Magnesium in PDB 8d8j: Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Other elements in 8d8j:
The structure of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
29;
Binding sites:
The binding sites of Magnesium atom in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
(pdb code 8d8j). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 29 binding sites of Magnesium where determined in the
Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1), PDB code: 8d8j:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 29 in 8d8j
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Magnesium Binding Sites List in 8d8j
Magnesium binding site 1 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1701
b:22.9
occ:1.00
|
O6
|
a:G75
|
4.1
|
53.9
|
1.0
|
N7
|
a:G75
|
4.1
|
53.9
|
1.0
|
O4
|
a:U76
|
4.2
|
59.7
|
1.0
|
O3'
|
a:A71
|
4.7
|
46.3
|
1.0
|
C1'
|
a:A71
|
4.8
|
46.3
|
1.0
|
O4
|
a:U99
|
4.8
|
53.2
|
1.0
|
C6
|
a:G75
|
4.8
|
53.9
|
1.0
|
C5
|
a:G75
|
4.8
|
53.9
|
1.0
|
N3
|
a:A71
|
4.9
|
46.3
|
1.0
|
N6
|
a:A98
|
4.9
|
62.2
|
1.0
|
OP2
|
a:U72
|
4.9
|
48.5
|
1.0
|
|
Magnesium binding site 2 out
of 29 in 8d8j
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Magnesium Binding Sites List in 8d8j
Magnesium binding site 2 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1702
b:36.7
occ:1.00
|
OP2
|
a:C70
|
4.1
|
36.4
|
1.0
|
OP2
|
a:A71
|
4.2
|
46.3
|
1.0
|
|
Magnesium binding site 3 out
of 29 in 8d8j
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Magnesium Binding Sites List in 8d8j
Magnesium binding site 3 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1703
b:18.1
occ:1.00
|
OP2
|
a:U101
|
3.2
|
49.9
|
1.0
|
OP2
|
a:G102
|
3.7
|
51.7
|
1.0
|
OP2
|
a:U103
|
4.3
|
48.0
|
1.0
|
O6
|
a:G104
|
4.3
|
42.3
|
1.0
|
N7
|
a:G104
|
4.4
|
42.3
|
1.0
|
P
|
a:U101
|
4.4
|
49.9
|
1.0
|
N3
|
a:A100
|
4.5
|
46.6
|
1.0
|
C5
|
a:U103
|
4.5
|
48.0
|
1.0
|
OP1
|
a:G102
|
4.6
|
51.7
|
1.0
|
P
|
a:G102
|
4.6
|
51.7
|
1.0
|
OP1
|
a:U101
|
4.7
|
49.9
|
1.0
|
O4
|
a:U103
|
4.8
|
48.0
|
1.0
|
|
Magnesium binding site 4 out
of 29 in 8d8j
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Magnesium Binding Sites List in 8d8j
Magnesium binding site 4 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1704
b:28.5
occ:1.00
|
OP2
|
a:A110
|
2.0
|
33.8
|
1.0
|
P
|
a:A110
|
3.4
|
33.8
|
1.0
|
O5'
|
a:A110
|
4.1
|
33.8
|
1.0
|
C4'
|
a:A109
|
4.2
|
49.0
|
1.0
|
OP1
|
a:A110
|
4.2
|
33.8
|
1.0
|
OP1
|
a:U336
|
4.3
|
37.4
|
1.0
|
C5'
|
a:A109
|
4.4
|
49.0
|
1.0
|
O3'
|
a:A109
|
4.4
|
49.0
|
1.0
|
N7
|
a:A110
|
4.5
|
33.8
|
1.0
|
N6
|
a:A111
|
4.6
|
29.9
|
1.0
|
O6
|
a:G321
|
4.6
|
28.5
|
1.0
|
C3'
|
a:A109
|
4.6
|
49.0
|
1.0
|
C8
|
a:A110
|
4.7
|
33.8
|
1.0
|
N7
|
a:A111
|
4.8
|
29.9
|
1.0
|
|
Magnesium binding site 5 out
of 29 in 8d8j
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Magnesium Binding Sites List in 8d8j
Magnesium binding site 5 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1705
b:21.7
occ:1.00
|
OP1
|
a:C54
|
3.3
|
28.8
|
1.0
|
OP1
|
a:A53
|
3.8
|
25.3
|
1.0
|
O3'
|
a:A312
|
3.8
|
28.3
|
1.0
|
OP1
|
a:A55
|
3.9
|
31.0
|
1.0
|
O2'
|
a:A312
|
4.1
|
28.3
|
1.0
|
OP1
|
a:A313
|
4.1
|
25.6
|
1.0
|
C5'
|
a:A53
|
4.2
|
25.3
|
1.0
|
P
|
a:C54
|
4.4
|
28.8
|
1.0
|
OP1
|
a:U114
|
4.5
|
33.1
|
1.0
|
O3'
|
a:A53
|
4.6
|
25.3
|
1.0
|
O5'
|
a:A53
|
4.6
|
25.3
|
1.0
|
P
|
a:A313
|
4.7
|
25.6
|
1.0
|
O5'
|
a:C54
|
4.7
|
28.8
|
1.0
|
C3'
|
a:A312
|
4.8
|
28.3
|
1.0
|
C5'
|
a:A313
|
4.9
|
25.6
|
1.0
|
P
|
a:A53
|
4.9
|
25.3
|
1.0
|
|
Magnesium binding site 6 out
of 29 in 8d8j
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Magnesium Binding Sites List in 8d8j
Magnesium binding site 6 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1706
b:13.4
occ:1.00
|
OP1
|
a:G115
|
1.9
|
28.4
|
1.0
|
OP2
|
a:A55
|
2.1
|
31.0
|
1.0
|
OP2
|
a:U56
|
2.7
|
34.3
|
1.0
|
P
|
a:G115
|
3.2
|
28.4
|
1.0
|
P
|
a:A55
|
3.5
|
31.0
|
1.0
|
O3'
|
a:U114
|
3.5
|
33.1
|
1.0
|
O3'
|
a:C54
|
3.9
|
28.8
|
1.0
|
OP2
|
a:G115
|
4.1
|
28.4
|
1.0
|
P
|
a:U56
|
4.1
|
34.3
|
1.0
|
O5'
|
a:G115
|
4.4
|
28.4
|
1.0
|
O5'
|
a:A55
|
4.4
|
31.0
|
1.0
|
OP1
|
a:A55
|
4.6
|
31.0
|
1.0
|
C5'
|
a:A55
|
4.6
|
31.0
|
1.0
|
C4'
|
a:A55
|
4.7
|
31.0
|
1.0
|
OP1
|
a:A58
|
4.7
|
35.0
|
1.0
|
C5'
|
a:G115
|
4.7
|
28.4
|
1.0
|
OP1
|
a:U56
|
4.7
|
34.3
|
1.0
|
C3'
|
a:U114
|
4.8
|
33.1
|
1.0
|
O2'
|
a:C54
|
4.8
|
28.8
|
1.0
|
O3'
|
a:A55
|
4.9
|
31.0
|
1.0
|
|
Magnesium binding site 7 out
of 29 in 8d8j
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Magnesium Binding Sites List in 8d8j
Magnesium binding site 7 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1707
b:27.6
occ:1.00
|
OP2
|
a:A294
|
2.0
|
34.1
|
1.0
|
OP2
|
a:G117
|
2.1
|
32.8
|
1.0
|
OP2
|
a:A116
|
2.4
|
32.1
|
1.0
|
P
|
a:A294
|
3.3
|
34.1
|
1.0
|
O5'
|
a:A294
|
3.5
|
34.1
|
1.0
|
P
|
a:G117
|
3.6
|
32.8
|
1.0
|
O4
|
a:U118
|
3.6
|
36.5
|
1.0
|
P
|
a:A116
|
3.8
|
32.1
|
1.0
|
MG
|
a:MG1729
|
4.1
|
23.9
|
1.0
|
C3'
|
a:A293
|
4.2
|
39.7
|
1.0
|
O3'
|
a:A293
|
4.3
|
39.7
|
1.0
|
C4
|
a:U118
|
4.3
|
36.5
|
1.0
|
O5'
|
a:A293
|
4.4
|
39.7
|
1.0
|
O3'
|
a:G115
|
4.4
|
28.4
|
1.0
|
O5'
|
a:G117
|
4.4
|
32.8
|
1.0
|
OP1
|
a:A294
|
4.4
|
34.1
|
1.0
|
OP1
|
a:G117
|
4.4
|
32.8
|
1.0
|
O3'
|
a:A116
|
4.4
|
32.1
|
1.0
|
C5
|
a:U118
|
4.5
|
36.5
|
1.0
|
OP2
|
a:A293
|
4.5
|
39.7
|
1.0
|
C3'
|
a:A116
|
4.5
|
32.1
|
1.0
|
O5'
|
a:A116
|
4.5
|
32.1
|
1.0
|
N7
|
a:G117
|
4.6
|
32.8
|
1.0
|
C5'
|
a:A116
|
4.8
|
32.1
|
1.0
|
C8
|
a:G117
|
4.8
|
32.8
|
1.0
|
C5'
|
a:A294
|
4.8
|
34.1
|
1.0
|
OP1
|
a:A116
|
4.9
|
32.1
|
1.0
|
C8
|
a:A293
|
4.9
|
39.7
|
1.0
|
P
|
a:A293
|
4.9
|
39.7
|
1.0
|
C2'
|
a:A293
|
5.0
|
39.7
|
1.0
|
|
Magnesium binding site 8 out
of 29 in 8d8j
Go back to
Magnesium Binding Sites List in 8d8j
Magnesium binding site 8 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1708
b:32.8
occ:1.00
|
N4
|
a:C153
|
4.0
|
60.3
|
1.0
|
OP2
|
a:A157
|
4.1
|
50.6
|
1.0
|
O6
|
a:G152
|
4.4
|
62.3
|
1.0
|
OP1
|
a:A157
|
4.5
|
50.6
|
1.0
|
OP2
|
a:U158
|
4.7
|
45.6
|
1.0
|
P
|
a:A157
|
4.7
|
50.6
|
1.0
|
N7
|
a:G152
|
4.7
|
62.3
|
1.0
|
O5'
|
a:A157
|
4.9
|
50.6
|
1.0
|
|
Magnesium binding site 9 out
of 29 in 8d8j
Go back to
Magnesium Binding Sites List in 8d8j
Magnesium binding site 9 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1709
b:40.8
occ:1.00
|
OP1
|
a:A159
|
2.7
|
49.7
|
1.0
|
OP1
|
a:A200
|
3.7
|
48.9
|
1.0
|
P
|
a:A159
|
4.0
|
49.7
|
1.0
|
OP2
|
a:C160
|
4.3
|
55.1
|
1.0
|
O5'
|
a:A159
|
4.3
|
49.7
|
1.0
|
N7
|
a:A200
|
4.4
|
48.9
|
1.0
|
O3'
|
a:A199
|
4.5
|
57.1
|
1.0
|
O3'
|
a:U158
|
4.6
|
45.6
|
1.0
|
P
|
a:A200
|
4.6
|
48.9
|
1.0
|
C8
|
a:A200
|
4.7
|
48.9
|
1.0
|
C5'
|
a:A199
|
4.8
|
57.1
|
1.0
|
OP1
|
a:C160
|
4.9
|
55.1
|
1.0
|
|
Magnesium binding site 10 out
of 29 in 8d8j
Go back to
Magnesium Binding Sites List in 8d8j
Magnesium binding site 10 out
of 29 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg1710
b:50.2
occ:1.00
|
OP2
|
a:U256
|
2.3
|
44.2
|
1.0
|
O3'
|
a:G255
|
3.2
|
45.3
|
1.0
|
P
|
a:U256
|
3.3
|
44.2
|
1.0
|
OP2
|
a:U271
|
3.8
|
55.1
|
1.0
|
OP2
|
a:U272
|
3.9
|
64.3
|
1.0
|
O2'
|
a:G270
|
4.0
|
46.8
|
1.0
|
O2'
|
a:G255
|
4.2
|
45.3
|
1.0
|
O5'
|
a:U256
|
4.2
|
44.2
|
1.0
|
O3'
|
a:G270
|
4.3
|
46.8
|
1.0
|
OP2
|
a:A257
|
4.3
|
44.5
|
1.0
|
C5'
|
a:U256
|
4.3
|
44.2
|
1.0
|
O3'
|
a:U271
|
4.4
|
55.1
|
1.0
|
C3'
|
a:G255
|
4.5
|
45.3
|
1.0
|
OP1
|
a:U256
|
4.5
|
44.2
|
1.0
|
P
|
a:U271
|
4.7
|
55.1
|
1.0
|
P
|
a:U272
|
4.7
|
64.3
|
1.0
|
C2'
|
a:G255
|
4.9
|
45.3
|
1.0
|
CD
|
Q:LYS68
|
4.9
|
43.5
|
1.0
|
|
Reference:
N.J.Harper,
C.Burnside,
S.Klinge.
Principles of Mitoribosomal Small Subunit Assembly in Eukaryotes. Nature 2022.
ISSN: ESSN 1476-4687
PubMed: 36482135
DOI: 10.1038/S41586-022-05621-0
Page generated: Thu Oct 3 23:41:21 2024
|