Magnesium in PDB 7qh7: Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4

The structure of Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 also contains other interesting chemical elements:

Zinc

(Zn)

3 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;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 (pdb code 7qh7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 50 binding sites of Magnesium where determined in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4, PDB code: 7qh7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:8.6 occ:1.00 OP1 A:A2462 2.0 8.5 1.0 NE2 E:HIS237 2.1 10.1 1.0 CE1 E:HIS237 3.0 10.1 1.0 CD2 E:HIS237 3.1 10.1 1.0 P A:A2462 3.2 8.5 1.0 OP2 A:A2462 3.8 8.5 1.0 O5' A:A2462 3.8 8.5 1.0 OP2 A:A2463 3.9 8.0 1.0 ND1 E:HIS237 4.1 10.1 1.0 CG E:HIS237 4.2 10.1 1.0 O E:GLN233 4.2 11.0 1.0 C5' A:A2462 4.4 8.5 1.0 O3' A:A2461 4.4 3.5 1.0 N E:LYS235 4.5 15.3 1.0 OP1 A:U1954 4.7 12.7 1.0 P A:A2463 4.9 8.0 1.0 O3' A:A1953 5.0 10.3 1.0 CA E:THR234 5.0 11.4 1.0

Magnesium binding site 2 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3301 b:17.5 occ:1.00 N7 A:A2827 4.1 48.5 1.0 N6 A:A2827 4.4 48.5 1.0 N4 A:C2829 4.7 41.9 1.0 C5 A:A2827 4.7 48.5 1.0 C8 A:A2827 4.9 48.5 1.0 C6 A:A2827 4.9 48.5 1.0

Magnesium binding site 3 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3302 b:11.0 occ:1.00 OP1 A:A2866 1.9 9.7 1.0 P A:A2866 3.0 9.7 1.0 OP2 A:A2866 3.3 9.7 1.0 OP2 A:C2867 3.6 6.3 1.0 O5' A:A2866 3.7 9.7 1.0 OP2 A:U2864 4.1 25.4 1.0 C5' A:U2864 4.1 25.4 1.0 O3' A:C2865 4.3 21.7 1.0 C5' A:A2866 4.5 9.7 1.0 N6 A:A2869 4.6 6.9 1.0 O2 A:U2863 4.7 15.8 1.0 N4 A:C2868 4.8 5.5 1.0 C3' A:U2864 4.8 25.4 1.0 C2' A:U2863 4.9 15.8 1.0 C2 A:U2863 4.9 15.8 1.0

Magnesium binding site 4 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3303 b:12.5 occ:1.00 OP2 A:A1757 2.4 10.9 1.0 O4 A:U1758 2.9 7.8 1.0 O4 A:U1759 3.6 16.4 1.0 P A:A1757 3.7 10.9 1.0 C4 A:U1758 3.9 7.8 1.0 OP1 A:A1757 4.1 10.9 1.0 N6 A:A1739 4.2 5.8 1.0 O5' A:A1756 4.3 10.9 1.0 C5 A:U1758 4.3 7.8 1.0 O3' A:A1756 4.5 10.9 1.0 OP1 A:A1756 4.5 10.9 1.0 N1 A:A1740 4.5 10.9 1.0 C4 A:U1759 4.7 16.4 1.0 C3' A:A1756 4.8 10.9 1.0 P A:A1756 4.8 10.9 1.0 O5' A:A1757 4.8 10.9 1.0 C2 A:A1740 4.9 10.9 1.0 C5' A:A1756 5.0 10.9 1.0

Magnesium binding site 5 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3304 b:7.8 occ:1.00 OP2 A:C1726 2.0 5.3 1.0 OP1 A:C1725 2.6 8.0 1.0 N7 A:A1723 3.2 5.4 1.0 P A:C1726 3.3 5.3 1.0 OP2 A:A1722 3.6 9.7 1.0 OP1 A:C1726 3.8 5.3 1.0 N6 A:A1723 3.9 5.4 1.0 N7 A:A1722 4.1 9.7 1.0 P A:C1725 4.1 8.0 1.0 C5 A:A1723 4.1 5.4 1.0 C8 A:A1723 4.2 5.4 1.0 C8 A:A1722 4.2 9.7 1.0 O3' A:C1725 4.2 8.0 1.0 OP2 A:A1723 4.4 5.4 1.0 O5' A:C1726 4.4 5.3 1.0 C6 A:A1723 4.4 5.4 1.0 C5' A:C1725 4.7 8.0 1.0 O5' A:C1725 4.8 8.0 1.0 P A:A1722 4.8 9.7 1.0 O5' A:A1722 4.8 9.7 1.0 C3' A:C1725 4.9 8.0 1.0 OP2 A:C1725 5.0 8.0 1.0

Magnesium binding site 6 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3305 b:5.6 occ:1.00 OP2 A:A1815 2.0 10.9 1.0 OP2 A:A1814 2.8 10.9 1.0 P A:A1815 3.4 10.9 1.0 P A:A1814 3.6 10.9 1.0 OP1 A:A1814 3.8 10.9 1.0 O5' A:A1814 4.1 10.9 1.0 OP1 A:A1815 4.2 10.9 1.0 O5' A:A1815 4.2 10.9 1.0 O6 A:G1816 4.3 10.9 1.0 C5' A:A1814 4.4 10.9 1.0 N7 A:G1816 4.4 10.9 1.0 O3' A:A1814 4.5 10.9 1.0 C3' A:A1814 4.5 10.9 1.0 N7 A:A1815 4.7 10.9 1.0 N4 A:C1817 4.8 10.9 1.0 C8 A:A1815 4.8 10.9 1.0

Magnesium binding site 7 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3306 b:3.5 occ:1.00 OP1 A:A1779 2.2 10.9 1.0 O6 A:G1776 2.5 10.9 1.0 C6 A:G1776 3.5 10.9 1.0 P A:A1779 3.6 10.9 1.0 MG A:MG3335 3.8 5.8 1.0 N7 A:G1776 4.1 10.9 1.0 C5' A:A1779 4.1 10.9 1.0 C5 A:G1776 4.2 10.9 1.0 N7 A:A1775 4.3 10.9 1.0 OP2 A:A1779 4.3 10.9 1.0 O5' A:A1779 4.4 10.9 1.0 OP2 A:A1775 4.5 10.9 1.0 O3' A:U1778 4.6 10.9 1.0 N1 A:G1776 4.6 10.9 1.0 N6 A:A1775 4.8 10.9 1.0 C5' A:U1774 4.9 10.9 1.0

Magnesium binding site 8 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3307 b:8.8 occ:1.00 OP2 A:G1918 1.9 10.9 1.0 P A:G1918 3.3 10.9 1.0 O3' A:A1917 3.9 10.9 1.0 OP2 A:C1919 4.0 11.0 1.0 O6 A:G1981 4.1 10.9 1.0 OP1 A:G1918 4.2 10.9 1.0 O6 A:G1982 4.2 10.9 1.0 O5' A:G1918 4.4 10.9 1.0 O4 A:U1920 4.6 14.4 1.0 NZ 2:LYS59 4.6 10.9 1.0 O2' A:A1917 4.7 10.9 1.0 N4 A:C1922 4.7 10.9 1.0 C5' A:G1918 4.8 10.9 1.0

Magnesium binding site 9 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3308 b:10.8 occ:1.00 OP2 A:G2011 2.2 10.9 1.0 P A:G2011 3.5 10.9 1.0 O3' A:U2010 4.1 10.9 1.0 O F:GLY122 4.1 9.2 1.0 OP1 A:G2011 4.2 10.9 1.0 O F:ALA118 4.4 10.9 1.0 OP1 A:G2008 4.4 10.9 1.0 NZ i:LYS112 4.6 3.8 1.0 OP2 A:G2009 4.6 10.9 1.0 O5' A:G2011 4.7 10.9 1.0 CA F:ALA118 4.8 10.9 1.0 C F:ALA118 5.0 10.9 1.0 C5' A:G2011 5.0 10.9 1.0

Magnesium binding site 10 out of 50 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


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 the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3309 b:9.6 occ:1.00 OP2 A:A2027 2.2 10.9 1.0 P A:A2027 3.5 10.9 1.0 OP2 A:C2263 3.9 13.2 1.0 OP1 A:A2027 3.9 10.9 1.0 N7 A:G2028 4.0 5.1 1.0 O3' A:A2026 4.5 10.9 1.0 O6 A:G2028 4.5 5.1 1.0 O5' A:A2027 4.6 10.9 1.0 N6 A:A2142 4.6 11.4 1.0 C3' A:A2026 4.7 10.9 1.0 C8 A:A2027 4.8 10.9 1.0 N7 A:A2027 4.8 10.9 1.0 C5' A:A2027 4.8 10.9 1.0 C8 A:G2028 5.0 5.1 1.0 C5 A:G2028 5.0 5.1 1.0

P.Rebelo-Guiomar, S.Pellegrino, K.C.Dent, A.Sas-Chen, L.Miller-Fleming, C.Garone, L.Van Haute, J.F.Rogan, A.Dinan, A.E.Firth, B.Andrews, A.J.Whitworth, S.Schwartz, A.J.Warren, M.Minczuk. A Late-Stage Assembly Checkpoint of the Human Mitochondrial Ribosome Large Subunit. Nat Commun V. 13 929 2022.
ISSN: ESSN 2041-1723
PubMed: 35177605
DOI: 10.1038/S41467-022-28503-5