Magnesium in PDB 6sw9: IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi

The structure of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi 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 - 34;

Binding sites:

The binding sites of Magnesium atom in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi (pdb code 6sw9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 34 binding sites of Magnesium where determined in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi, PDB code: 6sw9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1601 b:45.9 occ:1.00 OP1 2:G28 1.8 39.8 1.0 P 2:G28 2.9 39.8 1.0 OP2 2:G28 3.2 39.8 1.0 O3' 2:U27 3.7 42.0 1.0 O5' 2:G28 4.1 39.8 1.0 OP2 2:U527 4.4 41.7 1.0 C5' 2:G28 4.5 39.8 1.0 O2' 2:G533 4.9 44.9 1.0 C5' 2:U527 5.0 41.7 1.0

Magnesium binding site 2 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1602 b:45.7 occ:1.00 OP2 2:A539 1.8 44.5 1.0 OP2 2:A540 1.9 44.5 1.0 P 2:A539 2.3 44.5 1.0 OP1 2:A539 2.4 44.5 1.0 O5' 2:A539 3.1 44.5 1.0 P 2:A540 3.3 44.5 1.0 O3' 2:A538 3.8 46.1 1.0 O5' 2:A540 4.0 44.5 1.0 C5' 2:A539 4.1 44.5 1.0 OP1 2:A540 4.2 44.5 1.0 O3' 2:A539 4.3 44.5 1.0 C3' 2:A539 4.4 44.5 1.0 C3' 2:A538 4.5 46.1 1.0 C5' 2:A538 4.7 46.1 1.0 OP1 2:U537 4.7 49.7 1.0 OP2 2:A538 4.7 46.1 1.0 CG 0:PRO5 4.8 62.5 1.0 C4' 2:A539 4.9 44.5 1.0

Magnesium binding site 3 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1603 b:42.5 occ:1.00 OP1 2:C39 1.9 44.1 1.0 P 2:C39 2.2 44.1 1.0 O5' 2:C39 2.2 44.1 1.0 OP2 2:C39 2.6 44.1 1.0 C5' 2:C39 2.9 44.1 1.0 OP2 2:U40 3.6 43.5 1.0 O3' 2:A38 3.7 41.3 1.0 C4' 2:C39 4.2 44.1 1.0 C3' 2:C39 4.7 44.1 1.0 C3' 2:A38 4.7 41.3 1.0 O4' 2:C39 4.9 44.1 1.0 P 2:U40 4.9 43.5 1.0

Magnesium binding site 4 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1604 b:49.3 occ:1.00 OP2 2:A1370 1.9 54.5 1.0 P 2:A1370 2.8 54.5 1.0 O5' 2:A1370 3.0 54.5 1.0 OP1 2:A1370 3.5 54.5 1.0 OP1 2:G22 3.9 51.0 1.0 C8 2:A1370 4.0 54.5 1.0 O3' 2:C1369 4.2 43.8 1.0 C5' 2:A1370 4.2 54.5 1.0 O3' 2:U21 4.2 49.4 1.0 N7 2:A1370 4.6 54.5 1.0 C3' 2:C1369 4.7 43.8 1.0 P 2:G22 4.7 51.0 1.0 C2' 2:A1370 4.8 54.5 1.0

Magnesium binding site 5 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1605 b:51.0 occ:1.00 OP2 2:A574 1.8 53.3 1.0 P 2:A574 3.0 53.3 1.0 O5' 2:A574 3.2 53.3 1.0 C8 2:A574 3.5 53.3 1.0 N7 2:A574 3.5 53.3 1.0 N7 2:A575 3.5 56.0 1.0 OP1 2:A574 3.8 53.3 1.0 C8 2:A575 4.0 56.0 1.0 O3' 2:A573 4.3 54.5 1.0 C5' 2:A574 4.4 53.3 1.0 O4 2:U576 4.5 61.7 1.0 C3' 2:A573 4.6 54.5 1.0 C5 2:A575 4.7 56.0 1.0 N9 2:A574 4.7 53.3 1.0 C5 2:A574 4.8 53.3 1.0 C5 2:U576 4.8 61.7 1.0 C4 2:U576 4.9 61.7 1.0 C3' 2:A574 4.9 53.3 1.0

Magnesium binding site 6 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1606 b:53.7 occ:1.00 OP1 2:A587 1.8 62.9 1.0 O3' 2:C586 2.2 64.7 1.0 P 2:A587 2.3 62.9 1.0 OP2 2:A587 3.1 62.9 1.0 C3' 2:C586 3.5 64.7 1.0 O5' 2:A587 3.7 62.9 1.0 C4' 2:C586 4.1 64.7 1.0 O2' 2:C586 4.2 64.7 1.0 C5' 2:A587 4.3 62.9 1.0 C2' 2:C586 4.5 64.7 1.0 C5' 2:C586 4.5 64.7 1.0 O6 2:G583 4.8 64.0 1.0

Magnesium binding site 7 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1607 b:61.6 occ:1.00 OP2 2:4AC590 2.7 64.0 1.0 OP2 2:G591 2.9 64.7 1.0 O5' 2:4AC590 3.5 64.0 1.0 P 2:4AC590 3.5 64.0 1.0 OP1 2:4AC590 4.0 64.0 1.0 P 2:G591 4.3 64.7 1.0 C3' 2:4AC590 4.3 64.0 1.0 OP1 2:U576 4.4 61.7 1.0 O3' 2:4AC590 4.6 64.0 1.0 C5' 2:4AC590 4.6 64.0 1.0 O3' 2:C589 5.0 62.7 1.0 C6 2:4AC590 5.0 64.0 1.0

Magnesium binding site 8 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1608 b:56.9 occ:1.00 OP1 2:A726 1.8 51.9 1.0 OP2 2:G727 1.9 52.0 1.0 O5' 2:A726 1.9 51.9 1.0 C5' 2:A726 2.3 51.9 1.0 O3' 2:A726 2.3 51.9 1.0 P 2:A726 2.3 51.9 1.0 C3' 2:A726 2.4 51.9 1.0 P 2:G727 2.6 52.0 1.0 C4' 2:A726 2.7 51.9 1.0 OP2 2:A726 3.4 51.9 1.0 O5' 2:G727 3.4 52.0 1.0 O3' 2:G725 3.6 57.8 1.0 O4' 2:A726 3.9 51.9 1.0 C2' 2:A726 3.9 51.9 1.0 OP1 2:G727 3.9 52.0 1.0 C1' 2:A726 4.5 51.9 1.0 O2' 2:G725 4.6 57.8 1.0 O2' 2:A726 4.6 51.9 1.0 C3' 2:G725 4.8 57.8 1.0 C5' 2:G727 4.8 52.0 1.0 N4 2:C542 4.9 39.8 1.0 C8 2:A726 5.0 51.9 1.0

Magnesium binding site 9 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1609 b:75.0 occ:1.00 OP1 2:G1477 1.8 49.4 1.0 O1P 2:6MZ1469 1.8 43.7 1.0 OP1 2:G1474 1.9 54.6 1.0 P 2:G1477 3.0 49.4 1.0 P 2:G1474 3.1 54.6 1.0 O3' 2:A1476 3.3 50.8 1.0 P 2:6MZ1469 3.3 43.7 1.0 OP2 2:G1474 3.5 54.6 1.0 O5' 2:G1477 3.7 49.4 1.0 O3' 2:A1468 4.0 47.9 1.0 O3' 2:G1473 4.2 47.0 1.0 O5' 2:G1474 4.2 54.6 1.0 C3' 2:G1473 4.2 47.0 1.0 O5' 2:6MZ1469 4.3 43.7 1.0 OP2 2:G1477 4.3 49.4 1.0 O2P 2:6MZ1469 4.3 43.7 1.0 C5' 2:G1474 4.5 54.6 1.0 O2' 2:A1476 4.7 50.8 1.0 C3' 2:A1476 4.7 50.8 1.0 C5' 2:G1477 4.7 49.4 1.0 C5' 2:6MZ1469 4.8 43.7 1.0 MG 2:MG1616 4.8 44.0 1.0 O2' 2:G1473 4.9 47.0 1.0 O2' 2:U1475 4.9 50.9 1.0

Magnesium binding site 10 out of 34 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1610 b:43.9 occ:1.00 OP2 2:C106 1.8 47.4 1.0 P 2:C106 2.5 47.4 1.0 OP1 2:C106 2.6 47.4 1.0 O5' 2:C106 3.3 47.4 1.0 O3' 2:A105 4.0 46.8 1.0 C5' 2:C106 4.4 47.4 1.0 O6 2:G108 4.7 42.3 1.0 OP1 2:C339 4.8 50.0 1.0 C4' 2:A105 4.8 46.8 1.0 C3' 2:A105 4.8 46.8 1.0 N7 2:G107 5.0 46.9 1.0 CE E:LYS4 5.0 43.3 1.0

P.D.Coureux, C.Lazennec-Schurdevin, S.Bourcier, Y.Mechulam, E.Schmitt. Cryo-Em Study of An Archaeal 30S Initiation Complex Gives Insights Into Evolution of Translation Initiation. Commun Biol V. 3 58 2020.
ISSN: ESSN 2399-3642
PubMed: 32029867
DOI: 10.1038/S42003-020-0780-0