Magnesium in PDB 3j81: Cryoem Structure of A Partial Yeast 48S Preinitiation Complex

The structure of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex 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 - 81;

Binding sites:

The binding sites of Magnesium atom in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex (pdb code 3j81). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 81 binding sites of Magnesium where determined in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex, PDB code: 3j81:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:0.4 occ:1.00 OP1 2:G361 2.0 81.3 1.0 P 2:G361 2.8 80.0 1.0 O5' 2:G361 3.0 76.9 1.0 OP2 2:G362 3.4 87.7 1.0 OP2 2:G361 3.5 79.8 1.0 C5' 2:G361 3.6 75.9 1.0 OP1 2:G362 3.8 91.9 1.0 P 2:G362 3.9 88.8 1.0 O3' 2:G361 4.1 85.0 1.0 O3' 2:C360 4.3 77.8 1.0 C3' 2:G361 4.3 78.7 1.0 C4' 2:G361 4.5 77.9 1.0 O2' 2:A359 4.7 0.7 1.0

Magnesium binding site 2 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:98.4 occ:1.00 OP1 2:G402 2.4 0.5 1.0 O6 2:G95 3.1 97.9 1.0 O3' 2:C401 3.3 0.0 1.0 OP2 2:A93 3.4 88.3 1.0 P 2:G402 3.5 0.6 1.0 NH2 E:ARG3 3.6 0.0 1.0 C6 2:G95 4.3 97.0 1.0 O5' 2:G402 4.4 1.0 1.0 C3' 2:C401 4.5 0.9 1.0 O5' 2:C401 4.6 99.4 1.0 OP2 2:G402 4.6 0.9 1.0 N7 2:G402 4.6 0.5 1.0 CZ E:ARG3 4.7 0.8 1.0 C8 2:G402 4.7 0.4 1.0 C4' 2:C401 4.8 0.9 1.0 C5' 2:C401 4.8 0.1 1.0 N1 2:G96 4.8 89.3 1.0 P 2:A93 4.9 90.2 1.0 O6 2:G96 4.9 92.0 1.0 NH1 E:ARG3 5.0 0.9 1.0

Magnesium binding site 3 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:70.9 occ:1.00 OP2 2:A554 2.2 98.4 1.0 OP2 2:A555 2.4 99.6 1.0 OP1 2:G551 3.3 0.8 1.0 P 2:A554 3.4 96.5 1.0 OP2 2:G552 3.5 0.4 1.0 P 2:A555 3.7 0.3 1.0 O5' 2:A554 3.7 96.9 1.0 O3' 2:C553 4.0 95.1 1.0 O5' 2:G551 4.0 0.8 1.0 P 2:G551 4.2 0.9 1.0 OP1 2:A555 4.2 1.0 1.0 O2' 2:C553 4.3 92.0 1.0 C5' 2:G551 4.3 0.4 1.0 N7 2:A555 4.4 90.8 1.0 O5' 2:A555 4.6 99.6 1.0 C8 2:A555 4.6 91.6 1.0 C3' 2:C553 4.7 95.3 1.0 OP1 2:A554 4.7 96.0 1.0 O3' 2:A554 4.8 98.3 1.0 C3' 2:A554 4.8 96.5 1.0 OP2 2:G551 4.9 0.9 1.0 P 2:G552 4.9 0.7 1.0

Magnesium binding site 4 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:44.7 occ:1.00 OP1 2:A100 3.3 86.6 1.0 OP2 2:A100 3.5 86.4 1.0 OP1 2:C360 3.7 83.6 1.0 P 2:A100 3.8 87.0 1.0 C3' 2:C99 4.3 70.1 1.0 C4' 2:U44 4.4 0.3 1.0 O2' 2:A43 4.4 0.6 1.0 O3' 2:C99 4.5 77.6 1.0 O4' 2:U44 4.7 0.9 1.0 C5' 2:C99 4.8 71.2 1.0 OP1 2:U45 4.9 0.1 1.0 O4' 2:A377 4.9 89.8 1.0 C5' 2:U44 4.9 0.8 1.0 P 2:C360 5.0 83.4 1.0

Magnesium binding site 5 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:48.3 occ:1.00 OP2 2:A1024 2.2 97.8 1.0 OP2 2:G623 2.7 0.9 1.0 P 2:A1024 3.5 97.6 1.0 P 2:G623 3.9 0.7 1.0 OP1 2:A1024 4.0 99.1 1.0 O5' 2:A1024 4.2 92.5 1.0 OP1 2:G623 4.3 0.5 1.0 C5' 2:A1024 4.3 87.1 1.0 OP2 2:A1025 4.4 86.3 1.0 N7 2:A1026 4.6 77.2 1.0 O3' 2:U1023 4.7 98.1 1.0 C5' 2:U1023 4.8 99.8 1.0 O3' 2:A622 4.9 0.5 1.0 C3' 2:U1023 5.0 97.9 1.0

Magnesium binding site 6 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:81.4 occ:1.00 OP2 2:C582 3.6 0.3 1.0 N6 2:A584 3.8 0.4 1.0 O6 2:G585 3.8 0.7 1.0 O6 2:G556 4.2 0.3 1.0 N7 2:A584 4.5 0.2 1.0 OP1 2:U581 4.6 0.5 1.0 C6 2:A584 4.8 0.7 1.0 N4 2:C558 4.8 0.4 1.0 C5 2:A584 5.0 0.9 1.0

Magnesium binding site 7 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1807 b:77.7 occ:1.00 OP2 2:C49 2.3 0.2 1.0 P 2:C49 3.4 1.0 1.0 OP1 2:C49 3.6 0.1 1.0 N7 2:A424 3.8 98.1 1.0 OP1 2:A424 4.2 1.0 1.0 O4' 2:G387 4.3 0.2 1.0 O3' 2:G48 4.3 0.3 1.0 C4' 2:G387 4.5 0.4 1.0 C8 2:A424 4.5 97.5 1.0 O5' 2:C49 4.6 0.8 1.0 N6 2:A424 4.6 0.3 1.0 C5 2:A424 4.7 97.0 1.0 O2' 2:G387 4.8 0.1 1.0 C3' 2:G48 4.8 0.6 1.0

Magnesium binding site 8 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1808 b:57.1 occ:1.00 O3' 2:U1003 3.8 0.1 1.0 OP2 2:A1004 3.9 0.2 1.0 OP2 2:A992 4.0 0.6 1.0 OP1 2:C1005 4.5 0.1 1.0 OP1 2:A992 4.5 0.6 1.0 C4' 2:U1003 4.6 0.9 1.0 P 2:A1004 4.6 0.8 1.0 C5' 2:U1003 4.6 0.1 1.0 N7 2:G993 4.7 0.3 1.0 P 2:A992 4.8 0.3 1.0 C3' 2:U1003 4.8 0.8 1.0 O4 2:U995 4.9 0.0 1.0

Magnesium binding site 9 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1809 b:21.0 occ:1.00 OP2 2:G1329 2.0 0.6 1.0 P 2:G1329 3.4 0.8 1.0 N4 2:C1418 3.6 0.1 1.0 N3 2:C1418 3.8 0.5 1.0 O5' 2:G1329 3.9 0.7 1.0 OP1 2:A1328 3.9 99.5 1.0 O5' 2:A1328 4.0 99.8 1.0 N7 2:A1330 4.1 0.9 1.0 C4 2:C1418 4.1 0.4 1.0 N6 2:A1330 4.2 0.7 1.0 OP1 2:G1329 4.3 0.2 1.0 P 2:A1328 4.3 97.6 1.0 N3 2:C1331 4.3 0.6 1.0 N4 2:C1331 4.4 0.1 1.0 O3' 2:A1328 4.5 0.4 1.0 OP2 2:A1328 4.5 96.7 1.0 C5' 2:A1328 4.5 0.2 1.0 N7 2:G1329 4.5 0.3 1.0 C8 2:G1329 4.5 0.7 1.0 OG D:SER160 4.6 0.4 1.0 O6 2:G1417 4.6 0.3 1.0 C3' 2:A1328 4.6 0.1 1.0 C4 2:C1331 4.7 0.6 1.0 C5 2:A1330 4.9 0.6 1.0 C2 2:C1418 4.9 0.1 1.0 CB D:SER160 4.9 0.9 1.0 C6 2:A1330 5.0 0.4 1.0

Magnesium binding site 10 out of 81 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1810 b:62.5 occ:1.00 OP2 2:A11 3.5 0.1 1.0 OP2 2:U9 3.9 1.0 1.0 OP1 2:U8 4.0 0.0 1.0 OP2 2:G10 4.2 0.7 1.0 C5 2:U9 4.6 0.6 1.0 C6 2:U9 4.7 0.8 1.0 O5' 2:G10 4.7 0.3 1.0 O5' 2:U9 4.7 0.1 1.0 P 2:A11 4.8 0.4 1.0 P 2:U9 4.9 0.3 1.0 OP2 2:U8 5.0 0.1 1.0

T.Hussain, J.L.Llacer, I.S.Fernandez, A.Munoz, P.Martin-Marcos, C.G.Savva, J.R.Lorsch, A.G.Hinnebusch, V.Ramakrishnan. Structural Changes Enable Start Codon Recognition By the Eukaryotic Translation Initiation Complex Cell(Cambridge,Mass.) V. 159 597 2014.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2014.10.001