Magnesium in PDB 8css: Human Mitochondrial Small Subunit Assembly Intermediate (State D)

All present enzymatic activity of Human Mitochondrial Small Subunit Assembly Intermediate (State D):
2.3.1.39;

The structure of Human Mitochondrial Small Subunit Assembly Intermediate (State D) also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Iron	(Fe)	8 atoms
Potassium	(K)	7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Magnesium atom in the Human Mitochondrial Small Subunit Assembly Intermediate (State D) (pdb code 8css). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 32 binding sites of Magnesium where determined in the Human Mitochondrial Small Subunit Assembly Intermediate (State D), PDB code: 8css:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1708 b:33.3 occ:1.00 O1A A:NAD1738 2.0 29.7 1.0 O A:HOH1843 2.0 28.8 1.0 O A:HOH1881 2.0 38.1 1.0 O A:HOH1854 2.4 37.5 1.0 O A:HOH1806 2.5 30.0 1.0 O A:HOH1877 2.5 35.1 1.0 PA A:NAD1738 3.4 29.7 1.0 O2' A:A757 3.8 26.2 1.0 O2N A:NAD1738 4.0 29.7 1.0 O2A A:NAD1738 4.1 29.7 1.0 N4 A:C1048 4.1 32.3 1.0 O5B A:NAD1738 4.1 29.7 1.0 O1N A:NAD1738 4.3 29.7 1.0 N1 A:A783 4.3 27.5 1.0 N6 A:A783 4.3 27.5 1.0 O3 A:NAD1738 4.4 29.7 1.0 O A:HOH1867 4.4 32.1 1.0 O A:HOH1817 4.4 30.4 1.0 C5B A:NAD1738 4.4 29.7 1.0 PN A:NAD1738 4.5 29.7 1.0 C6 A:A783 4.9 27.5 1.0 C2' A:A757 4.9 26.2 1.0

Magnesium binding site 2 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1709 b:33.8 occ:1.00 O A:HOH1892 2.3 30.3 1.0 O A:HOH1803 2.8 25.9 1.0 OP1 A:A1046 3.2 27.8 1.0 O4' A:G1134 3.8 33.7 1.0 O A:HOH1860 3.8 20.8 1.0 O5' A:A1046 4.0 27.8 1.0 C5' A:A1046 4.1 27.8 1.0 P A:A1046 4.1 27.8 1.0 C4' A:G1134 4.2 33.7 1.0 O A:HOH1841 4.2 21.1 1.0 C1' A:G1134 4.2 33.7 1.0 O2' A:G1134 4.3 33.7 1.0 O A:HOH1887 4.3 34.0 1.0 OP2 A:A1047 4.3 31.7 1.0 N7 A:A942 4.4 36.0 1.0 MG A:MG1715 4.6 26.4 1.0 N2 A:G941 4.6 33.7 1.0 O2' A:C1133 4.7 33.7 1.0 OP2 A:A1046 4.8 27.8 1.0 C2' A:G1134 4.8 33.7 1.0 C3' A:A1046 4.9 27.8 1.0 O2 A:C1133 5.0 33.7 1.0

Magnesium binding site 3 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1710 b:33.2 occ:1.00 O A:HOH1882 2.0 32.2 1.0 O A:HOH1886 2.0 35.7 1.0 OP1 A:G1092 2.0 31.0 1.0 O A:HOH1893 2.0 33.5 1.0 O A:HOH1873 2.1 35.4 1.0 O A:HOH1833 2.3 30.8 1.0 P A:G1092 3.5 31.0 1.0 O A:HOH1855 3.8 30.3 1.0 O3' A:U1091 4.1 32.7 1.0 O A:HOH1872 4.1 32.7 1.0 OP2 A:G1092 4.4 31.0 1.0 OP2 A:C1093 4.4 39.2 1.0 N4 A:C1058 4.4 38.7 1.0 O5' A:G1092 4.4 31.0 1.0 C5' A:G1092 4.6 31.0 1.0 O6 A:G1057 4.7 31.1 1.0 N7 A:G1057 4.7 31.1 1.0

Magnesium binding site 4 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1711 b:28.1 occ:1.00 OP2 A:G791 2.0 31.7 1.0 O A:HOH1838 2.0 31.5 1.0 O A:HOH1820 2.0 26.3 1.0 OP2 A:A718 2.0 25.9 1.0 O A:HOH1861 2.1 28.0 1.0 OP2 A:G719 2.2 24.6 1.0 P A:G791 3.4 31.7 1.0 P A:A718 3.5 25.9 1.0 P A:G719 3.6 24.6 1.0 O5' A:G791 3.8 31.7 1.0 OP1 A:A718 4.3 25.9 1.0 O3' A:G717 4.3 33.7 1.0 O5' A:A790 4.3 25.2 1.0 OP1 A:G791 4.4 31.7 1.0 OP1 A:G719 4.4 24.6 1.0 O5' A:A718 4.4 25.9 1.0 K A:K1702 4.4 23.7 1.0 O3' A:A718 4.4 25.9 1.0 O3' A:A790 4.4 25.2 1.0 C3' A:A790 4.4 25.2 1.0 C5' A:A718 4.5 25.9 1.0 OP2 A:A790 4.5 25.2 1.0 C3' A:A718 4.6 25.9 1.0 O5' A:G719 4.6 24.6 1.0 O4 A:U720 4.7 23.8 1.0 P A:A790 4.9 25.2 1.0 N7 A:G719 4.9 24.6 1.0

Magnesium binding site 5 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1712 b:25.4 occ:1.00 OP2 A:A940 2.0 33.7 1.0 O A:HOH1870 2.0 32.3 1.0 O A:HOH1819 2.0 32.0 1.0 O A:HOH1811 2.1 29.0 1.0 OP2 A:A939 2.3 29.5 1.0 OP2 A:A938 2.9 34.8 1.0 P A:A940 3.3 33.7 1.0 P A:A939 3.5 29.5 1.0 P A:A938 3.7 34.8 1.0 OP1 A:A939 3.7 29.5 1.0 OP1 A:U937 3.8 28.0 1.0 O5' A:A938 3.8 34.8 1.0 OP1 A:A940 3.9 33.7 1.0 OP1 A:A938 4.0 34.8 1.0 C5' A:A938 4.1 34.8 1.0 O3' A:A939 4.3 29.5 1.0 C3' A:A939 4.4 29.5 1.0 O5' A:A940 4.4 33.7 1.0 O5' A:A939 4.5 29.5 1.0 O3' A:A938 4.6 34.8 1.0 P A:U937 4.7 28.0 1.0 OP2 A:U937 4.8 28.0 1.0 C5' A:A939 4.9 29.5 1.0 C3' A:A938 4.9 34.8 1.0

Magnesium binding site 6 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1713 b:34.1 occ:1.00 O A:HOH1874 2.0 30.0 1.0 O A:HOH1878 2.0 30.6 1.0 O A:HOH1866 2.0 31.1 1.0 O A:HOH1898 2.0 35.2 1.0 O A:HOH1827 2.1 29.5 1.0 O A:HOH1831 2.3 33.8 1.0 O A:HOH1844 3.8 30.7 1.0 OP2 A:G1028 4.0 33.7 1.0 OP1 A:A1027 4.0 33.7 1.0 OP1 A:G1028 4.2 33.7 1.0 OP2 A:A1104 4.3 33.7 1.0 P A:G1028 4.4 33.7 1.0 N1 A:A1102 4.5 33.7 1.0 O3' A:A1027 4.6 33.7 1.0 O3' A:C1591 4.6 33.7 1.0 C5' A:A1027 4.6 33.7 1.0 O2' A:C1591 4.8 33.7 1.0 O2' A:A1104 4.9 33.7 1.0 OP1 A:U1592 4.9 33.7 1.0

Magnesium binding site 7 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1714 b:30.7 occ:1.00 OP2 A:A1054 2.0 37.6 1.0 O A:HOH1879 2.0 33.6 1.0 O A:HOH1858 2.0 28.9 1.0 O A:HOH1885 2.0 38.4 1.0 O A:HOH1801 2.1 30.1 1.0 O A:HOH1805 2.7 30.2 1.0 P A:A1054 3.3 37.6 1.0 OP1 A:A1054 3.8 37.6 1.0 N4 A:C1099 4.0 34.2 1.0 N3 A:C1099 4.2 34.2 1.0 O3' A:A1053 4.2 26.6 1.0 O2 A:C1100 4.3 30.5 1.0 C3' A:A1053 4.3 26.6 1.0 O5' A:A1054 4.4 37.6 1.0 C4 A:C1099 4.6 34.2 1.0 O A:HOH1859 4.7 24.7 1.0 O4 A:U1055 4.7 33.7 1.0 N6 A:A1056 4.8 36.2 1.0 N3 A:C1100 4.8 30.5 1.0 C2 A:C1100 4.8 30.5 1.0 O4 A:U1101 4.9 31.0 1.0

Magnesium binding site 8 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1715 b:26.4 occ:1.00 OP1 A:G1045 2.1 23.9 1.0 O A:HOH1841 2.1 21.1 1.0 O A:HOH1860 2.1 20.8 1.0 O A:HOH1832 2.1 24.4 1.0 O A:HOH1850 2.3 24.2 1.0 O A:HOH1887 2.4 34.0 1.0 P A:G1045 3.5 23.9 1.0 O A:HOH1892 4.0 30.3 1.0 OP1 A:A1046 4.1 27.8 1.0 O5' A:G1045 4.1 23.9 1.0 C5' A:G1045 4.2 23.9 1.0 O3' A:U1044 4.3 32.1 1.0 O2' A:A1109 4.4 33.7 1.0 O2 A:C1133 4.4 33.7 1.0 O4' A:A1110 4.5 27.3 1.0 OP2 A:G1045 4.5 23.9 1.0 N2 A:G941 4.6 33.7 1.0 MG A:MG1709 4.6 33.8 1.0 N3 A:A1109 4.6 33.7 1.0

Magnesium binding site 9 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1716 b:23.0 occ:1.00 OP2 A:U947 2.0 26.5 1.0 O A:HOH1821 2.0 29.4 1.0 O A:HOH1823 2.2 23.4 1.0 O A:HOH1828 2.3 26.0 1.0 O A:HOH1888 2.4 24.4 1.0 N7 A:G1045 2.6 23.9 1.0 P A:U947 3.3 26.5 1.0 C8 A:G1045 3.5 23.9 1.0 C5 A:G1045 3.6 23.9 1.0 O6 A:G1045 3.7 23.9 1.0 OP1 A:U947 3.8 26.5 1.0 C6 A:G1045 4.0 23.9 1.0 OP2 A:U1044 4.2 32.1 1.0 OP2 A:U946 4.3 23.4 1.0 OP1 A:U946 4.3 23.4 1.0 O3' A:U946 4.3 23.4 1.0 OP2 A:G1045 4.3 23.9 1.0 O5' A:U946 4.3 23.4 1.0 O5' A:U947 4.3 26.5 1.0 C5 A:U947 4.4 26.5 1.0 P A:U946 4.5 23.4 1.0 C3' A:U946 4.5 23.4 1.0 N9 A:G1045 4.7 23.9 1.0 C4 A:G1045 4.8 23.9 1.0 O A:HOH1808 4.8 21.9 1.0 C6 A:U947 4.9 26.5 1.0 C5' A:U946 5.0 23.4 1.0

Magnesium binding site 10 out of 32 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1717 b:39.2 occ:1.00 O A:HOH1895 2.0 32.3 1.0 O A:HOH1883 2.2 30.4 1.0 OP1 A:U655 2.9 30.7 1.0 OP2 A:U656 3.1 30.9 1.0 C5 A:U656 3.4 30.9 1.0 O5' A:U655 3.4 30.7 1.0 P A:U655 3.7 30.7 1.0 C6 A:U656 4.0 30.9 1.0 C4 A:U656 4.2 30.9 1.0 P A:U656 4.4 30.9 1.0 O4 A:U656 4.4 30.9 1.0 OP2 A:U655 4.4 30.7 1.0 O5' A:U656 4.5 30.9 1.0 C5' A:U655 4.7 30.7 1.0 C3' A:U655 4.7 30.7 1.0 OP2 A:G658 4.9 33.7 1.0 OP1 A:G658 5.0 33.7 1.0

N.J.Harper, C.Burnside, S.Klinge. Principles of Mitoribosomal Small Subunit Assembly in Eukaryotes. Nature 2022.
ISSN: ESSN 1476-4687
PubMed: 36482135
DOI: 10.1038/S41586-022-05621-0