Magnesium in PDB 8s8j: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5) 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 - 115;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5) (pdb code 8s8j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 115 binding sites of Magnesium where determined in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5), PDB code: 8s8j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:55.7 occ:1.00 OP1 2:G361 2.0 53.0 1.0 O2' 2:A359 3.4 57.3 1.0 P 2:G361 3.4 53.0 1.0 C1' 2:A359 4.0 57.3 1.0 OP2 2:G361 4.1 53.0 1.0 O4' 2:A359 4.1 57.3 1.0 O3' 2:C360 4.3 54.2 1.0 C2' 2:A359 4.3 57.3 1.0 O5' 2:G361 4.4 53.0 1.0 C5' 2:G361 4.6 53.0 1.0 C4' 2:A359 4.6 57.3 1.0 OP2 2:G376 4.7 54.4 1.0 OP2 2:G362 4.9 52.9 1.0

Magnesium binding site 2 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:55.6 occ:1.00 O3' 2:C401 2.0 65.9 1.0 OP1 2:G402 2.0 67.4 1.0 P 2:G402 2.3 67.4 1.0 O5' 2:G402 2.9 67.4 1.0 C3' 2:C401 3.4 65.9 1.0 OP2 2:G402 3.8 67.4 1.0 C8 2:G402 3.9 67.4 1.0 C4' 2:C401 3.9 65.9 1.0 O2' 2:C401 4.0 65.9 1.0 O5' 2:C401 4.1 65.9 1.0 N7 2:G402 4.2 67.4 1.0 C2' 2:C401 4.3 65.9 1.0 C5' 2:G402 4.3 67.4 1.0 C5' 2:C401 4.4 65.9 1.0 OP2 2:A93 4.7 68.4 1.0

Magnesium binding site 3 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:77.7 occ:1.00 OP2 2:A554 2.0 72.8 1.0 P 2:A554 2.2 72.8 1.0 C8 2:A554 2.2 72.8 1.0 O3' 2:C553 2.2 68.8 1.0 O5' 2:A554 2.3 72.8 1.0 C3' 2:A554 2.3 72.8 1.0 C4' 2:A554 2.9 72.8 1.0 C5' 2:A554 3.0 72.8 1.0 N9 2:A554 3.0 72.8 1.0 C2' 2:A554 3.0 72.8 1.0 OP2 2:A555 3.0 73.6 1.0 O4' 2:A554 3.2 72.8 1.0 C1' 2:A554 3.2 72.8 1.0 N7 2:A554 3.3 72.8 1.0 O3' 2:A554 3.3 72.8 1.0 C3' 2:C553 3.6 68.8 1.0 OP1 2:A554 3.7 72.8 1.0 P 2:A555 3.8 73.6 1.0 O2' 2:C553 4.0 68.8 1.0 C4 2:A554 4.2 72.8 1.0 C2' 2:C553 4.3 68.8 1.0 C5 2:A554 4.3 72.8 1.0 O2' 2:A554 4.3 72.8 1.0 C4' 2:C553 4.5 68.8 1.0 C1' 2:C553 4.6 68.8 1.0 N7 2:A555 4.6 73.6 1.0 O5' 2:A555 4.7 73.6 1.0 O4' 2:C553 4.9 68.8 1.0 C8 2:A555 4.9 73.6 1.0 C5 2:A555 4.9 73.6 1.0 OP1 2:A555 5.0 73.6 1.0

Magnesium binding site 4 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:56.0 occ:1.00 OP1 2:C360 1.9 54.2 1.0 OP2 2:A100 2.0 54.9 1.0 O3' 2:C99 2.1 56.3 1.0 P 2:C360 2.2 54.2 1.0 P 2:A100 2.2 54.9 1.0 O5' 2:C360 2.3 54.2 1.0 OP2 2:C360 2.6 54.2 1.0 OP1 2:A100 2.7 54.9 1.0 O2' 2:C99 2.7 56.3 1.0 C3' 2:C99 2.9 56.3 1.0 MG 2:MG1825 3.1 60.1 1.0 C2' 2:C99 3.3 56.3 1.0 C5' 2:C360 3.4 54.2 1.0 O5' 2:A100 3.7 54.9 1.0 O3' 2:A359 3.7 57.3 1.0 C4' 2:C99 4.3 56.3 1.0 C1' 2:C99 4.4 56.3 1.0 C4' 2:C360 4.5 54.2 1.0 C5' 2:A100 4.6 54.9 1.0 O4' 2:C360 4.7 54.2 1.0 OP2 2:U101 4.7 56.7 1.0 C3' 2:A359 4.8 57.3 1.0 C8 2:A100 4.9 54.9 1.0 O4' 2:C99 5.0 56.3 1.0

Magnesium binding site 5 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:66.5 occ:1.00 OP2 2:A1024 1.9 62.3 1.0 OP1 2:A1025 1.9 60.1 1.0 O5' 2:A1024 2.0 62.3 1.0 C5' 2:A1024 2.3 62.3 1.0 P 2:A1024 2.3 62.3 1.0 OP1 2:A1024 3.1 62.3 1.0 P 2:A1025 3.2 60.1 1.0 C4' 2:A1024 3.5 62.3 1.0 O3' 2:U1023 3.7 64.8 1.0 O3' 2:A1024 3.8 62.3 1.0 OP2 2:A1025 3.8 60.1 1.0 C3' 2:A1024 3.9 62.3 1.0 C3' 2:U1023 4.2 64.8 1.0 N7 2:A1026 4.3 62.7 1.0 O5' 2:A1025 4.4 60.1 1.0 O4' 2:A1024 4.6 62.3 1.0 C8 2:A1026 4.7 62.7 1.0 OP2 2:G623 4.9 60.2 1.0

Magnesium binding site 6 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:88.7 occ:1.00 OP2 2:C582 4.0 74.9 1.0 O6 2:G556 4.3 75.5 1.0 O6 2:G585 4.5 72.9 1.0 N4 2:C558 4.5 73.8 1.0 OP1 2:C582 4.7 74.9 1.0 P 2:C582 4.8 74.9 1.0 C5' 2:U581 4.9 70.4 1.0

Magnesium binding site 7 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:55.3 occ:1.00 OP2 2:C49 1.9 59.7 1.0 P 2:C49 3.4 59.7 1.0 N7 2:A424 3.4 59.6 1.0 OP1 2:A424 3.4 59.6 1.0 C8 2:A424 4.0 59.6 1.0 OP1 2:C49 4.2 59.7 1.0 O3' 2:G48 4.2 58.4 1.0 C3' 2:G48 4.2 58.4 1.0 O5' 2:C49 4.3 59.7 1.0 P 2:A424 4.5 59.6 1.0 O3' 2:C423 4.5 64.3 1.0 C5 2:A424 4.6 59.6 1.0 N6 2:A424 4.9 59.6 1.0 C4' 2:G387 5.0 77.6 1.0 C5 2:C49 5.0 59.7 1.0

Magnesium binding site 8 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:85.3 occ:1.00 OP1 2:C1005 1.9 99.9 1.0 P 2:C1005 2.6 99.9 1.0 OP2 2:C1005 2.7 99.9 1.0 O3' 2:A1004 3.2 100.3 1.0 O5' 2:C1005 4.1 99.9 1.0 C3' 2:A1004 4.4 100.3 1.0 CM5 2:5MC1006 4.5 108.8 1.0 C5' 2:C1005 4.9 99.9 1.0 C5' 2:A1004 4.9 100.3 1.0

Magnesium binding site 9 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:88.7 occ:1.00 OP1 2:U8 3.1 58.3 1.0 OP2 2:A11 3.9 56.0 1.0 OP1 2:A11 4.1 56.0 1.0 O4 2:U9 4.4 57.5 1.0 C4 2:U9 4.4 57.5 1.0 P 2:A11 4.4 56.0 1.0 P 2:U8 4.5 58.3 1.0 C5 2:U9 4.6 57.5 1.0 O5' 2:U8 4.7 58.3 1.0 OP2 2:U9 4.8 57.5 1.0 N3 2:U9 4.9 57.5 1.0

Magnesium binding site 10 out of 115 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:82.8 occ:1.00 N3 2:C930 2.2 74.5 1.0 N6 2:A929 2.3 74.8 1.0 O2 2:C930 2.7 74.5 1.0 C2 2:C930 2.7 74.5 1.0 N7 2:A929 3.0 74.8 1.0 OP2 2:A928 3.1 75.8 1.0 C6 2:A929 3.1 74.8 1.0 C4 2:C930 3.2 74.5 1.0 C5 2:A929 3.3 74.8 1.0 N4 2:C930 3.6 74.5 1.0 N1 2:C930 4.0 74.5 1.0 C8 2:A929 4.2 74.8 1.0 P 2:A928 4.3 75.8 1.0 N1 2:A929 4.3 74.8 1.0 C5 2:C930 4.3 74.5 1.0 O5' 2:A928 4.4 75.8 1.0 C6 2:C930 4.6 74.5 1.0 C4 2:A929 4.6 74.8 1.0 N7 2:A928 4.8 75.8 1.0 C8 2:A928 4.9 75.8 1.0 C1' 2:C930 4.9 74.5 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