Magnesium in PDB 8s8d: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-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) (pdb code 8s8d). 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), PDB code: 8s8d:
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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:55.5 occ:1.00 OP1 2:G361 2.1 62.9 1.0 OP2 2:G361 2.2 62.9 1.0 P 2:G361 2.4 62.9 1.0 OP1 2:A377 3.2 58.8 1.0 O5' 2:G361 3.5 62.9 1.0 OP2 2:G362 3.6 62.9 1.0 O3' 2:C360 3.8 59.8 1.0 O2' 2:A359 4.0 58.4 1.0 C5' 2:G361 4.4 62.9 1.0 P 2:A377 4.5 58.8 1.0 N7 2:G376 4.7 62.9 1.0 C3' 2:C360 4.7 59.8 1.0 C8 2:G376 4.8 62.9 1.0 C3' 2:G376 4.9 62.9 1.0 OP2 2:A377 4.9 58.8 1.0 P 2:G362 4.9 62.9 1.0 OP2 2:G376 5.0 62.9 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:48.7 occ:1.00 OP1 2:G402 2.2 56.1 1.0 O6 2:G95 3.1 62.9 1.0 P 2:G402 3.7 56.1 1.0 OP2 2:A93 3.7 49.8 1.0 NH2 E:ARG3 4.1 47.8 1.0 C6 2:G95 4.3 62.9 1.0 O3' 2:C401 4.4 62.9 1.0 O5' 2:C401 4.4 62.9 1.0 O5' 2:G402 4.5 56.1 1.0 OP2 2:G402 4.5 56.1 1.0 N7 2:G402 4.7 56.1 1.0 N6 2:A386 4.8 62.9 1.0 O6 2:G96 4.9 62.9 1.0 C8 2:G402 5.0 56.1 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:40.4 occ:1.00 OP2 2:A555 2.0 55.7 1.0 OP2 2:A554 2.1 62.9 1.0 OP1 2:G551 3.4 56.4 1.0 P 2:A555 3.5 55.7 1.0 P 2:A554 3.5 62.9 1.0 O3' 2:C553 3.9 62.9 1.0 N7 2:A555 4.1 55.7 1.0 C3' 2:A554 4.1 62.9 1.0 OP2 2:G552 4.1 57.5 1.0 O3' 2:A554 4.3 62.9 1.0 O5' 2:A555 4.3 55.7 1.0 C8 2:A555 4.3 55.7 1.0 OP1 2:A555 4.4 55.7 1.0 O5' 2:A554 4.4 62.9 1.0 OP1 2:A554 4.6 62.9 1.0 P 2:G551 4.6 56.4 1.0 O2' 2:C553 4.7 62.9 1.0 C5' 2:A554 4.8 62.9 1.0 C3' 2:C553 4.9 62.9 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:42.8 occ:1.00 OP1 2:A100 2.0 62.9 1.0 OP1 2:C360 3.0 59.8 1.0 P 2:A100 3.2 62.9 1.0 C3' 2:C99 3.7 62.9 1.0 OP2 2:A100 3.7 62.9 1.0 O3' 2:C99 3.8 62.9 1.0 P 2:C360 4.1 59.8 1.0 OP2 2:C360 4.3 59.8 1.0 O5' 2:A100 4.5 62.9 1.0 C4' 2:C99 4.6 62.9 1.0 C5' 2:C99 4.7 62.9 1.0 O2' 2:A43 4.7 49.8 1.0 C2' 2:C99 4.9 62.9 1.0 O4' 2:A377 4.9 58.8 1.0 OP2 2:U45 4.9 49.5 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:46.6 occ:1.00 OP2 2:A1024 2.1 62.9 1.0 P 2:A1024 3.0 62.9 1.0 OP1 2:A1024 3.2 62.9 1.0 OP1 2:G623 4.0 62.9 1.0 O5' 2:A1024 4.1 62.9 1.0 C5' 2:A1024 4.1 62.9 1.0 O3' 2:U1023 4.3 62.9 1.0 OP1 2:A1025 4.5 62.9 1.0 OP2 2:A1025 4.6 62.9 1.0 N7 2:A1026 4.8 62.9 1.0 OP2 2:G623 5.0 62.9 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:36.2 occ:1.00 OP2 2:C582 3.8 52.3 1.0 O6 2:G556 4.6 56.4 1.0 N6 2:A584 4.8 52.6 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:38.2 occ:1.00 OP2 2:C49 2.2 47.0 1.0 P 2:C49 3.6 47.0 1.0 N7 2:A424 3.7 62.9 1.0 OP1 2:A424 3.7 62.9 1.0 O3' 2:C423 4.0 62.9 1.0 C8 2:A424 4.1 62.9 1.0 OP1 2:C49 4.3 47.0 1.0 O5' 2:C49 4.4 47.0 1.0 C5' 2:G387 4.4 58.2 1.0 C4' 2:G387 4.5 58.2 1.0 P 2:A424 4.5 62.9 1.0 O3' 2:G48 4.7 49.5 1.0 O4' 2:G387 4.8 58.2 1.0 C5 2:C49 4.8 47.0 1.0 C3' 2:G48 4.8 49.5 1.0 C5 2:A424 4.8 62.9 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:48.7 occ:1.00 O4 2:U995 4.0 61.8 1.0 O3' 2:U1003 4.1 89.7 1.0 OP2 2:A1004 4.2 68.8 1.0 OP2 2:C1005 4.7 64.1 1.0 C5' 2:A1004 4.8 68.8 1.0 P 2:A1004 4.8 68.8 1.0 OP2 2:A992 4.9 50.7 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:32.1 occ:1.00 OP1 2:U8 3.7 62.9 1.0 OP2 2:G10 4.0 62.9 1.0 OP2 2:A11 4.0 62.9 1.0 OP2 2:U9 4.1 62.9 1.0 OP1 2:A11 4.1 62.9 1.0 C5 2:U9 4.4 62.9 1.0 P 2:A11 4.6 62.9 1.0 C6 2:U9 4.7 62.9 1.0 O5' 2:U8 4.9 62.9 1.0 P 2:U8 5.0 62.9 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:41.1 occ:1.00 OP2 2:A928 2.1 62.9 1.0 P 2:A928 3.3 62.9 1.0 O3' 2:U927 3.5 62.9 1.0 N4 2:C930 3.7 62.9 1.0 O2' 2:U927 3.8 62.9 1.0 O5' 2:A928 3.9 62.9 1.0 N3 2:C930 4.0 62.9 1.0 N6 2:A929 4.1 58.7 1.0 N7 2:A929 4.4 58.7 1.0 C4 2:C930 4.4 62.9 1.0 C4' 2:U944 4.4 51.7 1.0 C5' 2:U944 4.5 51.7 1.0 OP1 2:A928 4.6 62.9 1.0 C3' 2:U927 4.6 62.9 1.0 O4' 2:U944 4.6 51.7 1.0 C2' 2:U927 4.7 62.9 1.0 C8 2:A928 4.7 62.9 1.0 N7 2:A928 4.8 62.9 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