Magnesium in PDB 8rw1: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation

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

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation 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 - 115;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (pdb code 8rw1). 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, PDB code: 8rw1:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:53.8 occ:1.00 OP1 2:G361 1.9 60.9 1.0 OP2 2:G361 2.1 60.9 1.0 P 2:G361 2.3 60.9 1.0 OP1 2:A377 3.3 56.4 1.0 O5' 2:G361 3.5 60.9 1.0 O3' 2:C360 3.6 57.7 1.0 OP2 2:G362 3.6 60.9 1.0 O2' 2:A359 3.9 54.3 1.0 C5' 2:G361 4.3 60.9 1.0 P 2:A377 4.6 56.4 1.0 C3' 2:C360 4.6 57.7 1.0 N7 2:G376 4.8 60.9 1.0 C8 2:G376 4.8 60.9 1.0 P 2:G362 4.9 60.9 1.0 OP2 2:A377 5.0 56.4 1.0 C3' 2:G376 5.0 60.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:47.5 occ:1.00 OP1 2:G402 2.1 54.1 1.0 O6 2:G95 3.1 60.9 1.0 P 2:G402 3.6 54.1 1.0 OP2 2:A93 3.8 47.4 1.0 NH2 E:ARG3 4.2 44.5 1.0 C6 2:G95 4.3 60.9 1.0 O3' 2:C401 4.3 60.9 1.0 O5' 2:C401 4.4 60.9 1.0 OP2 2:G402 4.4 54.1 1.0 O5' 2:G402 4.5 54.1 1.0 N7 2:G402 4.7 54.1 1.0 N6 2:A386 4.8 60.9 1.0 O6 2:G96 4.9 60.9 1.0 N1 2:G95 5.0 60.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:40.2 occ:1.00 OP2 2:A554 2.0 56.5 1.0 OP2 2:A555 2.1 60.9 1.0 P 2:A554 3.4 56.5 1.0 OP1 2:G551 3.4 54.7 1.0 P 2:A555 3.6 60.9 1.0 O3' 2:C553 3.8 60.9 1.0 C3' 2:A554 4.1 56.5 1.0 N7 2:A555 4.1 60.9 1.0 OP2 2:G552 4.2 56.4 1.0 O3' 2:A554 4.2 56.5 1.0 O5' 2:A555 4.2 60.9 1.0 C8 2:A555 4.3 60.9 1.0 O5' 2:A554 4.4 56.5 1.0 OP1 2:A554 4.4 56.5 1.0 OP1 2:A555 4.6 60.9 1.0 P 2:G551 4.7 54.7 1.0 O2' 2:C553 4.8 60.9 1.0 C8 2:A554 4.8 56.5 1.0 C3' 2:C553 4.9 60.9 1.0 C5' 2:A554 4.9 56.5 1.0 C2' 2:A554 5.0 56.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:39.9 occ:1.00 OP1 2:A100 2.0 59.5 1.0 OP1 2:C360 3.0 57.7 1.0 P 2:A100 3.2 59.5 1.0 OP2 2:A100 3.7 59.5 1.0 C3' 2:C99 3.7 60.9 1.0 O3' 2:C99 3.7 60.9 1.0 P 2:C360 4.1 57.7 1.0 OP2 2:C360 4.4 57.7 1.0 O5' 2:A100 4.5 59.5 1.0 C4' 2:C99 4.6 60.9 1.0 C5' 2:C99 4.7 60.9 1.0 O2' 2:A43 4.8 47.7 1.0 C2' 2:C99 4.8 60.9 1.0 O4' 2:A377 4.9 56.4 1.0 OP2 2:U45 4.9 46.8 1.0 MG 2:MG1826 4.9 46.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:45.9 occ:1.00 OP2 2:A1024 2.0 60.9 1.0 P 2:A1024 2.9 60.9 1.0 OP1 2:A1024 3.1 60.9 1.0 O5' 2:A1024 4.0 60.9 1.0 C5' 2:A1024 4.0 60.9 1.0 OP1 2:G623 4.1 60.9 1.0 O3' 2:U1023 4.2 60.9 1.0 OP1 2:A1025 4.5 60.9 1.0 OP2 2:A1025 4.5 60.9 1.0 N7 2:A1026 4.7 60.9 1.0 C3' 2:U1023 5.0 60.9 1.0 OP2 2:G623 5.0 60.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:34.2 occ:1.00 OP2 2:C582 3.8 49.9 1.0 O6 2:G556 4.6 56.5 1.0 N6 2:A584 4.7 49.9 1.0 N7 2:A584 5.0 49.9 1.0 O6 2:G585 5.0 53.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:37.2 occ:1.00 OP2 2:C49 2.2 45.4 1.0 P 2:C49 3.6 45.4 1.0 OP1 2:A424 3.7 60.9 1.0 N7 2:A424 3.7 60.9 1.0 O3' 2:C423 4.0 60.9 1.0 C8 2:A424 4.1 60.9 1.0 OP1 2:C49 4.2 45.4 1.0 O5' 2:C49 4.3 45.4 1.0 C5' 2:G387 4.4 56.5 1.0 C4' 2:G387 4.5 56.5 1.0 P 2:A424 4.6 60.9 1.0 O3' 2:G48 4.6 47.7 1.0 C3' 2:G48 4.8 47.7 1.0 O4' 2:G387 4.8 56.5 1.0 C5 2:C49 4.8 45.4 1.0 C5 2:A424 4.9 60.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:47.2 occ:1.00 O3' 2:U1003 4.1 85.8 1.0 O4 2:U995 4.1 58.2 1.0 OP2 2:A1004 4.2 66.1 1.0 C5' 2:A1004 4.8 66.1 1.0 P 2:A1004 4.8 66.1 1.0 OP2 2:C1005 4.8 61.5 1.0 OP2 2:A992 4.9 48.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:33.9 occ:1.00 OP1 2:U8 3.8 60.9 1.0 OP2 2:G10 4.0 60.9 1.0 OP2 2:A11 4.0 60.9 1.0 OP2 2:U9 4.1 60.9 1.0 OP1 2:A11 4.1 60.9 1.0 C5 2:U9 4.4 60.9 1.0 P 2:A11 4.6 60.9 1.0 C6 2:U9 4.7 60.9 1.0 O5' 2:U8 4.9 60.9 1.0 P 2:U8 5.0 60.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:37.9 occ:1.00 OP2 2:A928 2.0 50.3 1.0 P 2:A928 3.2 50.3 1.0 O3' 2:U927 3.5 60.9 1.0 N4 2:C930 3.6 60.9 1.0 O2' 2:U927 3.8 60.9 1.0 O5' 2:A928 3.9 50.3 1.0 N3 2:C930 4.0 60.9 1.0 N6 2:A929 4.1 53.0 1.0 N7 2:A929 4.3 53.0 1.0 C4 2:C930 4.3 60.9 1.0 C4' 2:U944 4.5 48.8 1.0 C5' 2:U944 4.5 48.8 1.0 OP1 2:A928 4.5 50.3 1.0 C3' 2:U927 4.6 60.9 1.0 O4' 2:U944 4.7 48.8 1.0 C8 2:A928 4.7 50.3 1.0 C2' 2:U927 4.7 60.9 1.0 N7 2:A928 4.8 50.3 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