Magnesium in PDB 8s8g: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.1)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.1):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.1) 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-2.1) (pdb code 8s8g). 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-2.1), PDB code: 8s8g:
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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:33.1 occ:1.00 OP1 2:G361 1.9 51.0 1.0 OP2 2:G361 2.2 51.0 1.0 P 2:G361 2.3 51.0 1.0 O5' 2:G361 3.0 51.0 1.0 OP1 2:A377 3.2 41.6 1.0 OP2 2:G362 3.4 41.4 1.0 O3' 2:C360 3.8 35.0 1.0 C5' 2:G361 4.0 51.0 1.0 O2' 2:A359 4.1 42.6 1.0 P 2:A377 4.5 41.6 1.0 P 2:G362 4.7 41.4 1.0 OP2 2:A377 4.7 41.6 1.0 C3' 2:C360 4.8 35.0 1.0 C3' 2:G361 4.8 51.0 1.0 N7 2:G376 4.9 39.0 1.0 O3' 2:G361 4.9 51.0 1.0 C8 2:G376 5.0 39.0 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:72.3 occ:1.00 OP1 2:G402 1.9 50.3 1.0 P 2:G402 3.3 50.3 1.0 O6 2:G95 3.4 46.1 1.0 OP2 2:A93 3.8 44.2 1.0 O3' 2:C401 3.9 48.5 1.0 N7 2:G402 4.0 50.3 1.0 O5' 2:G402 4.1 50.3 1.0 C8 2:G402 4.3 50.3 1.0 OP2 2:G402 4.4 50.3 1.0 O5' 2:C401 4.5 48.5 1.0 C6 2:G95 4.5 46.1 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:43.2 occ:1.00 OP2 2:A554 1.9 48.8 1.0 OP2 2:A555 2.0 48.4 1.0 P 2:A554 3.3 48.8 1.0 P 2:A555 3.4 48.4 1.0 O3' 2:C553 3.8 54.3 1.0 OP2 2:G552 3.9 50.7 1.0 O3' 2:A554 4.0 48.8 1.0 OP1 2:A555 4.0 48.4 1.0 OP1 2:G551 4.2 50.8 1.0 OP1 2:A554 4.2 48.8 1.0 C3' 2:A554 4.2 48.8 1.0 O5' 2:A554 4.4 48.8 1.0 O5' 2:A555 4.5 48.4 1.0 C5' 2:A554 4.8 48.8 1.0 OP1 2:G552 4.9 50.7 1.0 P 2:G552 4.9 50.7 1.0 C3' 2:C553 4.9 54.3 1.0 O2' 2:C553 5.0 54.3 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:35.4 occ:1.00 OP1 2:C360 1.9 35.0 1.0 OP1 2:A100 2.0 39.5 1.0 OP2 2:A100 2.0 39.5 1.0 P 2:A100 2.2 39.5 1.0 P 2:C360 2.9 35.0 1.0 OP2 2:C360 3.1 35.0 1.0 MG 2:MG1826 3.1 34.5 1.0 O3' 2:C99 3.2 42.3 1.0 O5' 2:A100 3.6 39.5 1.0 O5' 2:C360 3.9 35.0 1.0 C3' 2:C99 3.9 42.3 1.0 C5' 2:A100 4.1 39.5 1.0 O3' 2:A359 4.1 42.6 1.0 OP2 2:U101 4.6 41.1 1.0 C5' 2:A358 4.9 42.0 1.0 O2' 2:C99 4.9 42.3 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:43.6 occ:1.00 OP2 2:A1024 2.0 72.3 1.0 OP1 2:A1024 2.1 72.3 1.0 P 2:A1024 2.3 72.3 1.0 OP1 2:A1025 2.8 48.4 1.0 C5' 2:A1024 3.0 72.3 1.0 O5' 2:A1024 3.0 72.3 1.0 O3' 2:U1023 3.8 53.9 1.0 P 2:A1025 4.1 48.4 1.0 C4' 2:A1024 4.1 72.3 1.0 OP2 2:A1025 4.7 48.4 1.0 O3' 2:A1024 4.8 72.3 1.0 C3' 2:U1023 4.8 53.9 1.0 C3' 2:A1024 4.9 72.3 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:72.3 occ:1.00 OP2 2:C582 3.7 51.4 1.0 O6 2:G556 4.4 56.9 1.0 N6 2:A584 4.7 57.0 1.0 O6 2:G585 4.9 57.5 1.0 P 2:C582 5.0 51.4 1.0 N7 2:A549 5.0 48.6 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:72.3 occ:1.00 OP2 2:C49 1.9 43.5 1.0 P 2:C49 3.3 43.5 1.0 N7 2:A424 3.4 53.4 1.0 OP1 2:A424 3.4 53.4 1.0 C8 2:A424 3.8 53.4 1.0 OP1 2:C49 3.9 43.5 1.0 O5' 2:C49 4.2 43.5 1.0 O3' 2:G48 4.3 40.6 1.0 O3' 2:C423 4.5 45.3 1.0 C4' 2:G387 4.5 51.4 1.0 P 2:A424 4.6 53.4 1.0 C5' 2:G387 4.6 51.4 1.0 C3' 2:G48 4.6 40.6 1.0 O4' 2:G387 4.7 51.4 1.0 C5 2:A424 4.7 53.4 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:75.5 occ:1.00 OP2 2:A992 3.7 52.3 1.0 N7 2:G993 4.1 50.4 1.0 O3' 2:U1003 4.2 75.7 1.0 OP2 2:A1004 4.2 63.5 1.0 C8 2:G993 4.7 50.4 1.0 N7 2:A994 4.8 60.8 1.0 P 2:A1004 4.9 63.5 1.0 N6 2:A994 4.9 60.8 1.0 C5 2:G993 5.0 50.4 1.0 O4 2:U995 5.0 68.5 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:72.3 occ:1.00 OP1 2:U8 4.4 54.9 1.0 OP2 2:A11 4.5 49.1 1.0 OP2 2:G10 4.5 46.1 1.0 OP1 2:A11 4.5 49.1 1.0 C5 2:U9 4.6 53.4 1.0 O3' 2:G10 4.7 46.1 1.0 P 2:A11 4.7 49.1 1.0 OP2 2:U9 4.9 53.4 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:55.6 occ:1.00 N4 2:C930 2.0 57.0 1.0 OP2 2:A928 2.1 58.0 1.0 OP1 2:A928 2.4 58.0 1.0 P 2:A928 2.4 58.0 1.0 N3 2:C930 2.7 57.0 1.0 C4 2:C930 2.7 57.0 1.0 O5' 2:A928 2.9 58.0 1.0 O4 2:U931 3.5 50.5 1.0 O3' 2:U927 3.9 59.7 1.0 C5' 2:A928 3.9 58.0 1.0 C2 2:C930 4.0 57.0 1.0 C4 2:U931 4.1 50.5 1.0 C5 2:C930 4.1 57.0 1.0 N7 2:A929 4.1 59.0 1.0 N3 2:U931 4.2 50.5 1.0 O2 2:C930 4.5 57.0 1.0 O2' 2:U927 4.6 59.7 1.0 O2' 2:A943 4.6 48.8 1.0 C3' 2:U927 4.7 59.7 1.0 C8 2:A929 4.9 59.0 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