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:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 82 in 3jaq
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Magnesium Binding Sites List in 3jaq
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 Sites List in 3jaq
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 Sites List in 3jaq
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 Sites List in 3jaq
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
Go back to
Magnesium Binding Sites List in 3jaq
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
Go back to
Magnesium Binding Sites List in 3jaq
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
Go back to
Magnesium Binding Sites List in 3jaq
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
Go back to
Magnesium Binding Sites List in 3jaq
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
Go back to
Magnesium Binding Sites List in 3jaq
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
Go back to
Magnesium Binding Sites List in 3jaq
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
|