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Magnesium in PDB 3j80: Cryoem Structure of 40S-EIF1-EIF1A Preinitiation Complex

Other elements in 3j80:

The structure of Cryoem Structure of 40S-EIF1-EIF1A Preinitiation Complex also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

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 - 67;

Binding sites:

The binding sites of Magnesium atom in the Cryoem Structure of 40S-EIF1-EIF1A Preinitiation Complex (pdb code 3j80). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 67 binding sites of Magnesium where determined in the Cryoem Structure of 40S-EIF1-EIF1A Preinitiation Complex, PDB code: 3j80:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 67 in 3j80

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Magnesium binding site 1 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A Preinitiation Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1801

b:68.5
occ:1.00
OP1 2:G361 2.7 43.2 1.0
OP1 2:G362 3.3 60.5 1.0
OP2 2:G362 3.6 56.2 1.0
P 2:G361 3.8 42.4 1.0
P 2:G362 3.9 56.3 1.0
O5' 2:G361 4.1 40.6 1.0
C5' 2:G361 4.2 41.5 1.0
N7 2:G376 4.3 55.5 1.0
OP2 2:G361 4.4 44.6 1.0
C5 2:G376 4.7 55.1 1.0
O3' 2:G361 4.7 49.8 1.0
O6 2:G376 4.7 56.9 1.0
C8 2:G376 4.9 54.7 1.0
C6 2:G376 4.9 56.7 1.0

Magnesium binding site 2 out of 67 in 3j80

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Magnesium binding site 2 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A Preinitiation Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1802

b:50.0
occ:1.00
OP1 2:G402 1.9 92.6 1.0
P 2:G402 3.2 93.0 1.0
OP2 2:A93 3.3 67.3 1.0
NH2 E:ARG3 3.6 55.9 1.0
O3' 2:C401 3.6 87.3 1.0
O5' 2:A93 4.0 58.7 1.0
O5' 2:G402 4.1 98.2 1.0
O6 2:G95 4.3 79.1 1.0
P 2:A93 4.3 64.2 1.0
OP2 2:G402 4.4 93.8 1.0
O5' 2:C401 4.4 57.7 1.0
CZ E:ARG3 4.8 55.0 1.0
C3' 2:C401 4.8 79.4 1.0
C8 2:G402 4.9 90.2 1.0
N7 2:G402 5.0 86.8 1.0

Magnesium binding site 3 out of 67 in 3j80

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Magnesium binding site 3 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A 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 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1803

b:29.5
occ:1.00
OP2 2:A555 2.2 91.6 1.0
OP2 2:A554 2.3 93.9 1.0
OP2 2:G552 3.4 0.5 1.0
P 2:A554 3.5 92.6 1.0
P 2:A555 3.6 90.1 1.0
O3' 2:C553 3.8 87.2 1.0
OP1 2:G551 3.9 0.9 1.0
O2' 2:C553 4.0 80.9 1.0
N7 2:A555 4.1 91.1 1.0
O5' 2:A554 4.1 91.2 1.0
O5' 2:A555 4.3 86.6 1.0
C8 2:A555 4.3 90.8 1.0
C3' 2:A554 4.4 89.5 1.0
O3' 2:A554 4.4 92.6 1.0
O5' 2:G551 4.5 0.4 1.0
P 2:G551 4.5 0.9 1.0
P 2:G552 4.6 0.7 1.0
OP1 2:A555 4.6 91.0 1.0
OP2 2:G551 4.7 0.0 1.0
C3' 2:C553 4.8 86.5 1.0
OP1 2:G552 4.8 0.7 1.0
OP1 2:A554 4.8 96.1 1.0
C2' 2:C553 5.0 82.3 1.0
C5' 2:A554 5.0 85.2 1.0

Magnesium binding site 4 out of 67 in 3j80

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Magnesium binding site 4 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A 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 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1804

b:44.8
occ:1.00
OP1 2:A100 2.3 53.8 1.0
OP1 2:C360 3.5 50.9 1.0
P 2:A100 3.7 52.5 1.0
C3' 2:C99 4.0 45.4 1.0
O3' 2:C99 4.2 48.1 1.0
O2' 2:A43 4.3 71.4 1.0
OP2 2:A100 4.5 54.1 1.0
C4' 2:U44 4.6 96.0 1.0
P 2:C360 4.7 51.6 1.0
C5' 2:C99 4.7 51.1 1.0
O5' 2:A100 4.7 56.7 1.0
C5' 2:U44 4.8 88.6 1.0
C4' 2:C99 4.8 45.4 1.0
O4' 2:A377 4.9 62.1 1.0
OP2 2:C360 4.9 53.6 1.0

Magnesium binding site 5 out of 67 in 3j80

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Magnesium binding site 5 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A 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 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1805

b:28.9
occ:1.00
OP2 2:A1024 2.0 84.2 1.0
OP2 2:G623 3.3 92.7 1.0
P 2:A1024 3.3 85.0 1.0
OP1 2:A1024 3.9 87.7 1.0
O5' 2:A1024 4.2 72.7 1.0
C5' 2:A1024 4.2 61.7 1.0
OP1 2:A1025 4.2 74.9 1.0
C5' 2:U1023 4.3 78.6 1.0
O3' 2:U1023 4.5 80.0 1.0
P 2:G623 4.6 92.0 1.0
N7 2:A1026 4.6 40.5 1.0
C3' 2:U1023 4.7 73.6 1.0
OP1 2:C1127 4.8 0.5 1.0
O5' 2:U1023 4.9 83.0 1.0
OP1 2:G623 4.9 92.1 1.0

Magnesium binding site 6 out of 67 in 3j80

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Magnesium binding site 6 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A 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 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1806

b:34.6
occ:1.00
O6 2:G585 3.8 1.0 1.0
O6 2:G556 4.0 0.8 1.0
N4 2:C586 4.3 0.1 1.0
N7 2:A549 4.3 68.4 1.0
N6 2:A549 4.4 68.3 1.0
N4 2:C558 4.5 0.0 1.0
OP2 2:C582 4.6 0.5 1.0
C5 2:A549 4.7 65.7 1.0
C6 2:A549 4.8 63.9 1.0
N7 2:G556 4.8 95.5 1.0
C6 2:G556 4.9 96.2 1.0
C6 2:G585 5.0 0.8 1.0

Magnesium binding site 7 out of 67 in 3j80

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Magnesium binding site 7 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A 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 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1807

b:35.8
occ:1.00
OP2 2:C49 1.8 96.2 1.0
P 2:C49 2.9 97.7 1.0
O5' 2:C49 3.4 98.5 1.0
OP1 2:C49 3.5 0.1 1.0
OP1 2:A424 4.1 94.5 1.0
O3' 2:G48 4.3 0.7 1.0
O4' 2:G387 4.4 75.3 1.0
C4' 2:G387 4.4 75.4 1.0
C5' 2:G387 4.5 72.9 1.0
N7 2:A424 4.6 59.0 1.0
C3' 2:G48 4.7 0.9 1.0
C5' 2:C49 4.7 99.3 1.0
P 2:A424 4.8 89.0 1.0
O3' 2:C423 4.9 89.8 1.0
C8 2:A424 4.9 59.6 1.0

Magnesium binding site 8 out of 67 in 3j80

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Magnesium binding site 8 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A 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 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1808

b:65.0
occ:1.00
N7 2:G993 4.0 0.9 1.0
O3' 2:U1003 4.0 0.6 1.0
O4 2:U995 4.2 0.5 1.0
O2' 2:U1003 4.3 0.6 1.0
OP2 2:A1004 4.4 0.8 1.0
N7 2:A994 4.4 99.4 1.0
OP2 2:A992 4.5 0.8 1.0
C8 2:G993 4.6 0.5 1.0
P 2:A1004 4.9 0.3 1.0
C4' 2:U1003 4.9 0.5 1.0
C5 2:G993 5.0 0.8 1.0
C3' 2:U1003 5.0 0.2 1.0

Magnesium binding site 9 out of 67 in 3j80

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Magnesium binding site 9 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A 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 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1809

b:15.3
occ:1.00
OP2 2:G1329 2.3 69.3 1.0
P 2:G1329 3.3 66.8 1.0
N4 2:C1331 3.5 66.0 1.0
OP1 2:G1329 3.5 65.5 1.0
N3 2:C1418 3.6 71.7 1.0
N6 2:A1330 3.7 58.9 1.0
O5' 2:G1329 3.9 64.7 1.0
C4 2:C1331 4.0 62.2 1.0
N4 2:C1418 4.0 67.9 1.0
N7 2:A1330 4.1 62.4 1.0
OP1 2:A1328 4.1 55.4 1.0
N3 2:C1331 4.1 58.5 1.0
C4 2:C1418 4.2 67.4 1.0
O6 2:G1417 4.2 65.9 1.0
C2 2:C1418 4.4 77.6 1.0
OP2 2:A1328 4.5 55.0 1.0
O2 2:C1418 4.5 76.1 1.0
N1 2:G1417 4.6 61.9 1.0
C6 2:A1330 4.6 57.1 1.0
C6 2:G1417 4.7 61.7 1.0
O3' 2:A1328 4.7 61.1 1.0
P 2:A1328 4.7 54.9 1.0
C5 2:A1330 4.7 58.0 1.0
C5 2:C1331 5.0 63.8 1.0

Magnesium binding site 10 out of 67 in 3j80

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Magnesium binding site 10 out of 67 in the Cryoem Structure of 40S-EIF1-EIF1A 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 40S-EIF1-EIF1A Preinitiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1810

b:95.5
occ:1.00
OP2 2:G10 3.1 0.8 1.0
OP2 2:U9 3.4 0.2 1.0
O5' 2:U9 4.0 0.1 1.0
OP2 2:A11 4.1 0.3 1.0
OP1 2:U8 4.2 0.4 1.0
P 2:U9 4.3 0.1 1.0
P 2:G10 4.6 0.9 1.0
C3' 2:U9 4.7 0.5 1.0
O5' 2:U8 4.9 90.1 1.0

Reference:

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
Page generated: Mon Dec 14 08:18:23 2020

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