Magnesium in PDB 8s8h: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) 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; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 116;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) (pdb code 8s8h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 116 binding sites of Magnesium where determined in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2), PDB code: 8s8h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:45.0 occ:1.00 OP1 2:G361 2.9 52.3 1.0 OP2 2:G376 3.4 71.4 1.0 N7 2:G376 4.0 71.4 1.0 P 2:G361 4.2 52.3 1.0 C8 2:G376 4.3 71.4 1.0 OP2 2:G361 4.5 52.3 1.0 P 2:G376 4.6 71.4 1.0 O5' 2:G376 4.6 71.4 1.0 OP2 2:G362 4.7 71.4 1.0 O2' 2:A359 4.9 45.5 1.0

Magnesium binding site 2 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:35.8 occ:1.00 OP1 2:G402 1.8 53.0 1.0 P 2:G402 2.9 53.0 1.0 O3' 2:C401 3.1 44.4 1.0 O5' 2:G402 3.5 53.0 1.0 N7 2:G402 3.8 53.0 1.0 OP2 2:A93 3.8 40.3 1.0 C8 2:G402 3.9 53.0 1.0 OP2 2:G402 4.2 53.0 1.0 O6 2:G95 4.4 40.6 1.0 C3' 2:C401 4.4 44.4 1.0 O5' 2:C401 4.6 44.4 1.0 C5' 2:G402 4.9 53.0 1.0 C4' 2:C401 5.0 44.4 1.0

Magnesium binding site 3 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:71.4 occ:1.00 OP2 2:A555 1.9 47.6 1.0 OP2 2:A554 1.9 47.5 1.0 P 2:A555 3.1 47.6 1.0 P 2:A554 3.3 47.5 1.0 OP1 2:A555 3.6 47.6 1.0 O3' 2:A554 3.8 47.5 1.0 O3' 2:C553 3.9 46.3 1.0 C3' 2:A554 4.2 47.5 1.0 OP2 2:G552 4.2 48.8 1.0 OP1 2:A554 4.2 47.5 1.0 O5' 2:A555 4.4 47.6 1.0 O5' 2:A554 4.4 47.5 1.0 OP1 2:G551 4.4 44.6 1.0 C5' 2:A554 4.8 47.5 1.0

Magnesium binding site 4 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:32.8 occ:1.00 OP1 2:A100 2.0 47.5 1.0 OP1 2:C360 2.7 51.2 1.0 P 2:A100 3.2 47.5 1.0 OP2 2:A100 3.8 47.5 1.0 C3' 2:C99 3.8 46.8 1.0 O3' 2:C99 3.9 46.8 1.0 P 2:C360 4.1 51.2 1.0 O5' 2:A100 4.4 47.5 1.0 MG 2:MG1826 4.7 49.2 1.0 OP2 2:C360 4.7 51.2 1.0 O4' 2:A377 4.8 53.4 1.0 C4' 2:C99 4.9 46.8 1.0 C2' 2:C99 4.9 46.8 1.0 O2' 2:A43 4.9 46.5 1.0 O3' 2:A359 4.9 45.5 1.0 C5' 2:C99 5.0 46.8 1.0

Magnesium binding site 5 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:71.4 occ:1.00 OP2 2:A1024 1.9 53.4 1.0 P 2:A1024 2.9 53.4 1.0 OP2 2:G623 3.2 51.3 1.0 OP1 2:A1024 3.2 53.4 1.0 OP1 2:G623 3.9 51.3 1.0 P 2:G623 4.0 51.3 1.0 O5' 2:A1024 4.0 53.4 1.0 O3' 2:U1023 4.1 58.7 1.0 OP2 2:A1025 4.4 41.7 1.0 C5' 2:A1024 4.5 53.4 1.0 C3' 2:U1023 4.7 58.7 1.0 N7 2:A1026 4.7 53.8 1.0 C5' 2:U1023 4.9 58.7 1.0 N6 2:A1026 5.0 53.8 1.0

Magnesium binding site 6 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:71.4 occ:1.00 OP2 2:C582 3.9 49.5 1.0 N6 2:A584 4.3 58.5 1.0 N7 2:A584 4.4 58.5 1.0 O6 2:G585 4.9 58.7 1.0

Magnesium binding site 7 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:33.2 occ:1.00 OP2 2:C49 2.0 46.3 1.0 P 2:C49 3.4 46.3 1.0 OP1 2:A424 3.5 40.7 1.0 N7 2:A424 3.9 40.7 1.0 O5' 2:C49 4.1 46.3 1.0 OP1 2:C49 4.1 46.3 1.0 C8 2:A424 4.3 40.7 1.0 O3' 2:G48 4.4 49.2 1.0 C5' 2:G387 4.5 48.5 1.0 C3' 2:G48 4.6 49.2 1.0 C5 2:C49 4.7 46.3 1.0 C4' 2:G387 4.7 48.5 1.0 P 2:A424 4.8 40.7 1.0 C6 2:C49 4.9 46.3 1.0 O4' 2:G387 5.0 48.5 1.0

Magnesium binding site 8 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:41.7 occ:1.00 OP2 2:A992 3.6 51.2 1.0 N7 2:G993 3.8 55.3 1.0 OP2 2:A1004 4.2 54.9 1.0 C5' 2:A992 4.4 51.2 1.0 C8 2:G993 4.5 55.3 1.0 O3' 2:U1003 4.7 66.1 1.0 C5 2:G993 4.7 55.3 1.0 P 2:A992 4.8 51.2 1.0 O6 2:G993 4.8 55.3 1.0 OP2 2:G993 4.8 55.3 1.0 O4 2:U995 4.8 65.4 1.0 N6 2:A994 4.8 59.8 1.0 O5' 2:A992 5.0 51.2 1.0

Magnesium binding site 9 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:71.4 occ:1.00 OP2 2:U9 3.5 44.4 1.0 OP2 2:G10 4.1 39.0 1.0 OP1 2:U8 4.3 57.8 1.0 OP2 2:A11 4.3 52.2 1.0 P 2:U9 4.8 44.4 1.0 O5' 2:U9 4.9 44.4 1.0 OP1 2:A11 4.9 52.2 1.0

Magnesium binding site 10 out of 116 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)


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 Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:34.5 occ:1.00 OP2 2:A928 2.0 53.1 1.0 P 2:A928 3.4 53.1 1.0 N4 2:C930 3.4 47.0 1.0 N3 2:C930 3.6 47.0 1.0 C4 2:C930 4.0 47.0 1.0 N6 2:A929 4.2 53.9 1.0 O3' 2:U927 4.2 57.2 1.0 OP1 2:A928 4.3 53.1 1.0 O5' 2:A928 4.3 53.1 1.0 C4' 2:U944 4.4 58.0 1.0 N7 2:A929 4.5 53.9 1.0 C5' 2:U944 4.5 58.0 1.0 O2' 2:U927 4.5 57.2 1.0 C2 2:C930 4.7 47.0 1.0 O4 2:U931 4.7 43.7 1.0 O4' 2:U944 4.9 58.0 1.0 O2 2:C930 5.0 47.0 1.0

L.Villamayor-Belinchon, P.Sharma, Y.Gordiyenko, J.L.Llacer, T.Hussain. Structural Basis of Auc Codon Discrimination During Translation Initiation in Yeast. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39193907
DOI: 10.1093/NAR/GKAE737