Magnesium in PDB 8s8i: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1) 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 - 117;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1) (pdb code 8s8i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1), PDB code: 8s8i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:127.8 occ:1.00 OP1 2:G361 1.9 94.6 1.0 P 2:G361 3.2 94.6 1.0 OP2 2:G361 3.8 94.6 1.0 O2' 2:A359 3.9 86.0 1.0 O5' 2:G361 4.1 94.6 1.0 OP2 2:G362 4.2 78.5 1.0 O3' 2:C360 4.3 99.6 1.0 C5' 2:G361 4.5 94.6 1.0 OP2 2:G376 4.5 73.6 1.0 OP1 2:A377 4.7 76.7 1.0 C1' 2:A359 4.8 86.0 1.0 O4' 2:A359 4.8 86.0 1.0 C2' 2:A359 5.0 86.0 1.0

Magnesium binding site 2 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:127.8 occ:1.00 OP1 2:G402 1.9 88.1 1.0 O6 2:G95 3.2 85.9 1.0 P 2:G402 3.3 88.1 1.0 OP2 2:A93 3.9 93.4 1.0 OP2 2:G402 4.0 88.1 1.0 O5' 2:G402 4.1 88.1 1.0 C6 2:G95 4.2 85.9 1.0 O3' 2:C401 4.3 89.7 1.0 N7 2:G402 4.4 88.1 1.0 O5' 2:C401 4.5 89.7 1.0 C8 2:G402 4.6 88.1 1.0 NH2 E:ARG3 4.8 89.9 1.0 N1 2:G95 4.8 85.9 1.0

Magnesium binding site 3 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:97.1 occ:1.00 OP2 2:A555 1.8 104.3 1.0 OP2 2:A554 1.9 99.8 1.0 P 2:A555 2.7 104.3 1.0 OP1 2:A555 3.1 104.3 1.0 P 2:A554 3.3 99.8 1.0 O3' 2:A554 3.4 99.8 1.0 O3' 2:C553 3.7 97.3 1.0 C3' 2:A554 3.8 99.8 1.0 OP2 2:G552 3.9 90.8 1.0 O5' 2:A555 4.1 104.3 1.0 OP1 2:G551 4.2 95.3 1.0 O5' 2:A554 4.2 99.8 1.0 OP1 2:A554 4.2 99.8 1.0 C5' 2:A554 4.7 99.8 1.0 C4' 2:A554 4.8 99.8 1.0 C3' 2:C553 4.8 97.3 1.0 C2' 2:A554 4.9 99.8 1.0 O2' 2:C553 5.0 97.3 1.0

Magnesium binding site 4 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:89.7 occ:1.00 OP1 2:C360 1.9 99.6 1.0 OP1 2:A100 1.9 90.8 1.0 OP2 2:A100 2.0 90.8 1.0 P 2:A100 2.2 90.8 1.0 P 2:C360 2.7 99.6 1.0 OP2 2:C360 2.8 99.6 1.0 MG 2:MG1826 3.1 100.6 1.0 O3' 2:C99 3.2 91.6 1.0 O5' 2:A100 3.6 90.8 1.0 O3' 2:A359 3.8 86.0 1.0 O5' 2:C360 3.9 99.6 1.0 C3' 2:C99 3.9 91.6 1.0 C5' 2:A100 4.0 90.8 1.0 OP2 2:U101 4.5 95.9 1.0 O2' 2:C99 4.7 91.6 1.0 C3' 2:A359 4.8 86.0 1.0 C2' 2:C99 4.9 91.6 1.0 C5' 2:C360 4.9 99.6 1.0

Magnesium binding site 5 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:78.4 occ:1.00 OP1 2:A1024 2.0 92.2 1.0 OP2 2:A1024 2.1 92.2 1.0 P 2:A1024 2.3 92.2 1.0 O5' 2:A1024 3.2 92.2 1.0 O3' 2:U1023 3.7 94.7 1.0 OP1 2:G623 3.9 87.4 1.0 OP1 2:A1025 3.9 98.9 1.0 C5' 2:A1024 4.2 92.2 1.0 OP2 2:A1025 4.5 98.9 1.0 C3' 2:U1023 4.6 94.7 1.0 P 2:A1025 4.8 98.9 1.0 N7 2:A1026 5.0 93.8 1.0

Magnesium binding site 6 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:127.8 occ:1.00 O6 2:G556 4.2 118.1 1.0 N7 2:A549 4.4 99.1 1.0 OP2 2:C582 4.4 100.4 1.0 C5 2:A549 4.6 99.1 1.0 N6 2:A549 4.7 99.1 1.0 O6 2:G585 4.7 100.7 1.0 C6 2:A549 4.8 99.1 1.0 C8 2:A549 5.0 99.1 1.0

Magnesium binding site 7 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:127.8 occ:1.00 OP2 2:C49 2.1 79.0 1.0 OP1 2:A424 3.3 88.9 1.0 P 2:C49 3.4 79.0 1.0 OP1 2:C49 3.9 79.0 1.0 N7 2:A424 4.0 88.9 1.0 O5' 2:C49 4.3 79.0 1.0 C8 2:A424 4.3 88.9 1.0 O3' 2:G48 4.5 85.0 1.0 P 2:A424 4.6 88.9 1.0 O3' 2:C423 4.8 81.5 1.0 C3' 2:G48 4.8 85.0 1.0 C5 2:C49 4.9 79.0 1.0 C4' 2:G387 5.0 95.9 1.0 C5' 2:G387 5.0 95.9 1.0

Magnesium binding site 8 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:88.0 occ:1.00 OP2 2:A1004 3.4 127.2 1.0 O3' 2:U1003 3.4 151.8 1.0 P 2:A1004 4.1 127.2 1.0 C5' 2:A1004 4.2 127.2 1.0 O2' 2:U1003 4.3 151.8 1.0 O4 2:U995 4.5 118.0 1.0 OP1 2:A992 4.5 110.1 1.0 C3' 2:U1003 4.6 151.8 1.0 O5' 2:A1004 4.7 127.2 1.0 C4' 2:U1003 4.9 151.8 1.0

Magnesium binding site 9 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:66.0 occ:1.00 OP2 2:U9 3.7 102.2 1.0 OP1 2:U8 4.4 111.6 1.0 OP2 2:A11 4.5 96.3 1.0 OP2 2:G10 4.6 95.1 1.0 OP1 2:A11 4.6 96.3 1.0 C5 2:U9 4.7 102.2 1.0 P 2:A11 5.0 96.3 1.0 OP2 3:U36 5.0 469.6 1.0

Magnesium binding site 10 out of 117 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:98.2 occ:1.00 OP2 2:A928 2.0 103.9 1.0 N3 2:C930 2.3 99.0 1.0 N4 2:C930 2.6 99.0 1.0 C4 2:C930 2.8 99.0 1.0 P 2:A928 2.9 103.9 1.0 O5' 2:A928 3.3 103.9 1.0 OP1 2:A928 3.4 103.9 1.0 C2 2:C930 3.4 99.0 1.0 O2 2:C930 3.7 99.0 1.0 N7 2:A929 3.8 99.3 1.0 O4 2:U931 3.8 94.0 1.0 N6 2:A929 4.1 99.3 1.0 C5 2:C930 4.2 99.0 1.0 O3' 2:U927 4.4 117.0 1.0 C4 2:U931 4.4 94.0 1.0 N3 2:U931 4.6 94.0 1.0 C5 2:A929 4.6 99.3 1.0 N1 2:C930 4.6 99.0 1.0 C5' 2:A928 4.6 103.9 1.0 C8 2:A929 4.7 99.3 1.0 C6 2:A929 4.8 99.3 1.0 C6 2:C930 4.9 99.0 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