Magnesium in PDB 7zah: Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B

The structure of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B also contains other interesting chemical elements:

Zinc

(Zn)

6 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 - 60; Page 7, Binding sites: 61 - 63;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B (pdb code 7zah). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 63 binding sites of Magnesium where determined in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B, PDB code: 7zah:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1601 b:46.2 occ:1.00 O 2:HOH2004 1.9 42.4 1.0 O 2:HOH1855 1.9 42.9 1.0 O F:HOH404 1.9 43.9 1.0 O 2:HOH1854 1.9 41.8 1.0 O 2:HOH1790 1.9 39.4 1.0 O 2:HOH1993 1.9 42.3 1.0 OP1 2:A836 4.0 46.4 1.0 N7 2:G834 4.1 31.6 1.0 OP1 2:U1043 4.4 36.4 1.0 O6 2:G834 4.6 31.6 1.0 C5 2:G834 4.8 31.6 1.0 OP2 2:A836 4.8 46.4 1.0 C8 2:G834 4.9 31.6 1.0 P 2:A836 4.9 46.4 1.0 C6 2:G834 4.9 31.6 1.0

Magnesium binding site 2 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1602 b:71.6 occ:1.00 O 2:HOH1734 1.8 76.6 1.0 OP2 2:A209 1.9 63.8 1.0 O 2:HOH1958 1.9 74.2 1.0 O 2:HOH1716 1.9 68.2 1.0 O 2:HOH1840 1.9 69.0 1.0 P 2:A209 3.3 63.8 1.0 O4 2:U177 3.7 73.2 1.0 C2' 2:G208 3.9 62.5 1.0 C3' 2:G208 4.0 62.5 1.0 O5' 2:A209 4.1 63.8 1.0 O3' 2:G208 4.2 62.5 1.0 C5' 2:A209 4.2 63.8 1.0 OP1 2:A209 4.3 63.8 1.0 N7 2:A176 4.4 76.5 1.0 N9 2:G208 4.6 62.5 1.0 C4 2:G208 4.7 62.5 1.0 O2' 2:G208 4.8 62.5 1.0 C4 2:U177 4.8 73.2 1.0 C1' 2:G208 4.9 62.5 1.0 N3 2:G208 4.9 62.5 1.0 C8 2:G208 5.0 62.5 1.0

Magnesium binding site 3 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1603 b:61.7 occ:1.00 O 2:HOH1947 1.9 56.8 1.0 O 2:HOH2005 1.9 56.3 1.0 O 2:HOH1862 2.0 56.1 1.0 O 2:HOH1924 2.0 55.8 1.0 O 2:HOH2014 2.0 59.5 1.0 N7 2:G650 3.5 47.0 1.0 O6 2:G650 3.8 47.0 1.0 C5 2:G650 4.2 47.0 1.0 C6 2:G650 4.3 47.0 1.0 C8 2:G650 4.4 47.0 1.0 N7 2:G649 4.5 48.4 1.0 N7 2:G651 4.5 45.5 1.0 O6 2:G651 4.5 45.5 1.0 O6 2:G649 4.5 48.4 1.0 C5 2:G649 4.8 48.4 1.0 C6 2:G649 4.8 48.4 1.0 O6 2:G652 4.8 47.3 1.0 OP1 2:A671 4.9 48.5 1.0

Magnesium binding site 4 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1604 b:38.0 occ:1.00 OP1 2:C1048 1.9 26.5 1.0 O 2:HOH1822 1.9 34.3 1.0 O 2:HOH1962 1.9 37.6 1.0 O 2:HOH1831 1.9 37.5 1.0 O 2:HOH1773 2.0 36.5 1.0 O 2:HOH1985 2.2 36.0 1.0 P 2:C1048 3.3 26.5 1.0 C5' 2:C1048 3.7 26.5 1.0 O3' 2:G1047 3.8 27.1 1.0 O5' 2:C1048 3.8 26.5 1.0 OP2 2:G1049 4.4 26.1 1.0 OP2 2:C1048 4.4 26.5 1.0 OP1 2:U1364 4.9 28.3 1.0

Magnesium binding site 5 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1605 b:44.5 occ:1.00 O4 2:U825 1.9 33.6 1.0 O 2:HOH1997 1.9 44.6 1.0 O 2:HOH1793 1.9 43.2 1.0 O 2:HOH1813 1.9 41.6 1.0 O 2:HOH1941 1.9 41.6 1.0 O 2:HOH1973 2.0 44.5 1.0 C4 2:U825 2.9 33.6 1.0 C5 2:U825 3.4 33.6 1.0 N7 2:G824 3.9 31.9 1.0 N3 2:U825 4.1 33.6 1.0 C8 2:G824 4.5 31.9 1.0 OP1 2:U842 4.6 34.7 1.0 C5 2:G824 4.7 31.9 1.0 C6 2:U825 4.7 33.6 1.0 C5 2:U842 4.7 34.7 1.0 O6 2:G824 4.9 31.9 1.0 OP2 2:U842 4.9 34.7 1.0

Magnesium binding site 6 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1606 b:37.1 occ:1.00 O 2:HOH1799 1.9 35.4 1.0 O 2:HOH1957 1.9 36.6 1.0 O 2:HOH1875 2.0 37.9 1.0 O 2:HOH1713 2.0 37.4 1.0 OP1 2:G948 2.0 34.5 1.0 P 2:G948 3.1 34.5 1.0 O5' 2:G948 3.1 34.5 1.0 O3' 2:G947 4.2 36.6 1.0 OP2 2:G948 4.2 34.5 1.0 C3' 2:G947 4.2 36.6 1.0 N6 2:A1337 4.3 33.2 1.0 OP2 2:G947 4.4 36.6 1.0 N1 2:A1337 4.4 33.2 1.0 C5' 2:G948 4.5 34.5 1.0 O4' 2:G948 4.5 34.5 1.0 O5' 2:G947 4.6 36.6 1.0 O2' 2:G946 4.6 37.4 1.0 O2 2:C1339 4.8 30.9 1.0 O3' 2:G946 4.9 37.4 1.0 C6 2:A1337 4.9 33.2 1.0 N2 2:G943 4.9 30.8 1.0 P 2:G947 4.9 36.6 1.0

Magnesium binding site 7 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1607 b:41.5 occ:1.00 O 2:HOH1867 1.9 38.1 1.0 O 2:HOH1710 1.9 36.9 1.0 O 2:HOH1988 1.9 40.2 1.0 O 2:HOH1844 1.9 36.1 1.0 OP1 2:A1210 2.0 30.9 1.0 P 2:A1210 3.3 30.9 1.0 OE2 U:GLU88 3.9 33.5 1.0 O5' 2:A1210 4.0 30.9 1.0 OP2 2:A1210 4.0 30.9 1.0 O3' 2:U1209 4.4 28.4 1.0 OP1 2:G1216 4.4 38.2 1.0 CE1 H:HIS90 4.7 38.4 1.0 C5' 2:A1210 4.7 30.9 1.0 ND1 H:HIS90 5.0 38.4 1.0 CD U:GLU88 5.0 33.5 1.0

Magnesium binding site 8 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1608 b:32.9 occ:1.00 O 2:HOH1754 1.9 31.5 1.0 O 2:HOH1845 1.9 32.8 1.0 O 2:HOH1892 1.9 30.8 1.0 OP2 2:G917 2.1 31.3 1.0 OP1 2:G916 2.7 30.9 1.0 O 2:HOH1967 3.3 33.2 1.0 P 2:G917 3.4 31.3 1.0 P 2:G916 3.8 30.9 1.0 OP1 2:G917 3.9 31.3 1.0 O5' 2:G917 4.1 31.3 1.0 OP2 2:G916 4.1 30.9 1.0 O5' 2:G916 4.2 30.9 1.0 N7 2:A918 4.3 30.6 1.0 OP2 2:A918 4.4 30.6 1.0 C5' 2:G916 4.4 30.9 1.0 O3' 2:G916 4.6 30.9 1.0 C8 2:A918 4.9 30.6 1.0 C3' 2:G916 5.0 30.9 1.0

Magnesium binding site 9 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1609 b:45.4 occ:1.00 O 2:HOH1945 1.9 43.3 1.0 OP2 2:A59 1.9 36.0 1.0 O 2:HOH1865 1.9 41.5 1.0 O 2:HOH1841 1.9 40.6 1.0 O 2:HOH1954 1.9 43.3 1.0 O 2:HOH1772 1.9 41.8 1.0 P 2:A59 3.1 36.0 1.0 O3' 2:A58 3.7 42.3 1.0 OP1 2:A59 3.8 36.0 1.0 O5' 2:A59 4.3 36.0 1.0 N7 2:G60 4.5 39.8 1.0 OP1 2:C56 4.7 41.1 1.0 OP2 2:A55 4.7 35.5 1.0 C5' 2:A59 4.8 36.0 1.0 O2' 2:A58 4.8 42.3 1.0 C3' 2:A58 4.8 42.3 1.0

Magnesium binding site 10 out of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


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 A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1610 b:54.9 occ:1.00 O 2:HOH1794 1.9 47.7 1.0 O 0:HOH103 1.9 58.9 1.0 O 2:HOH1969 1.9 49.1 1.0 O 2:HOH1971 1.9 48.0 1.0 O 2:HOH2019 2.0 45.9 1.0 O 2:HOH1876 3.7 39.9 1.0 O6 2:G866 4.4 40.5 1.0 N7 2:G865 4.7 40.3 1.0 O6 2:G865 4.8 40.3 1.0

R.Kazan, G.Bourgeois, C.Lazennec-Schurdevin, E.Larquet, Y.Mechulam, P.D.Coureux, E.Schmitt. Role of AIF5B in Archaeal Translation Initiation. Nucleic Acids Res. V. 50 6532 2022.
ISSN: ESSN 1362-4962
PubMed: 35694843
DOI: 10.1093/NAR/GKAC490