Magnesium in PDB 5oom: Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna

All present enzymatic activity of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna:
3.1.1.29;

The structure of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna also contains other interesting chemical elements:

Zinc

(Zn)

2 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 - 49;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna (pdb code 5oom). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 49 binding sites of Magnesium where determined in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna, PDB code: 5oom:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3301 b:23.3 occ:1.00 OP1 A:A2866 2.2 25.4 1.0 OP2 A:U2864 2.3 26.0 1.0 OP2 A:C2867 3.6 28.9 1.0 P A:A2866 3.6 25.4 1.0 P A:U2864 3.8 26.0 1.0 C2' A:U2863 4.0 21.9 1.0 C2 A:U2863 4.2 21.9 1.0 C3' A:U2863 4.3 21.9 1.0 C5' A:U2864 4.3 26.0 1.0 O2 A:U2863 4.3 21.9 1.0 O5' A:U2864 4.4 26.0 1.0 OP2 A:A2866 4.4 25.4 1.0 O3' A:U2863 4.4 21.9 1.0 O5' A:A2866 4.4 25.4 1.0 O3' A:C2865 4.5 28.3 1.0 N3 A:U2863 4.5 21.9 1.0 N1 A:U2863 4.5 21.9 1.0 C5' A:A2866 4.5 25.4 1.0 OP1 A:U2864 4.9 26.0 1.0 C1' A:U2863 4.9 21.9 1.0 P A:C2867 4.9 28.9 1.0 O2' A:U2863 4.9 21.9 1.0 N6 A:A2869 4.9 22.3 1.0 C6 A:U2863 5.0 21.9 1.0 C4 A:U2863 5.0 21.9 1.0

Magnesium binding site 2 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3302 b:26.5 occ:1.00 O4 A:U1758 1.8 30.5 1.0 OP2 A:A1757 2.4 25.8 1.0 C4 A:U1758 2.9 30.5 1.0 O4 A:U1759 3.1 34.3 1.0 C5 A:U1758 3.6 30.5 1.0 N6 A:A1739 3.7 31.4 1.0 P A:A1757 3.8 25.8 1.0 N3 A:U1758 4.0 30.5 1.0 C4 A:U1759 4.1 34.3 1.0 N1 A:A1740 4.4 28.9 1.0 OP1 A:A1757 4.5 25.8 1.0 O5' A:A1757 4.7 25.8 1.0 C6 A:A1739 4.7 31.4 1.0 C2 A:A1740 4.8 28.9 1.0 N1 A:A1739 4.8 31.4 1.0 C5 A:U1759 4.8 34.3 1.0 O3' A:A1756 4.8 28.9 1.0 O5' A:A1756 4.9 28.9 1.0 N3 A:U1759 4.9 34.3 1.0 C6 A:U1758 4.9 30.5 1.0 C3' A:A1756 5.0 28.9 1.0

Magnesium binding site 3 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3303 b:27.6 occ:1.00 N7 A:A1723 1.9 30.4 1.0 OP1 A:C1725 1.9 35.1 1.0 OP2 A:C1726 2.5 31.9 1.0 C8 A:A1723 2.7 30.4 1.0 C5 A:A1723 3.1 30.4 1.0 P A:C1725 3.3 35.1 1.0 N6 A:A1723 3.7 30.4 1.0 N7 A:A1722 3.8 27.0 1.0 C6 A:A1723 3.8 30.4 1.0 OP2 A:C1725 3.9 35.1 1.0 P A:C1726 3.9 31.9 1.0 N9 A:A1723 4.0 30.4 1.0 C8 A:A1722 4.0 27.0 1.0 C4 A:A1723 4.1 30.4 1.0 OP2 A:A1723 4.2 30.4 1.0 O5' A:C1725 4.2 35.1 1.0 OP2 A:A1722 4.3 27.0 1.0 O3' A:A1724 4.3 29.0 1.0 C5 A:A1722 4.4 27.0 1.0 C5' A:C1725 4.6 35.1 1.0 N9 A:A1722 4.7 27.0 1.0 OP1 A:C1726 4.7 31.9 1.0 O3' A:C1725 4.8 35.1 1.0 C5 A:C1726 4.8 31.9 1.0 O5' A:A1722 4.8 27.0 1.0 O5' A:A1723 4.8 30.4 1.0 O5' A:C1726 4.8 31.9 1.0 C4 A:A1722 4.9 27.0 1.0

Magnesium binding site 4 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3304 b:15.3 occ:1.00 OP2 A:G1776 2.0 28.9 1.0 OP2 A:U1778 3.3 28.9 1.0 P A:G1776 3.3 28.9 1.0 OP1 A:G1776 4.0 28.9 1.0 O5' A:G1776 4.0 28.9 1.0 O F:GLY149 4.0 32.6 1.0 O F:GLY148 4.1 33.0 1.0 OP2 A:A1777 4.1 28.9 1.0 O3' A:A1775 4.5 28.9 1.0 OP2 A:A1775 4.5 28.9 1.0 C F:GLY148 4.5 33.0 1.0 CG2 F:VAL120 4.6 36.7 1.0 OP1 A:A1775 4.7 28.9 1.0 N7 A:G1776 4.7 28.9 1.0 C8 A:G1776 4.7 28.9 1.0 P A:U1778 4.8 28.9 1.0 CA F:GLY148 4.8 33.0 1.0 C5' A:A1777 4.9 28.9 1.0 C3' A:A1775 4.9 28.9 1.0

Magnesium binding site 5 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3305 b:23.0 occ:1.00 OP1 A:A1814 2.0 28.9 1.0 OP2 A:A1815 2.3 28.9 1.0 P A:A1814 3.3 28.9 1.0 O6 A:G1816 3.7 28.9 1.0 P A:A1815 3.8 28.9 1.0 N7 A:G1816 3.9 28.9 1.0 O5' A:A1814 4.0 28.9 1.0 OP2 A:A1814 4.1 28.9 1.0 N7 A:A1815 4.3 28.9 1.0 N4 A:C1817 4.3 28.9 1.0 O5' A:A1815 4.4 28.9 1.0 O3' A:C1813 4.5 40.1 1.0 C6 A:G1816 4.5 28.9 1.0 C5' A:A1814 4.5 28.9 1.0 C5 A:G1816 4.5 28.9 1.0 OP1 A:A1815 4.6 28.9 1.0 C8 A:A1815 4.6 28.9 1.0 C3' A:A1814 4.7 28.9 1.0 O3' A:A1814 4.7 28.9 1.0 C8 A:G1816 5.0 28.9 1.0

Magnesium binding site 6 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3306 b:14.3 occ:1.00 O6 A:G1776 2.0 28.9 1.0 OP1 A:A1779 2.4 28.9 1.0 C6 A:G1776 3.1 28.9 1.0 P A:A1779 3.8 28.9 1.0 C5 A:G1776 3.9 28.9 1.0 OP2 A:A1775 4.0 28.9 1.0 N7 A:G1776 4.1 28.9 1.0 N7 A:A1775 4.1 28.9 1.0 N1 A:G1776 4.1 28.9 1.0 MG A:MG3339 4.2 19.5 1.0 OP2 A:A1779 4.5 28.9 1.0 O5' A:A1779 4.6 28.9 1.0 NH2 F:ARG147 4.8 32.8 1.0 C8 A:A1775 4.8 28.9 1.0 O3' A:U1778 4.8 28.9 1.0 C5' A:U1774 4.8 28.9 1.0 N6 A:A1775 4.9 28.9 1.0 C5' A:A1779 4.9 28.9 1.0 C5 A:A1775 5.0 28.9 1.0

Magnesium binding site 7 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3307 b:24.9 occ:1.00 OP2 A:G1918 2.1 28.9 1.0 P A:G1918 3.4 28.9 1.0 O3' A:A1917 3.8 28.9 1.0 O6 A:G1981 4.0 28.9 1.0 OP2 A:C1919 4.0 27.4 1.0 O5' A:G1918 4.1 28.9 1.0 O6 A:G1982 4.3 28.9 1.0 O4 A:U1920 4.5 26.2 1.0 OP1 A:G1918 4.6 28.9 1.0 N4 A:C1922 4.8 25.1 1.0 NZ 2:LYS59 4.9 45.3 1.0 C6 A:G1981 4.9 28.9 1.0 N7 A:G1981 4.9 28.9 1.0

Magnesium binding site 8 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3308 b:11.8 occ:1.00 OP2 A:G2011 2.0 28.9 1.0 P A:G2011 3.5 28.9 1.0 O F:GLY123 4.1 39.8 1.0 O3' A:U2010 4.2 28.9 1.0 OP1 A:G2011 4.2 28.9 1.0 O F:ALA118 4.3 36.0 1.0 O F:GLY122 4.3 38.0 1.0 O5' A:G2011 4.4 28.9 1.0 OP1 A:G2008 4.5 28.9 1.0 C5' A:G2011 4.5 28.9 1.0 OP2 A:G2009 4.6 28.9 1.0 C F:GLY123 4.8 39.8 1.0 NZ i:LYS112 4.8 42.0 1.0 CA F:GLY124 4.9 43.6 1.0 CA F:ALA118 4.9 36.0 1.0

Magnesium binding site 9 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3309 b:26.1 occ:1.00 OP2 A:A2027 1.9 24.5 1.0 P A:A2027 3.3 24.5 1.0 OP1 A:A2027 4.0 24.5 1.0 O5' A:A2027 4.1 24.5 1.0 OP2 A:C2263 4.1 29.5 1.0 N7 A:G2028 4.2 26.8 1.0 N7 A:A2027 4.2 24.5 1.0 O6 A:G2028 4.3 26.8 1.0 O3' A:A2026 4.3 23.8 1.0 OP1 A:C2263 4.4 29.5 1.0 C8 A:A2027 4.4 24.5 1.0 C3' A:A2026 4.4 23.8 1.0 O5' A:A2026 4.6 23.8 1.0 N6 A:A2142 4.7 35.5 1.0 P A:C2263 4.7 29.5 1.0 C5 A:C2263 4.9 29.5 1.0

Magnesium binding site 10 out of 49 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3310 b:26.0 occ:1.00 OP1 A:C2252 1.7 28.9 1.0 OP1 A:U2141 2.1 35.6 1.0 OP2 A:U2253 2.2 28.9 1.0 P A:C2252 2.8 28.9 1.0 OP2 A:C2252 3.2 28.9 1.0 O5' A:U2141 3.2 35.6 1.0 P A:U2141 3.3 35.6 1.0 O5' A:C2252 3.6 28.9 1.0 P A:U2253 3.6 28.9 1.0 C5' A:C2252 3.9 28.9 1.0 O3' A:G2140 4.1 32.4 1.0 O3' A:A2251 4.1 28.9 1.0 OP1 A:A2142 4.1 35.5 1.0 O5' A:A2142 4.2 35.5 1.0 OP1 A:U2253 4.4 28.9 1.0 O3' A:C2252 4.4 28.9 1.0 OP2 A:U2141 4.5 35.6 1.0 C5' A:U2141 4.6 35.6 1.0 C3' A:C2252 4.6 28.9 1.0 O5' A:U2253 4.7 28.9 1.0 C4' A:C2252 4.8 28.9 1.0 P A:A2142 4.9 35.5 1.0 C3' A:U2141 5.0 35.6 1.0

A.Brown, S.Rathore, D.Kimanius, S.Aibara, X.C.Bai, J.Rorbach, A.Amunts, V.Ramakrishnan. Structures of the Human Mitochondrial Ribosome in Native States of Assembly. Nat. Struct. Mol. Biol. V. 24 866 2017.
ISSN: ESSN 1545-9985
PubMed: 28892042
DOI: 10.1038/NSMB.3464