 b:63.8 occ:1.00 OP2 2:A1360 2.6 45.5 1.0 P 2:A1360 3.8 52.3 1.0 OP2 2:C1359 4.1 44.9 1.0 OP1 2:G10 4.2 44.4 1.0 O5' 2:A1360 4.2 38.4 1.0 OP1 2:A1360 4.4 35.4 1.0 OP1 2:C1359 4.5 41.0 1.0 P 2:C1359 4.7 50.7 1.0 O3' 2:U9 4.7 52.5 1.0 O5' 2:C1359 4.9 38.0 1.0 P 2:G10 5.0 55.0 1.0

Magnesium binding site 3 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1545 b:55.0 occ:1.00 O 2:HOH1699 1.8 38.2 1.0 O 2:HOH1737 1.9 46.5 1.0 O 2:HOH1645 1.9 49.9 1.0 O 2:HOH1623 1.9 43.8 1.0 OP2 2:A567 2.2 43.0 1.0 P 2:A567 3.6 42.5 1.0 O 2:HOH1644 3.7 49.7 1.0 OP1 2:A566 4.1 41.2 1.0 O5' 2:A567 4.2 33.1 1.0 OP1 2:A567 4.2 39.0 1.0 N7 2:A568 4.3 31.1 1.0 N7 2:G569 4.3 40.2 1.0 N6 2:A568 4.3 31.8 1.0 O 2:HOH1638 4.4 41.7 1.0 N7 2:A567 4.6 27.1 1.0 O3' 2:A566 4.7 29.2 1.0 C8 2:A567 4.8 28.3 1.0 O6 2:G569 4.8 53.6 1.0

Magnesium binding site 4 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1546 b:48.1 occ:1.00 OP2 2:G719 2.0 52.6 1.0 OP1 2:A718 2.2 36.5 1.0 P 2:G719 3.4 51.3 1.0 P 2:A718 3.5 42.3 1.0 O5' 2:A718 3.9 39.6 1.0 OP2 2:A718 4.1 41.9 1.0 OP1 2:G719 4.1 42.2 1.0 O6 2:G720 4.2 44.7 1.0 O5' 2:G719 4.2 50.9 1.0 N3 2:C535 4.3 35.9 1.0 N7 2:G720 4.3 40.0 1.0 O3' 2:A718 4.4 35.7 1.0 C5' 2:A718 4.5 35.3 1.0 O3' 2:G717 4.7 25.6 1.0 N4 2:C535 4.7 29.4 1.0 C3' 2:A718 4.9 39.3 1.0 C6 2:G720 5.0 38.5 1.0

Magnesium binding site 5 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1547 b:52.7 occ:1.00 O1P 2:6MZ1457 1.6 46.1 1.0 O 2:HOH1676 1.8 50.8 1.0 O 2:HOH1667 1.8 54.9 1.0 O 2:HOH1642 1.9 50.8 1.0 OP1 2:G1462 2.0 53.2 1.0 OP1 2:G1465 2.1 56.9 1.0 P 2:6MZ1457 3.1 42.9 1.0 N14 2:SPM1522 3.2 55.9 1.0 P 2:G1465 3.3 51.7 1.0 O3' 2:A1464 3.4 51.4 1.0 P 2:G1462 3.4 47.2 1.0 O2P 2:6MZ1457 3.9 46.9 1.0 O5' 2:6MZ1457 4.0 46.9 1.0 OP1 2:G1461 4.0 44.1 1.0 OP2 2:G1462 4.0 43.3 1.0 C5' 2:G1465 4.1 53.2 1.0 O5' 2:G1465 4.2 57.5 1.0 O3' 2:A1456 4.2 38.7 1.0 O5' 2:G1462 4.3 45.4 1.0 O3' 2:G1461 4.3 39.4 1.0 C5' 2:G1462 4.3 47.1 1.0 C3' 2:G1461 4.3 35.3 1.0 OP2 2:G1465 4.4 53.9 1.0 O2' 2:U1463 4.4 60.3 1.0 OP2 2:C1458 4.4 44.0 1.0 C5' 2:6MZ1457 4.6 39.7 1.0 O2' 2:G1461 4.6 51.1 1.0 C13 2:SPM1522 4.6 48.2 1.0 C3' 2:A1464 4.7 53.1 1.0 C2' 2:G1461 4.9 37.0 1.0 C2' 2:U1463 4.9 55.0 1.0

Magnesium binding site 6 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1548 b:28.0 occ:1.00 O 2:HOH1718 1.6 48.9 1.0 O 2:HOH1777 1.6 43.6 1.0 O b:HOH201 1.9 0.8 1.0 O b:HOH202 1.9 30.9 1.0 O 2:HOH1782 1.9 35.7 1.0 O 2:HOH1700 2.2 30.6 1.0 O b:GLY16 3.7 42.1 1.0 O3' 2:G1483 4.0 38.9 1.0 OP1 2:C1484 4.2 49.4 1.0 OP2 2:A775 4.2 14.8 1.0 OP1 2:A689 4.3 29.4 1.0 OP2 2:G690 4.3 34.2 1.0 O2' 2:G1483 4.4 49.6 1.0 OP1 2:G690 4.6 44.7 1.0 C5' 2:C1484 4.7 44.5 1.0 N1 2:A773 4.7 25.4 1.0 P 2:C1484 4.7 50.9 1.0 C b:GLY16 4.8 37.7 1.0 P 2:G690 4.8 40.9 1.0 C2 2:A773 4.9 25.6 1.0 C5' 2:A689 4.9 20.0 1.0 O3' 2:A689 5.0 30.5 1.0

Magnesium binding site 7 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1549 b:52.8 occ:1.00 OP2 2:A96 1.6 41.8 1.0 O 2:HOH1649 1.8 48.8 1.0 O 2:HOH1675 1.8 41.5 1.0 O 2:HOH1693 1.8 46.9 1.0 OP2 2:G97 2.0 43.6 1.0 OP2 2:G294 2.3 51.0 1.0 P 2:A96 3.0 49.5 1.0 P 2:G97 3.4 60.6 1.0 P 2:G294 3.6 44.5 1.0 O5' 2:A96 3.7 42.3 1.0 O3' 2:G95 3.8 44.8 1.0 C5' 2:A96 3.9 36.1 1.0 C3' 2:A96 4.0 38.7 1.0 O 2:HOH1698 4.0 40.8 1.0 O3' 2:A96 4.0 44.8 1.0 OP1 2:A96 4.0 43.0 1.0 O5' 2:G294 4.1 42.7 1.0 O5' 2:G97 4.4 39.9 1.0 OP1 2:G97 4.4 45.2 1.0 OP1 2:G294 4.4 43.0 1.0 C4' 2:A96 4.5 40.0 1.0 N7 2:G97 4.6 36.4 1.0 O4 2:U98 4.6 42.4 1.0 O3' 2:A293 4.7 38.6 1.0 C8 2:G97 4.7 35.3 1.0 C3' 2:A293 4.8 41.8 1.0 O5' 2:A293 5.0 51.1 1.0

Magnesium binding site 8 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1550 b:32.8 occ:1.00 O6 2:G469 4.1 72.6 1.0 O6 2:G498 4.4 72.4 1.0 N6 2:A497 4.5 68.5 1.0 N7 2:A497 4.7 66.6 1.0 OP2 2:C495 4.7 54.5 1.0 N4 2:C499 4.8 66.6 1.0

Magnesium binding site 9 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1551 b:63.2 occ:1.00 OP1 2:C1011 1.9 69.8 1.0 OP1 2:G1160 1.9 65.9 1.0 OP2 2:G1161 2.1 62.4 1.0 P 2:C1011 3.1 72.2 1.0 P 2:G1160 3.1 68.1 1.0 P 2:G1161 3.2 71.7 1.0 O2' 2:A1159 3.4 75.6 1.0 OP1 2:G1161 3.5 67.3 1.0 OP2 2:G1160 3.5 68.0 1.0 OP2 2:C1011 3.6 70.7 1.0 O3' 2:G1160 4.0 67.3 1.0 O5' 2:C1011 4.1 73.6 1.0 O3' 2:A1159 4.1 69.8 1.0 O3' 2:G1010 4.2 67.1 1.0 O5' 2:G1160 4.2 58.2 1.0 C5' 2:G1160 4.3 56.5 1.0 C3' 2:G1160 4.5 56.8 1.0 O5' 2:G1161 4.5 61.9 1.0 C2' 2:A1159 4.5 76.4 1.0 C3' 2:A1159 4.6 70.2 1.0 C3' 2:G1010 4.6 63.7 1.0 MG 2:MG1553 4.8 49.1 1.0 O2' 2:G1010 4.9 67.0 1.0 C4' 2:G1160 5.0 53.0 1.0

Magnesium binding site 10 out of 47 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1552 b:81.2 occ:1.00 OP2 2:C944 1.9 82.8 1.0 O4 2:U945 2.1 87.0 1.0 OP1 2:U943 2.2 86.2 1.0 O6 2:G1185 2.8 90.5 1.0 C4 2:U945 3.2 82.9 1.0 P 2:C944 3.2 81.5 1.0 P 2:U943 3.4 87.7 1.0 OP1 2:C944 3.7 81.6 1.0 C5 2:U945 3.8 83.5 1.0 O5' 2:U943 3.9 86.0 1.0 N4 2:C1186 4.0 78.3 1.0 C6 2:G1185 4.0 90.8 1.0 C5' 2:U943 4.1 83.4 1.0 OP2 2:U943 4.1 88.8 1.0 O5' 2:C944 4.2 88.5 1.0 N3 2:U945 4.3 81.6 1.0 O3' 2:U943 4.3 83.1 1.0 O2 2:U946 4.4 88.8 1.0 O6 2:G1184 4.5 92.6 1.0 C3' 2:U943 4.7 82.9 1.0 O3' 2:A942 4.7 81.6 1.0 C8 2:SPM1513 4.7 97.7 1.0 N3 2:U946 4.8 81.2 1.0 C4 2:C1186 4.8 77.6 1.0 C2 2:U946 4.8 83.2 1.0 C5 2:G1185 4.9 88.3 1.0 C4' 2:U943 4.9 84.0 1.0 N1 2:G1185 5.0 89.9 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