Magnesium in PDB 9frk: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd Mrna

The structure of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 - 59;

Binding sites:

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

Magnesium binding site 1 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1501 b:86.2 occ:1.00 OP2 2:A532 1.8 69.6 1.0 O 2:HOH1628 1.9 62.5 1.0 O 2:HOH1642 1.9 76.8 1.0 O 2:HOH1674 1.9 80.9 1.0 OP2 2:A531 2.3 57.2 1.0 OP2 2:A533 2.3 64.0 1.0 P 2:A532 2.9 64.4 1.0 P 2:A531 3.0 61.3 1.0 OP1 2:A532 3.2 45.4 1.0 OP1 2:A531 3.3 69.5 1.0 O5' 2:A531 3.3 57.9 1.0 P 2:A533 3.6 63.0 1.0 C5' 2:A531 3.7 51.2 1.0 O5' 2:A532 4.0 65.1 1.0 O3' 2:A531 4.0 60.5 1.0 OP1 2:A533 4.1 55.2 1.0 OP1 2:U530 4.2 56.8 1.0 C3' 2:A531 4.3 49.8 1.0 C3' 2:A532 4.3 53.0 1.0 C5' 2:A532 4.4 57.9 1.0 O3' 2:A532 4.5 63.9 1.0 O3' 2:U530 4.5 52.5 1.0 N7 2:A533 4.5 53.6 1.0 C4' 2:A531 4.6 51.6 1.0 OP2 2:U530 4.7 60.5 1.0 O 2:HOH1679 4.7 30.0 1.0 O 2:HOH1700 4.8 90.2 1.0 O5' 2:A533 4.8 55.6 1.0 P 2:U530 4.8 61.0 1.0 C8 2:A533 4.8 52.3 1.0 MG 2:MG1534 4.9 103.4 1.0 O5' 2:U530 5.0 55.2 1.0 C4' 2:A532 5.0 51.3 1.0

Magnesium binding site 2 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1502 b:73.6 occ:1.00 O 2:HOH1621 1.8 71.7 1.0 O 2:HOH1622 1.9 71.9 1.0 O 2:HOH1650 1.9 82.4 1.0 O 2:HOH1688 1.9 76.0 1.0 OP2 2:A567 2.2 66.9 1.0 P 2:A567 3.4 56.7 1.0 N7 2:A568 3.7 67.4 1.0 O5' 2:A567 3.8 47.1 1.0 OP1 2:A567 4.0 58.0 1.0 N7 2:G569 4.0 74.2 1.0 N6 2:A568 4.2 68.5 1.0 N7 2:A567 4.4 60.1 1.0 C8 2:A567 4.4 61.3 1.0 OP2 2:A568 4.5 65.4 1.0 OP1 2:A566 4.6 69.0 1.0 O3' 2:A566 4.7 56.5 1.0 C8 2:G569 4.7 75.3 1.0 C5 2:A568 4.7 60.3 1.0 C8 2:A568 4.7 65.3 1.0 C6 2:A568 4.9 62.8 1.0 C5 2:G569 4.9 75.5 1.0

Magnesium binding site 3 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1503 b:49.1 occ:1.00 OP2 2:G719 2.0 77.6 1.0 OP1 2:A718 2.2 56.6 1.0 P 2:A718 3.4 62.4 1.0 P 2:G719 3.4 73.5 1.0 O5' 2:A718 3.9 65.6 1.0 OP2 2:A718 4.0 67.2 1.0 O6 2:G720 4.1 68.8 1.0 O5' 2:G719 4.2 73.9 1.0 N7 2:G720 4.2 68.4 1.0 OP1 2:G719 4.2 67.6 1.0 N3 2:C535 4.3 59.2 1.0 O3' 2:A718 4.4 60.0 1.0 C5' 2:A718 4.5 62.7 1.0 N4 2:C535 4.6 59.5 1.0 O3' 2:G717 4.6 55.0 1.0 C3' 2:A718 4.8 60.2 1.0 C6 2:G720 4.9 67.0 1.0 C5 2:G720 4.9 67.8 1.0 C4 2:C535 5.0 62.0 1.0

Magnesium binding site 4 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1504 b:79.2 occ:1.00 O1P 2:6MZ1457 1.8 62.2 1.0 O 2:HOH1613 1.9 71.0 1.0 O 2:HOH1624 1.9 75.6 1.0 O 2:HOH1659 1.9 75.8 1.0 OP1 2:G1462 2.0 66.9 1.0 OP1 2:G1465 2.1 73.8 1.0 N14 2:SPM1579 3.1 75.6 1.0 P 2:6MZ1457 3.2 61.4 1.0 P 2:G1465 3.3 68.7 1.0 O3' 2:A1464 3.4 76.0 1.0 P 2:G1462 3.4 64.6 1.0 O5' 2:6MZ1457 3.9 54.7 1.0 OP1 2:G1461 3.9 66.7 1.0 C5' 2:G1465 4.0 65.6 1.0 O2P 2:6MZ1457 4.0 73.4 1.0 OP2 2:G1462 4.0 58.2 1.0 O5' 2:G1465 4.1 67.2 1.0 O3' 2:A1456 4.2 18.7 1.0 C3' 2:G1461 4.2 57.7 1.0 OP2 2:C1458 4.2 63.1 1.0 O3' 2:G1461 4.2 62.9 1.0 C5' 2:6MZ1457 4.3 56.4 1.0 C13 2:SPM1579 4.4 71.6 1.0 O5' 2:G1462 4.4 54.7 1.0 O2' 2:G1461 4.4 69.0 1.0 OP2 2:G1465 4.5 63.4 1.0 C5' 2:G1462 4.5 54.8 1.0 O2' 2:U1463 4.5 68.6 1.0 C3' 2:A1464 4.7 72.6 1.0 C2' 2:G1461 4.8 53.3 1.0 P 2:G1461 4.9 78.5 1.0 OP2 2:G1461 4.9 73.5 1.0

Magnesium binding site 5 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1505 b:82.0 occ:1.00 O 2:HOH1718 1.8 36.2 1.0 O 2:HOH1729 1.9 79.2 1.0 O 2:HOH1710 1.9 96.9 1.0 O 2:HOH1662 1.9 78.0 1.0 O 2:HOH1673 1.9 83.0 1.0 O 2:HOH1669 1.9 89.5 1.0 OP2 2:G690 3.6 67.2 1.0 OP1 2:G690 4.0 69.2 1.0 P 2:G690 4.1 74.0 1.0 OP1 2:A689 4.2 69.3 1.0 O3' 2:A689 4.2 71.8 1.0 N1 2:A773 4.2 56.4 1.0 O3' 2:G1483 4.3 77.3 1.0 C5' 2:A689 4.5 53.5 1.0 O2' 2:G1483 4.6 76.5 1.0 C2 2:A773 4.6 57.5 1.0 OP2 2:A775 4.7 49.9 1.0 OP1 2:C1484 4.7 76.7 1.0 O5' 2:A689 4.9 61.8 1.0

Magnesium binding site 6 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1506 b:59.5 occ:1.00 OP2 2:G1462 1.9 58.2 1.0 O 2:HOH1625 1.9 62.8 1.0 O 2:HOH1683 1.9 37.1 1.0 O 2:HOH1645 1.9 61.6 1.0 O2P 2:6MZ1457 1.9 73.4 1.0 OP2 2:A1456 2.6 52.2 1.0 P 2:G1462 3.3 64.6 1.0 P 2:6MZ1457 3.4 61.4 1.0 O3' 2:U1455 3.4 30.0 1.0 P 2:A1456 3.6 30.6 1.0 O3' 2:G1461 3.8 62.9 1.0 C3' 2:A1456 4.0 36.4 1.0 O2' 2:U1455 4.0 43.1 1.0 O3' 2:A1456 4.1 18.7 1.0 O1P 2:6MZ1457 4.1 62.2 1.0 OP1 2:G1462 4.2 66.9 1.0 O5' 2:G1462 4.3 54.7 1.0 O5' 2:A1456 4.3 53.1 1.0 O5' 2:6MZ1457 4.3 54.7 1.0 O2' 2:G1461 4.5 69.0 1.0 C3' 2:U1455 4.5 39.9 1.0 C5' 2:A1456 4.5 54.9 1.0 OP1 2:A1456 4.8 48.7 1.0 C4' 2:A1456 4.8 43.4 1.0 C2' 2:U1455 4.9 29.3 1.0

Magnesium binding site 7 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1507 b:98.7 occ:1.00 OP2 2:A468 1.7 79.5 1.0 O 2:HOH1626 1.8 75.5 1.0 O 2:HOH1696 1.8 65.8 1.0 O 2:HOH1639 1.8 84.3 1.0 OP2 2:A467 1.9 78.1 1.0 O 2:HOH1618 1.9 90.7 1.0 P 2:A468 3.1 76.3 1.0 P 2:A467 3.3 71.9 1.0 O3' 2:C466 3.8 73.8 1.0 OP1 2:G464 3.9 76.1 1.0 C3' 2:A467 3.9 62.4 1.0 OP1 2:A468 3.9 73.1 1.0 O3' 2:A467 4.0 60.9 1.0 O5' 2:A468 4.0 72.6 1.0 O5' 2:A467 4.2 68.2 1.0 OP1 2:A467 4.3 63.6 1.0 N7 2:A468 4.4 63.4 1.0 C8 2:A468 4.4 62.7 1.0 C5' 2:A467 4.5 60.8 1.0 OP2 2:G465 4.5 73.4 1.0 C4' 2:A467 4.8 56.8 1.0 C2' 2:A467 5.0 71.9 1.0

Magnesium binding site 8 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1508 b:71.8 occ:1.00 O 2:HOH1620 1.8 71.2 1.0 O 2:HOH1607 1.9 69.7 1.0 OP2 2:A96 1.9 69.4 1.0 OP2 2:G294 2.1 67.2 1.0 OP2 2:G97 2.2 70.1 1.0 P 2:G294 3.3 64.9 1.0 P 2:A96 3.3 71.1 1.0 O5' 2:G294 3.5 60.9 1.0 P 2:G97 3.7 81.2 1.0 O3' 2:G95 3.9 61.5 1.0 O5' 2:A96 4.1 61.8 1.0 O4 2:U98 4.1 71.9 1.0 N7 2:G97 4.2 58.2 1.0 OP1 2:G294 4.3 59.9 1.0 C3' 2:A96 4.4 63.5 1.0 O3' 2:A293 4.4 68.1 1.0 O5' 2:G97 4.4 67.2 1.0 O3' 2:A96 4.5 66.3 1.0 OP1 2:A96 4.5 64.9 1.0 C3' 2:A293 4.5 65.5 1.0 C5' 2:A96 4.5 55.2 1.0 C8 2:G97 4.5 63.9 1.0 OP1 2:G97 4.6 68.8 1.0 C4 2:U98 4.8 63.0 1.0 O5' 2:A293 4.9 75.1 1.0 C5 2:U98 4.9 60.1 1.0 C5' 2:G294 4.9 51.9 1.0

Magnesium binding site 9 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1509 b:78.9 occ:1.00 O6 2:G469 4.1 96.8 1.0 OP2 2:C495 4.6 80.5 1.0 N6 2:A497 4.6 93.7 1.0 O6 2:G498 4.6 99.5 1.0 N7 2:A497 4.6 95.5 1.0 N4 2:C499 4.9 95.8 1.0

Magnesium binding site 10 out of 59 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1510 b:116.5 occ:1.00 OP2 2:C1011 1.5 84.3 1.0 P 2:C1011 1.9 88.0 1.0 OP1 2:C1011 1.9 84.7 1.0 OP1 2:G1160 2.1 81.7 1.0 OP2 2:G1160 2.2 85.1 1.0 P 2:G1160 2.4 88.8 1.0 OP2 2:G1161 2.7 67.8 1.0 O3' 2:G1010 3.0 76.7 1.0 O3' 2:A1159 3.0 83.4 1.0 O2' 2:A1159 3.1 92.5 1.0 O5' 2:C1011 3.2 82.0 1.0 O 2:HOH1637 3.2 78.5 1.0 O 2:HOH1641 3.3 64.2 1.0 O5' 2:G1160 3.9 73.4 1.0 C3' 2:G1010 3.9 71.5 1.0 O2' 2:G1010 4.0 75.5 1.0 C3' 2:A1159 4.0 84.8 1.0 C2' 2:A1159 4.1 87.4 1.0 P 2:G1161 4.2 76.3 1.0 C5' 2:C1011 4.2 78.4 1.0 C2' 2:G1010 4.5 67.2 1.0 C5' 2:G1160 4.6 73.0 1.0 C3' 2:G1160 4.6 72.3 1.0 O3' 2:G1160 4.8 77.8 1.0 C1' 2:A1159 4.8 85.2 1.0 O5' 2:G1161 5.0 67.8 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