Magnesium in PDB 7oib: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
Enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
All present enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D:
3.1.1.29;
Other elements in 7oib:
The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 49 in 7oib
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Magnesium Binding Sites List in 7oib
Magnesium binding site 1 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Mg201
b:5.5
occ:1.00
|
O
|
W:SER46
|
3.8
|
35.3
|
1.0
|
O
|
W:GLY44
|
4.0
|
44.6
|
1.0
|
N4
|
A:C1159
|
4.3
|
46.1
|
1.0
|
N7
|
A:A1157
|
4.7
|
56.4
|
1.0
|
C
|
W:SER46
|
4.8
|
35.3
|
1.0
|
N
|
W:SER46
|
4.8
|
35.3
|
1.0
|
CB
|
W:SER46
|
4.9
|
35.3
|
1.0
|
C
|
W:GLY44
|
4.9
|
44.6
|
1.0
|
|
Magnesium binding site 2 out
of 49 in 7oib
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Magnesium Binding Sites List in 7oib
Magnesium binding site 2 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
g:Mg201
b:12.1
occ:1.00
|
OD1
|
g:ASP99
|
2.3
|
18.8
|
1.0
|
CG
|
g:ASP99
|
3.4
|
18.8
|
1.0
|
OD2
|
g:ASP99
|
3.9
|
18.8
|
1.0
|
OP2
|
A:G224
|
4.2
|
23.4
|
1.0
|
N7
|
A:G224
|
4.3
|
23.4
|
1.0
|
O
|
g:ILE100
|
4.4
|
16.1
|
1.0
|
CB
|
g:ASP99
|
4.5
|
18.8
|
1.0
|
N
|
g:ILE100
|
4.7
|
16.1
|
1.0
|
O2'
|
A:A223
|
4.8
|
16.8
|
1.0
|
CA
|
g:ASP99
|
4.8
|
18.8
|
1.0
|
C8
|
A:G224
|
5.0
|
23.4
|
1.0
|
|
Magnesium binding site 3 out
of 49 in 7oib
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Magnesium Binding Sites List in 7oib
Magnesium binding site 3 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1601
b:18.0
occ:1.00
|
OP1
|
A:A1196
|
2.4
|
18.7
|
1.0
|
OP2
|
A:U1194
|
2.7
|
23.2
|
1.0
|
OP2
|
A:C1197
|
3.4
|
18.7
|
1.0
|
P
|
A:A1196
|
3.9
|
18.7
|
1.0
|
C2'
|
A:U1193
|
4.0
|
22.0
|
1.0
|
P
|
A:U1194
|
4.1
|
23.2
|
1.0
|
C3'
|
A:U1193
|
4.2
|
22.0
|
1.0
|
P
|
A:C1197
|
4.4
|
18.7
|
1.0
|
O3'
|
A:U1193
|
4.4
|
22.0
|
1.0
|
C2
|
A:U1193
|
4.5
|
22.0
|
1.0
|
OP1
|
A:C1197
|
4.5
|
18.7
|
1.0
|
N1
|
A:U1193
|
4.5
|
22.0
|
1.0
|
OP2
|
A:A1196
|
4.6
|
18.7
|
1.0
|
O3'
|
A:C1195
|
4.7
|
25.4
|
1.0
|
O5'
|
A:A1196
|
4.8
|
18.7
|
1.0
|
N3
|
A:U1193
|
4.8
|
22.0
|
1.0
|
O2
|
A:U1193
|
4.8
|
22.0
|
1.0
|
C6
|
A:U1193
|
4.8
|
22.0
|
1.0
|
C5'
|
A:A1196
|
4.9
|
18.7
|
1.0
|
C1'
|
A:U1193
|
4.9
|
22.0
|
1.0
|
O2'
|
A:U1193
|
4.9
|
22.0
|
1.0
|
O5'
|
A:U1194
|
4.9
|
23.2
|
1.0
|
|
Magnesium binding site 4 out
of 49 in 7oib
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Magnesium Binding Sites List in 7oib
Magnesium binding site 4 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1602
b:41.1
occ:1.00
|
O4
|
A:U88
|
2.3
|
31.8
|
1.0
|
OP2
|
A:A87
|
2.6
|
34.2
|
1.0
|
C4
|
A:U88
|
3.3
|
31.8
|
1.0
|
O4
|
A:U89
|
3.8
|
31.9
|
1.0
|
N6
|
A:A69
|
3.9
|
37.0
|
1.0
|
P
|
A:A87
|
3.9
|
34.2
|
1.0
|
C5
|
A:U88
|
3.9
|
31.8
|
1.0
|
N1
|
A:A70
|
4.3
|
22.0
|
1.0
|
OP1
|
A:A87
|
4.4
|
34.2
|
1.0
|
N3
|
A:U88
|
4.5
|
31.8
|
1.0
|
O5'
|
A:A86
|
4.5
|
22.0
|
1.0
|
C2
|
A:A70
|
4.8
|
22.0
|
1.0
|
C4
|
A:U89
|
4.8
|
31.9
|
1.0
|
O3'
|
A:A86
|
4.8
|
22.0
|
1.0
|
OP2
|
A:A86
|
4.8
|
22.0
|
1.0
|
OP1
|
A:A86
|
4.9
|
22.0
|
1.0
|
O5'
|
A:A87
|
4.9
|
34.2
|
1.0
|
C3'
|
A:A86
|
5.0
|
22.0
|
1.0
|
P
|
A:A86
|
5.0
|
22.0
|
1.0
|
|
Magnesium binding site 5 out
of 49 in 7oib
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Magnesium Binding Sites List in 7oib
Magnesium binding site 5 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_05.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1603
b:22.7
occ:1.00
|
OP1
|
A:C55
|
2.1
|
28.7
|
1.0
|
OP2
|
A:C56
|
2.1
|
29.6
|
1.0
|
N7
|
A:A53
|
2.6
|
23.4
|
1.0
|
C8
|
A:A53
|
3.5
|
23.4
|
1.0
|
P
|
A:C55
|
3.6
|
28.7
|
1.0
|
P
|
A:C56
|
3.6
|
29.6
|
1.0
|
C5
|
A:A53
|
3.7
|
23.4
|
1.0
|
OP2
|
A:A52
|
3.7
|
21.8
|
1.0
|
N6
|
A:A53
|
3.9
|
23.4
|
1.0
|
N7
|
A:A52
|
4.1
|
21.8
|
1.0
|
OP2
|
A:A53
|
4.2
|
23.4
|
1.0
|
C8
|
A:A52
|
4.2
|
21.8
|
1.0
|
C6
|
A:A53
|
4.3
|
23.4
|
1.0
|
OP2
|
A:C55
|
4.3
|
28.7
|
1.0
|
OP1
|
A:C56
|
4.4
|
29.6
|
1.0
|
O3'
|
A:C55
|
4.5
|
28.7
|
1.0
|
O5'
|
A:C55
|
4.5
|
28.7
|
1.0
|
O5'
|
A:C56
|
4.5
|
29.6
|
1.0
|
O3'
|
A:A54
|
4.5
|
24.6
|
1.0
|
C5'
|
A:C55
|
4.5
|
28.7
|
1.0
|
O5'
|
A:A52
|
4.6
|
21.8
|
1.0
|
N9
|
A:A53
|
4.8
|
23.4
|
1.0
|
P
|
A:A52
|
4.8
|
21.8
|
1.0
|
C3'
|
A:C55
|
4.8
|
28.7
|
1.0
|
C5
|
A:A52
|
4.8
|
21.8
|
1.0
|
C4
|
A:A53
|
4.9
|
23.4
|
1.0
|
C5
|
A:C56
|
4.9
|
29.6
|
1.0
|
|
Magnesium binding site 6 out
of 49 in 7oib
Go back to
Magnesium Binding Sites List in 7oib
Magnesium binding site 6 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_06.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1604
b:41.1
occ:1.00
|
OP2
|
A:G106
|
2.1
|
41.1
|
1.0
|
P
|
A:G106
|
3.5
|
41.1
|
1.0
|
O
|
F:GLY149
|
3.5
|
41.1
|
1.0
|
O
|
F:GLY148
|
3.6
|
25.8
|
1.0
|
C
|
F:GLY148
|
3.9
|
25.8
|
1.0
|
OP2
|
A:U108
|
4.0
|
19.4
|
1.0
|
OP1
|
A:G106
|
4.0
|
41.1
|
1.0
|
OP1
|
A:A105
|
4.2
|
14.5
|
1.0
|
CA
|
F:GLY148
|
4.2
|
25.8
|
1.0
|
O5'
|
A:G106
|
4.3
|
41.1
|
1.0
|
C
|
F:GLY149
|
4.5
|
41.1
|
1.0
|
O3'
|
A:A105
|
4.6
|
14.5
|
1.0
|
N
|
F:GLY149
|
4.6
|
41.1
|
1.0
|
OP2
|
A:A107
|
4.6
|
22.3
|
1.0
|
CG1
|
F:VAL120
|
4.7
|
15.9
|
1.0
|
OP2
|
A:A105
|
4.7
|
14.5
|
1.0
|
P
|
A:A105
|
4.8
|
14.5
|
1.0
|
CG2
|
F:VAL120
|
4.9
|
15.9
|
1.0
|
O5'
|
A:A105
|
5.0
|
14.5
|
1.0
|
|
Magnesium binding site 7 out
of 49 in 7oib
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Magnesium Binding Sites List in 7oib
Magnesium binding site 7 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_07.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1605
b:16.4
occ:1.00
|
OP1
|
A:A144
|
2.2
|
32.8
|
1.0
|
OP2
|
A:A145
|
2.9
|
24.7
|
1.0
|
P
|
A:A144
|
3.6
|
32.8
|
1.0
|
N4
|
A:C147
|
3.8
|
15.4
|
1.0
|
O6
|
A:G146
|
3.9
|
16.0
|
1.0
|
OP2
|
A:A144
|
4.2
|
32.8
|
1.0
|
P
|
A:A145
|
4.3
|
24.7
|
1.0
|
N7
|
A:G146
|
4.4
|
16.0
|
1.0
|
O5'
|
A:A144
|
4.4
|
32.8
|
1.0
|
O3'
|
A:C143
|
4.7
|
58.9
|
1.0
|
C6
|
A:G146
|
4.7
|
16.0
|
1.0
|
OP1
|
A:A145
|
4.9
|
24.7
|
1.0
|
C4
|
A:C147
|
4.9
|
15.4
|
1.0
|
O6
|
A:G1
|
4.9
|
17.3
|
1.0
|
C5
|
A:G146
|
5.0
|
16.0
|
1.0
|
O5'
|
A:A145
|
5.0
|
24.7
|
1.0
|
|
Magnesium binding site 8 out
of 49 in 7oib
Go back to
Magnesium Binding Sites List in 7oib
Magnesium binding site 8 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_08.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1606
b:14.7
occ:1.00
|
O6
|
A:G106
|
2.1
|
41.1
|
1.0
|
OP1
|
A:A109
|
2.3
|
20.6
|
1.0
|
C6
|
A:G106
|
3.3
|
41.1
|
1.0
|
P
|
A:A109
|
3.7
|
20.6
|
1.0
|
C5
|
A:G106
|
4.0
|
41.1
|
1.0
|
N7
|
A:G106
|
4.0
|
41.1
|
1.0
|
N7
|
A:A105
|
4.3
|
14.5
|
1.0
|
OP2
|
A:A109
|
4.3
|
20.6
|
1.0
|
N1
|
A:G106
|
4.4
|
41.1
|
1.0
|
OP2
|
A:A105
|
4.4
|
14.5
|
1.0
|
MG
|
A:MG1639
|
4.6
|
41.1
|
1.0
|
O5'
|
A:A109
|
4.6
|
20.6
|
1.0
|
N6
|
A:A105
|
4.7
|
14.5
|
1.0
|
O3'
|
A:U108
|
4.7
|
19.4
|
1.0
|
C5'
|
A:A109
|
4.8
|
20.6
|
1.0
|
C5
|
A:A105
|
5.0
|
14.5
|
1.0
|
|
Magnesium binding site 9 out
of 49 in 7oib
Go back to
Magnesium Binding Sites List in 7oib
Magnesium binding site 9 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_09.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1607
b:15.1
occ:1.00
|
OP2
|
A:G248
|
2.1
|
22.5
|
1.0
|
P
|
A:G248
|
3.2
|
22.5
|
1.0
|
O5'
|
A:G248
|
3.3
|
22.5
|
1.0
|
OP2
|
A:C249
|
3.5
|
25.7
|
1.0
|
O3'
|
A:A247
|
4.0
|
27.6
|
1.0
|
O4
|
A:U250
|
4.4
|
26.4
|
1.0
|
OP1
|
A:G248
|
4.5
|
22.5
|
1.0
|
C5'
|
A:G248
|
4.5
|
22.5
|
1.0
|
O6
|
A:G311
|
4.6
|
27.1
|
1.0
|
C4'
|
A:G248
|
4.6
|
22.5
|
1.0
|
O6
|
A:G312
|
4.8
|
27.4
|
1.0
|
P
|
A:C249
|
4.9
|
25.7
|
1.0
|
|
Magnesium binding site 10 out
of 49 in 7oib
Go back to
Magnesium Binding Sites List in 7oib
Magnesium binding site 10 out
of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D
![](/pictures/MG/pdb/oi/7oib-MG-sphere_10.jpg) Mono view
![](/pictures/MG/pdb/oi/7oib-MG-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1608
b:41.1
occ:1.00
|
OP2
|
A:G341
|
2.2
|
11.3
|
1.0
|
P
|
A:G341
|
3.6
|
11.3
|
1.0
|
OP2
|
A:G339
|
4.1
|
16.0
|
1.0
|
OP1
|
A:G338
|
4.2
|
18.0
|
1.0
|
OP1
|
A:G341
|
4.2
|
11.3
|
1.0
|
NZ
|
i:LYS112
|
4.3
|
12.1
|
1.0
|
O
|
F:ALA118
|
4.4
|
11.1
|
1.0
|
O3'
|
A:U340
|
4.4
|
15.8
|
1.0
|
O
|
F:GLY122
|
4.5
|
41.1
|
1.0
|
OP1
|
A:G339
|
4.6
|
16.0
|
1.0
|
O5'
|
A:G341
|
4.6
|
11.3
|
1.0
|
OP2
|
A:G338
|
4.8
|
18.0
|
1.0
|
CA
|
F:GLY124
|
4.8
|
28.8
|
1.0
|
P
|
A:G338
|
4.8
|
18.0
|
1.0
|
P
|
A:G339
|
4.9
|
16.0
|
1.0
|
O
|
F:GLY123
|
4.9
|
41.1
|
1.0
|
C5'
|
A:G341
|
4.9
|
11.3
|
1.0
|
|
Reference:
J.Cheng,
O.Berninghausen,
R.Beckmann.
A Distinct Assembly Pathway of the Human 39S Late Pre-Mitoribosome. Nat Commun V. 12 4544 2021.
ISSN: ESSN 2041-1723
PubMed: 34315873
DOI: 10.1038/S41467-021-24818-X
Page generated: Fri Sep 24 15:33:51 2021
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