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Magnesium in PDB 3jaq: Structure of A Partial Yeast 48S Preinitiation Complex in Open Conformation

Other elements in 3jaq:

The structure of Structure of A Partial Yeast 48S Preinitiation Complex in Open Conformation also contains other interesting chemical elements:

Zinc (Zn) 4 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 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 82;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Partial Yeast 48S Preinitiation Complex in Open Conformation (pdb code 3jaq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 82 binding sites of Magnesium where determined in the Structure of A Partial Yeast 48S Preinitiation Complex in Open Conformation, PDB code: 3jaq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 82 in 3jaq

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Magnesium binding site 1 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1801

b:50.0
occ:1.00
OP2 2:G362 2.0 50.0 1.0
P 2:G362 3.2 50.0 1.0
O6 2:G376 3.5 50.0 1.0
C6 2:G376 3.5 50.0 1.0
OP1 2:G362 3.6 50.0 1.0
C5 2:G376 3.6 50.0 1.0
OP1 2:G361 3.7 50.0 1.0
N7 2:G376 3.8 50.0 1.0
OP2 2:G361 3.9 50.0 1.0
P 2:G361 4.1 50.0 1.0
O3' 2:G361 4.1 50.0 1.0
N1 2:G376 4.2 50.0 1.0
O5' 2:G361 4.2 50.0 1.0
O5' 2:G362 4.3 50.0 1.0
C4 2:G376 4.4 50.0 1.0
C3' 2:G361 4.6 50.0 1.0
C8 2:G376 4.6 50.0 1.0
C5' 2:G361 4.8 50.0 1.0
C2 2:G376 4.9 50.0 1.0
N9 2:G376 5.0 50.0 1.0

Magnesium binding site 2 out of 82 in 3jaq

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Magnesium binding site 2 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1802

b:50.0
occ:1.00
OP2 2:A93 2.5 50.0 1.0
N7 2:G402 3.0 50.0 1.0
P 2:A93 3.3 50.0 1.0
OP1 2:A93 3.4 50.0 1.0
OP1 2:G402 3.4 50.0 1.0
C8 2:G402 3.5 50.0 1.0
O3' 2:A92 3.8 50.0 1.0
O5' 2:G402 4.1 50.0 1.0
C5 2:G402 4.2 50.0 1.0
P 2:G402 4.3 50.0 1.0
O2' 2:A92 4.4 50.0 1.0
N9 2:G402 4.7 50.0 1.0
O5' 2:A93 4.7 50.0 1.0
O3' 2:C401 4.8 50.0 1.0
C2' 2:A92 4.8 50.0 1.0
O6 2:G402 4.9 50.0 1.0
C3' 2:A92 4.9 50.0 1.0
C6 2:G402 4.9 50.0 1.0
O6 2:G95 5.0 50.0 1.0
O4 2:U94 5.0 50.0 1.0

Magnesium binding site 3 out of 82 in 3jaq

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Magnesium binding site 3 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1803

b:50.0
occ:1.00
OP2 2:A555 2.0 50.0 1.0
O5' 2:A555 2.3 50.0 1.0
P 2:A555 2.5 50.0 1.0
OP2 2:G556 3.0 50.0 1.0
OP1 2:A555 3.3 50.0 1.0
C8 2:A555 3.5 50.0 1.0
C5' 2:A555 3.7 50.0 1.0
OP1 2:G551 3.7 50.0 1.0
O3' 2:A554 3.9 50.0 1.0
C3' 2:A555 4.0 50.0 1.0
N7 2:A555 4.0 50.0 1.0
P 2:G556 4.3 50.0 1.0
C4' 2:A555 4.3 50.0 1.0
OP2 2:A554 4.3 50.0 1.0
C3' 2:A554 4.4 50.0 1.0
N9 2:A555 4.6 50.0 1.0
O3' 2:A555 4.6 50.0 1.0
O4' 2:A555 4.7 50.0 1.0
P 2:G551 4.8 50.0 1.0
OP1 2:G556 4.9 50.0 1.0
O5' 2:A554 4.9 50.0 1.0
C2' 2:A555 5.0 50.0 1.0
OP2 2:G551 5.0 50.0 1.0

Magnesium binding site 4 out of 82 in 3jaq

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Magnesium binding site 4 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1804

b:50.0
occ:1.00
OP1 2:A100 2.0 50.0 1.0
P 2:A100 2.7 50.0 1.0
OP2 2:A100 2.7 50.0 1.0
OP2 2:C360 3.0 50.0 1.0
O5' 2:A100 3.9 50.0 1.0
O3' 2:C99 4.0 50.0 1.0
OP1 2:U45 4.1 50.0 1.0
C5' 2:A100 4.1 50.0 1.0
P 2:C360 4.1 50.0 1.0
C5' 2:A358 4.2 50.0 1.0
OP1 2:C360 4.3 50.0 1.0
OP2 2:A358 4.5 50.0 1.0
C3' 2:C99 4.6 50.0 1.0
MG 2:MG1826 4.7 50.0 1.0
O5' 2:A358 4.8 50.0 1.0

Magnesium binding site 5 out of 82 in 3jaq

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Magnesium binding site 5 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1805

b:50.0
occ:1.00
OP2 2:G623 3.5 50.0 1.0
OP2 2:A1024 4.2 50.0 1.0
P 2:G623 4.6 50.0 1.0
O3' 2:A622 4.6 50.0 1.0
OP1 2:A1024 4.8 50.0 1.0
OP1 2:A1025 4.9 50.0 1.0
P 2:A1024 5.0 50.0 1.0

Magnesium binding site 6 out of 82 in 3jaq

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Magnesium binding site 6 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1806

b:50.0
occ:1.00
N6 2:A584 1.7 50.0 1.0
N4 2:C583 2.8 50.0 1.0
C6 2:A584 2.9 50.0 1.0
C4 2:C583 3.5 50.0 1.0
C5 2:A584 3.6 50.0 1.0
C5 2:C583 3.7 50.0 1.0
N7 2:A584 3.7 50.0 1.0
O4 2:U559 3.8 50.0 1.0
N1 2:A584 4.0 50.0 1.0
OP2 2:C582 4.0 50.0 1.0
OP1 2:U581 4.0 50.0 1.0
O6 2:G585 4.1 50.0 1.0
N4 2:C558 4.3 50.0 1.0
N4 2:C582 4.5 50.0 1.0
O6 2:G560 4.5 50.0 1.0
OP2 2:U581 4.5 50.0 1.0
N3 2:C583 4.7 50.0 1.0
C4 2:C582 4.7 50.0 1.0
P 2:U581 4.8 50.0 1.0
C5 2:C582 4.8 50.0 1.0
C6 2:C583 4.9 50.0 1.0
C6 2:G585 5.0 50.0 1.0
C4 2:A584 5.0 50.0 1.0

Magnesium binding site 7 out of 82 in 3jaq

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Magnesium binding site 7 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1807

b:50.0
occ:1.00
OP2 2:C49 2.0 50.0 1.0
P 2:C49 2.9 50.0 1.0
O5' 2:C49 3.0 50.0 1.0
OP1 2:C49 3.5 50.0 1.0
C6 2:C49 4.1 50.0 1.0
OP1 2:A424 4.1 50.0 1.0
O3' 2:G48 4.3 50.0 1.0
C5 2:C49 4.3 50.0 1.0
C5' 2:C49 4.3 50.0 1.0
OP2 2:A424 4.6 50.0 1.0
C3' 2:G48 4.7 50.0 1.0
P 2:A424 4.9 50.0 1.0
C3' 2:C49 5.0 50.0 1.0

Magnesium binding site 8 out of 82 in 3jaq

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Magnesium binding site 8 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1808

b:50.0
occ:1.00
OP2 2:A1004 2.6 50.0 1.0
OP2 2:C1005 3.4 50.0 1.0
C5' 2:U1003 3.7 50.0 1.0
MG 2:MG1842 4.0 50.0 1.0
P 2:A1004 4.0 50.0 1.0
OP1 2:C1005 4.1 50.0 1.0
P 2:C1005 4.2 50.0 1.0
OP2 2:U1003 4.3 50.0 1.0
O5' 2:U1003 4.4 50.0 1.0
O3' 2:U1003 4.5 50.0 1.0
C4' 2:U1003 4.5 50.0 1.0
O6 2:G1007 4.5 50.0 1.0
O3' 2:A1004 4.7 50.0 1.0
O4 2:U995 4.7 50.0 1.0
C5' 2:A1004 4.8 50.0 1.0
O5' 2:A1004 5.0 50.0 1.0

Magnesium binding site 9 out of 82 in 3jaq

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Magnesium binding site 9 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1809

b:50.0
occ:1.00
OP1 2:G573 1.9 50.0 1.0
O3' 2:C572 2.4 50.0 1.0
P 2:G573 2.6 50.0 1.0
OP1 2:U8 3.2 50.0 1.0
O3' 2:G7 3.3 50.0 1.0
O2' 2:C572 3.5 50.0 1.0
O5' 2:G573 3.6 50.0 1.0
C3' 2:C572 3.7 50.0 1.0
P 2:U8 3.8 50.0 1.0
OP2 2:G573 3.8 50.0 1.0
C2' 2:C572 4.1 50.0 1.0
C4' 2:C572 4.4 50.0 1.0
C3' 2:G7 4.5 50.0 1.0
OP2 2:U8 4.5 50.0 1.0
C4' 2:G7 4.6 50.0 1.0
OP2 2:U9 4.6 50.0 1.0
O2' 2:G7 4.7 50.0 1.0
OP2 2:A1137 4.9 50.0 1.0
C5' 2:G7 4.9 50.0 1.0
C5' 2:G573 5.0 50.0 1.0

Magnesium binding site 10 out of 82 in 3jaq

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Magnesium binding site 10 out of 82 in the Structure of A Partial Yeast 48S Preinitiation Complex in Open 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 Partial Yeast 48S Preinitiation Complex in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1810

b:50.0
occ:1.00
OP2 2:A928 2.1 50.0 1.0
O2' 2:U927 2.7 50.0 1.0
O3' 2:U927 3.1 50.0 1.0
P 2:A928 3.1 50.0 1.0
C2' 2:U927 3.7 50.0 1.0
C3' 2:U927 3.7 50.0 1.0
C5' 2:U944 3.8 50.0 1.0
O5' 2:A928 4.1 50.0 1.0
N7 2:A928 4.1 50.0 1.0
C4' 2:U944 4.3 50.0 1.0
OP1 2:A928 4.3 50.0 1.0
C8 2:A928 4.3 50.0 1.0
N4 2:C930 4.4 50.0 1.0
N6 2:A929 4.4 50.0 1.0
O2' 2:A943 4.5 50.0 1.0
N3 2:C930 4.7 50.0 1.0
C1' 2:U927 4.8 50.0 1.0
N7 2:A929 4.9 50.0 1.0
O4' 2:U944 4.9 50.0 1.0

Reference:

J.L.Llacer, T.Hussain, L.Marler, C.E.Aitken, A.Thakur, J.R.Lorsch, A.G.Hinnebusch, V.Ramakrishnan. Conformational Differences Between Open and Closed States of the Eukaryotic Translation Initiation Complex. Mol.Cell V. 59 399 2015.
ISSN: ISSN 1097-2765
PubMed: 26212456
DOI: 10.1016/J.MOLCEL.2015.06.033
Page generated: Mon Dec 14 08:19:11 2020

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