Magnesium in PDB 8s8e: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.1)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.1):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.1) 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-3.1) (pdb code 8s8e). 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-3.1), PDB code: 8s8e:
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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:61.4 occ:1.00 OP1 2:G361 1.8 78.6 1.0 P 2:G361 3.0 78.6 1.0 OP2 2:G361 3.4 78.6 1.0 O2' 2:A359 3.7 56.8 1.0 O5' 2:G361 3.9 78.6 1.0 O3' 2:C360 4.2 74.9 1.0 OP2 2:G362 4.2 72.4 1.0 C5' 2:G361 4.4 78.6 1.0 OP1 2:A377 4.4 63.3 1.0 OP2 2:G376 4.5 71.5 1.0 N7 2:G376 4.7 71.5 1.0 C1' 2:A359 4.8 56.8 1.0 C2' 2:A359 4.8 56.8 1.0 C8 2:G376 4.9 71.5 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:90.1 occ:1.00 OP1 2:G402 1.8 55.7 1.0 P 2:G402 2.9 55.7 1.0 O3' 2:C401 3.0 49.3 1.0 O6 2:G95 3.8 55.8 1.0 OP2 2:A93 3.8 51.0 1.0 O5' 2:G402 3.9 55.7 1.0 OP2 2:G402 4.0 55.7 1.0 NH2 E:ARG3 4.0 52.8 1.0 O5' 2:C401 4.2 49.3 1.0 C3' 2:C401 4.2 49.3 1.0 N7 2:G402 4.4 55.7 1.0 C4' 2:C401 4.6 49.3 1.0 C8 2:G402 4.6 55.7 1.0 C5' 2:C401 4.6 49.3 1.0 C6 2:G95 5.0 55.8 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:67.2 occ:1.00 OP2 2:A555 2.1 56.4 1.0 OP2 2:A554 3.1 52.4 1.0 OP1 2:G551 3.2 49.7 1.0 P 2:A555 3.4 56.4 1.0 N7 2:A555 3.4 56.4 1.0 C8 2:A555 3.5 56.4 1.0 O5' 2:A555 3.6 56.4 1.0 C3' 2:A554 4.0 52.4 1.0 O3' 2:A554 4.2 52.4 1.0 O3' 2:C553 4.2 47.5 1.0 P 2:A554 4.2 52.4 1.0 C8 2:A554 4.3 52.4 1.0 C5 2:A555 4.5 56.4 1.0 P 2:G551 4.5 49.7 1.0 C2' 2:A554 4.5 52.4 1.0 OP1 2:A555 4.6 56.4 1.0 N9 2:A555 4.6 56.4 1.0 OP2 2:G551 4.8 49.7 1.0 O2' 2:C553 4.8 47.5 1.0 O5' 2:A554 4.9 52.4 1.0 OP2 2:G552 4.9 50.9 1.0 N7 2:A554 4.9 52.4 1.0 C5' 2:A555 5.0 56.4 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:49.2 occ:1.00 OP1 2:C360 1.9 74.9 1.0 OP1 2:A100 1.9 54.2 1.0 P 2:A100 2.2 54.2 1.0 OP2 2:A100 2.3 54.2 1.0 O3' 2:C99 2.8 63.3 1.0 P 2:C360 2.9 74.9 1.0 OP2 2:C360 3.1 74.9 1.0 C3' 2:C99 3.3 63.3 1.0 MG 2:MG1826 3.6 61.7 1.0 O5' 2:A100 3.7 54.2 1.0 O5' 2:C360 4.0 74.9 1.0 O3' 2:A359 4.0 56.8 1.0 O2' 2:C99 4.3 63.3 1.0 C2' 2:C99 4.3 63.3 1.0 C5' 2:A100 4.4 54.2 1.0 C4' 2:C99 4.5 63.3 1.0 C5' 2:C360 5.0 74.9 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:61.8 occ:1.00 OP2 2:A1024 1.9 90.1 1.0 OP1 2:A1024 2.1 90.1 1.0 P 2:A1024 2.2 90.1 1.0 O5' 2:A1024 3.2 90.1 1.0 O3' 2:U1023 3.6 100.8 1.0 C5' 2:A1024 4.1 90.1 1.0 OP2 2:A1025 4.3 71.7 1.0 C3' 2:U1023 4.5 100.8 1.0 OP1 2:G623 4.6 63.5 1.0 OP1 2:A1025 4.7 71.7 1.0 N6 2:A1026 4.8 84.0 1.0 OP1 2:C1127 4.8 63.9 1.0 C5' 2:U1023 5.0 100.8 1.0 N7 2:A1026 5.0 84.0 1.0 P 2:A1025 5.0 71.7 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:26.1 occ:1.00 OP2 2:C582 4.4 58.8 1.0 O6 2:G556 4.7 71.9 1.0 N7 2:A584 4.7 61.8 1.0 N6 2:A584 4.8 61.8 1.0 O6 2:G585 4.9 67.0 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:50.8 occ:1.00 OP2 2:C49 2.0 53.5 1.0 OP1 2:A424 3.2 55.7 1.0 P 2:C49 3.3 53.5 1.0 O5' 2:C49 3.9 53.5 1.0 OP1 2:C49 4.1 53.5 1.0 N7 2:A424 4.1 55.7 1.0 C8 2:A424 4.2 55.7 1.0 O3' 2:G48 4.5 53.5 1.0 C5 2:C49 4.5 53.5 1.0 P 2:A424 4.6 55.7 1.0 C3' 2:G48 4.8 53.5 1.0 C6 2:C49 4.8 53.5 1.0 O3' 2:C423 4.8 52.8 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:44.8 occ:1.00 OP2 2:A992 4.0 65.8 1.0 OP2 2:A1004 4.1 69.5 1.0 O4 2:U995 4.4 73.3 1.0 O3' 2:U1003 4.4 78.6 1.0 OP2 2:C1005 4.8 70.9 1.0 C5' 2:A1004 4.8 69.5 1.0 P 2:A1004 4.9 69.5 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:41.1 occ:1.00 OP1 2:U8 4.0 60.1 1.0 OP2 2:G10 4.1 50.4 1.0 OP2 2:U9 4.1 48.6 1.0 OP2 2:A11 4.1 50.1 1.0 OP1 2:A11 4.3 50.1 1.0 P 2:A11 4.6 50.1 1.0 C5 2:U9 4.8 48.6 1.0 OP2 3:U36 5.0 275.4 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:61.2 occ:1.00 OP2 2:A928 1.9 67.3 1.0 N3 2:C930 2.5 72.1 1.0 N6 2:A929 2.9 67.8 1.0 N7 2:A929 3.0 67.8 1.0 N4 2:C930 3.2 72.1 1.0 P 2:A928 3.2 67.3 1.0 C4 2:C930 3.3 72.1 1.0 C2 2:C930 3.5 72.1 1.0 C5 2:A929 3.6 67.8 1.0 O5' 2:A928 3.6 67.3 1.0 C6 2:A929 3.6 67.8 1.0 O2 2:C930 3.6 72.1 1.0 C8 2:A929 4.1 67.8 1.0 O3' 2:U927 4.2 75.0 1.0 OP1 2:A928 4.3 67.3 1.0 C5 2:C930 4.6 72.1 1.0 N7 2:A928 4.6 67.3 1.0 C8 2:A928 4.7 67.3 1.0 O4 2:U931 4.7 69.6 1.0 N1 2:C930 4.7 72.1 1.0 N1 2:A929 4.8 67.8 1.0 C4 2:A929 4.9 67.8 1.0 C5' 2:A928 5.0 67.3 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