Magnesium in PDB 8s8f: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.2)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.2):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.2) also contains other interesting chemical elements:

Zinc

(Zn)

4 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-3.2) (pdb code 8s8f). 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-3.2), PDB code: 8s8f:
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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:14.8 occ:1.00 OP1 2:G361 2.0 26.9 1.0 P 2:G361 3.3 26.9 1.0 OP2 2:G361 3.8 26.9 1.0 O5' 2:G361 4.2 26.9 1.0 OP2 2:G362 4.2 21.7 1.0 O2' 2:A359 4.3 30.6 1.0 OP2 2:G376 4.3 30.5 1.0 N7 2:G376 4.4 30.5 1.0 O3' 2:C360 4.4 23.7 1.0 OP1 2:A377 4.6 25.7 1.0 C5' 2:G361 4.6 26.9 1.0 C8 2:G376 4.7 30.5 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:67.1 occ:1.00 OP1 2:G402 2.1 27.9 1.0 O6 2:G95 3.5 48.4 1.0 P 2:G402 3.6 27.9 1.0 OP2 2:A93 3.7 35.6 1.0 O3' 2:C401 4.1 23.9 1.0 O5' 2:C401 4.2 23.9 1.0 O5' 2:G402 4.4 27.9 1.0 NH2 E:ARG3 4.5 56.1 1.0 OP2 2:G402 4.6 27.9 1.0 C6 2:G95 4.6 48.4 1.0 N7 2:G402 4.7 27.9 1.0 OP1 2:C401 4.8 23.9 1.0 C8 2:G402 4.9 27.9 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:54.0 occ:1.00 OP2 2:A555 2.0 43.0 1.0 OP2 2:A554 2.0 44.0 1.0 OP1 2:G551 3.3 33.1 1.0 P 2:A555 3.4 43.0 1.0 P 2:A554 3.4 44.0 1.0 O3' 2:C553 3.8 40.0 1.0 C3' 2:A554 4.0 44.0 1.0 N7 2:A555 4.0 43.0 1.0 O5' 2:A555 4.1 43.0 1.0 O3' 2:A554 4.1 44.0 1.0 C8 2:A555 4.2 43.0 1.0 O5' 2:A554 4.3 44.0 1.0 OP1 2:A554 4.5 44.0 1.0 OP1 2:A555 4.5 43.0 1.0 O2' 2:C553 4.5 40.0 1.0 P 2:G551 4.6 33.1 1.0 C3' 2:C553 4.7 40.0 1.0 C8 2:A554 4.8 44.0 1.0 C5' 2:A554 4.9 44.0 1.0 OP2 2:G552 4.9 33.0 1.0 C2' 2:A554 4.9 44.0 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:31.4 occ:1.00 OP1 2:A100 2.3 23.4 1.0 OP1 2:C360 3.0 23.7 1.0 P 2:A100 3.7 23.4 1.0 C3' 2:C99 4.3 37.9 1.0 OP2 2:A100 4.3 23.4 1.0 P 2:C360 4.4 23.7 1.0 O3' 2:C99 4.4 37.9 1.0 O4' 2:A377 4.6 25.7 1.0 O2' 2:A43 4.6 26.9 1.0 C4' 2:U44 4.6 28.0 1.0 O5' 2:A100 4.7 23.4 1.0 OP2 2:C360 4.9 23.7 1.0 O4' 2:U44 4.9 28.0 1.0 C5' 2:U44 5.0 28.0 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:25.3 occ:1.00 OP2 2:A1024 2.2 33.9 1.0 OP1 2:G623 3.3 42.2 1.0 P 2:A1024 3.5 33.9 1.0 OP1 2:A1024 3.8 33.9 1.0 C5' 2:A1024 4.5 33.9 1.0 P 2:G623 4.5 42.2 1.0 O3' 2:U1023 4.5 39.9 1.0 O5' 2:A1024 4.5 33.9 1.0 OP2 2:A1025 4.7 33.7 1.0 OP2 2:G623 4.8 42.2 1.0 N7 2:A1026 4.9 39.8 1.0 N6 2:A1026 4.9 39.8 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:67.1 occ:1.00 OP2 2:C582 4.3 46.3 1.0 O6 2:G556 4.4 49.0 1.0 N7 2:A584 4.6 37.9 1.0 N7 2:A549 4.8 40.4 1.0 N6 2:A584 4.8 37.9 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:67.1 occ:1.00 OP2 2:C49 2.2 31.7 1.0 OP1 2:A424 3.5 36.6 1.0 P 2:C49 3.6 31.7 1.0 N7 2:A424 4.1 36.6 1.0 O5' 2:C49 4.3 31.7 1.0 OP1 2:C49 4.4 31.7 1.0 C8 2:A424 4.5 36.6 1.0 C5 2:C49 4.6 31.7 1.0 O3' 2:G48 4.7 38.1 1.0 C3' 2:G48 4.8 38.1 1.0 P 2:A424 4.9 36.6 1.0 C6 2:C49 5.0 31.7 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:34.3 occ:1.00 O4 2:U995 4.3 62.8 1.0 O3' 2:U1003 4.5 90.7 1.0 OP2 2:C1005 4.7 54.2 1.0 OP2 2:A1004 4.8 67.8 1.0 C5' 2:A1004 4.8 67.8 1.0 N7 2:G993 4.9 53.7 1.0 OP2 2:A992 4.9 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:12.6 occ:1.00 OP1 2:A11 3.7 26.0 1.0 OP2 2:A11 4.0 26.0 1.0 OP1 2:U8 4.1 55.1 1.0 P 2:A11 4.3 26.0 1.0 OP2 2:G10 4.6 28.5 1.0 OP2 2:U9 4.8 35.3 1.0 C5 2:U9 5.0 35.3 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:30.2 occ:1.00 OP2 2:A928 2.0 43.5 1.0 N4 2:C930 2.4 56.5 1.0 N3 2:C930 2.8 56.5 1.0 O4 2:U931 2.9 55.9 1.0 C4 2:C930 3.0 56.5 1.0 P 2:A928 3.4 43.5 1.0 C4 2:U931 3.9 55.9 1.0 C2 2:C930 4.0 56.5 1.0 O3' 2:U927 4.1 55.0 1.0 N7 2:A929 4.2 47.5 1.0 N6 2:A929 4.2 47.5 1.0 OP1 2:A928 4.2 43.5 1.0 N3 2:U931 4.3 55.9 1.0 C5 2:C930 4.4 56.5 1.0 O2 2:C930 4.5 56.5 1.0 O5' 2:A928 4.5 43.5 1.0 C5' 2:A928 4.7 43.5 1.0 C5 2:A929 4.9 47.5 1.0 C6 2:A929 5.0 47.5 1.0 O2' 2:A943 5.0 67.1 1.0 C5 2:U931 5.0 55.9 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