Magnesium in PDB 6swd: IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Other elements in 6swd:
The structure of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
25;
Binding sites:
The binding sites of Magnesium atom in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
(pdb code 6swd). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 25 binding sites of Magnesium where determined in the
IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi, PDB code: 6swd:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 1 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1601
b:19.7
occ:1.00
|
OP1
|
2:G28
|
2.4
|
21.7
|
1.0
|
P
|
2:G28
|
3.8
|
21.7
|
1.0
|
O2'
|
2:G533
|
4.1
|
21.7
|
1.0
|
N3
|
2:G533
|
4.4
|
21.7
|
1.0
|
OP2
|
2:U527
|
4.4
|
21.7
|
1.0
|
N1
|
2:A539
|
4.4
|
21.7
|
1.0
|
N2
|
2:G533
|
4.4
|
21.7
|
1.0
|
O3'
|
2:U27
|
4.5
|
21.7
|
1.0
|
OP2
|
2:G28
|
4.6
|
21.7
|
1.0
|
N6
|
2:A539
|
4.7
|
21.7
|
1.0
|
O4'
|
2:G534
|
4.9
|
21.7
|
1.0
|
O5'
|
2:G28
|
4.9
|
21.7
|
1.0
|
C2
|
2:G533
|
4.9
|
21.7
|
1.0
|
C2'
|
2:G533
|
4.9
|
21.7
|
1.0
|
O2'
|
2:G534
|
5.0
|
21.7
|
1.0
|
|
Magnesium binding site 2 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 2 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1602
b:10.6
occ:1.00
|
OP2
|
2:A540
|
2.3
|
19.0
|
1.0
|
OP2
|
2:A539
|
2.8
|
21.7
|
1.0
|
P
|
2:A540
|
3.7
|
19.0
|
1.0
|
OP1
|
2:U537
|
3.8
|
21.7
|
1.0
|
OP2
|
2:A538
|
4.0
|
21.7
|
1.0
|
P
|
2:A539
|
4.0
|
21.7
|
1.0
|
O5'
|
2:A540
|
4.4
|
19.0
|
1.0
|
OP1
|
2:A539
|
4.4
|
21.7
|
1.0
|
OP1
|
2:A540
|
4.4
|
19.0
|
1.0
|
C8
|
2:A540
|
4.7
|
19.0
|
1.0
|
C2
|
2:A786
|
4.7
|
24.4
|
1.0
|
P
|
2:U537
|
4.8
|
21.7
|
1.0
|
O5'
|
2:A539
|
4.8
|
21.7
|
1.0
|
N7
|
2:A540
|
4.8
|
19.0
|
1.0
|
OP2
|
2:U537
|
4.8
|
21.7
|
1.0
|
C5'
|
2:A538
|
4.9
|
21.7
|
1.0
|
O3'
|
2:A539
|
4.9
|
21.7
|
1.0
|
|
Magnesium binding site 3 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 3 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1603
b:14.6
occ:1.00
|
OP1
|
2:C39
|
2.7
|
21.7
|
1.0
|
P
|
2:C39
|
3.9
|
21.7
|
1.0
|
O4'
|
2:A374
|
4.1
|
16.6
|
1.0
|
O2'
|
2:A2M373
|
4.3
|
15.9
|
1.0
|
OP2
|
2:C39
|
4.4
|
21.7
|
1.0
|
O5'
|
2:C39
|
4.5
|
21.7
|
1.0
|
OP2
|
2:U40
|
4.7
|
13.8
|
1.0
|
CM'
|
2:A2M373
|
4.8
|
15.9
|
1.0
|
O3'
|
2:A2M373
|
4.9
|
15.9
|
1.0
|
C5'
|
2:C39
|
4.9
|
21.7
|
1.0
|
C4'
|
2:A374
|
4.9
|
16.6
|
1.0
|
|
Magnesium binding site 4 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 4 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1604
b:32.4
occ:1.00
|
OP2
|
2:A1370
|
2.3
|
75.2
|
1.0
|
P
|
2:A1370
|
3.6
|
75.2
|
1.0
|
OP1
|
2:A1370
|
4.3
|
75.2
|
1.0
|
O5'
|
2:A1370
|
4.3
|
75.2
|
1.0
|
OP1
|
2:C1369
|
4.4
|
66.9
|
1.0
|
OP2
|
2:C1369
|
4.4
|
66.9
|
1.0
|
O3'
|
2:C1369
|
4.7
|
66.9
|
1.0
|
P
|
2:C1369
|
4.8
|
66.9
|
1.0
|
C3'
|
2:C1369
|
4.8
|
66.9
|
1.0
|
OP1
|
2:G22
|
4.8
|
65.8
|
1.0
|
C5'
|
2:C1369
|
4.9
|
66.9
|
1.0
|
O5'
|
2:C1369
|
4.9
|
66.9
|
1.0
|
|
Magnesium binding site 5 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 5 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1605
b:11.5
occ:1.00
|
OP2
|
2:A574
|
2.1
|
21.7
|
1.0
|
P
|
2:A574
|
3.6
|
21.7
|
1.0
|
N3
|
2:C597
|
4.3
|
22.1
|
1.0
|
O5'
|
2:A574
|
4.4
|
21.7
|
1.0
|
OP1
|
2:A574
|
4.4
|
21.7
|
1.0
|
O3'
|
2:A573
|
4.5
|
21.7
|
1.0
|
OP1
|
2:A573
|
4.5
|
21.7
|
1.0
|
O2
|
2:C597
|
4.7
|
22.1
|
1.0
|
N7
|
2:A574
|
4.8
|
21.7
|
1.0
|
O6
|
2:G596
|
4.8
|
19.0
|
1.0
|
O4
|
2:U576
|
4.8
|
21.7
|
1.0
|
C3'
|
2:A573
|
4.8
|
21.7
|
1.0
|
C8
|
2:A574
|
4.9
|
21.7
|
1.0
|
N7
|
2:A575
|
4.9
|
21.7
|
1.0
|
C2
|
2:C597
|
5.0
|
22.1
|
1.0
|
|
Magnesium binding site 6 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 6 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1606
b:15.8
occ:1.00
|
OP1
|
2:A587
|
2.0
|
21.7
|
1.0
|
P
|
2:A587
|
3.4
|
21.7
|
1.0
|
O6
|
2:G582
|
4.0
|
20.2
|
1.0
|
OP2
|
2:A587
|
4.1
|
21.7
|
1.0
|
O5'
|
2:A587
|
4.3
|
21.7
|
1.0
|
O3'
|
2:C586
|
4.4
|
22.8
|
1.0
|
C5'
|
2:A587
|
4.6
|
21.7
|
1.0
|
O6
|
2:G583
|
4.8
|
19.5
|
1.0
|
C6
|
2:G582
|
4.8
|
20.2
|
1.0
|
N7
|
2:G582
|
4.9
|
20.2
|
1.0
|
|
Magnesium binding site 7 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 7 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1607
b:14.7
occ:1.00
|
OP2
|
2:G591
|
2.4
|
18.3
|
1.0
|
P
|
2:G591
|
3.8
|
18.3
|
1.0
|
OP1
|
2:U576
|
4.1
|
21.7
|
1.0
|
OP2
|
2:U576
|
4.4
|
21.7
|
1.0
|
OP2
|
2:4AC590
|
4.4
|
20.8
|
1.0
|
O5'
|
2:G591
|
4.6
|
18.3
|
1.0
|
C3'
|
2:4AC590
|
4.7
|
20.8
|
1.0
|
OP1
|
2:G591
|
4.7
|
18.3
|
1.0
|
O3'
|
2:4AC590
|
4.7
|
20.8
|
1.0
|
P
|
2:U576
|
4.8
|
21.7
|
1.0
|
O5'
|
2:4AC590
|
4.9
|
20.8
|
1.0
|
|
Magnesium binding site 8 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 8 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1608
b:13.5
occ:1.00
|
OP2
|
2:G727
|
1.8
|
18.1
|
1.0
|
P
|
2:G727
|
3.3
|
18.1
|
1.0
|
OP1
|
2:A726
|
3.4
|
24.6
|
1.0
|
O3'
|
2:A726
|
4.1
|
24.6
|
1.0
|
OP1
|
2:G727
|
4.2
|
18.1
|
1.0
|
O5'
|
2:G727
|
4.2
|
18.1
|
1.0
|
P
|
2:A726
|
4.4
|
24.6
|
1.0
|
O5'
|
2:A726
|
4.5
|
24.6
|
1.0
|
C5'
|
2:A726
|
4.6
|
24.6
|
1.0
|
CM7
|
2:4AC546
|
4.7
|
22.1
|
1.0
|
C3'
|
2:A726
|
4.7
|
24.6
|
1.0
|
N3
|
2:C542
|
4.7
|
20.8
|
1.0
|
O6
|
2:G728
|
4.8
|
24.2
|
1.0
|
N7
|
2:G728
|
4.9
|
24.2
|
1.0
|
OP2
|
2:A726
|
5.0
|
24.6
|
1.0
|
|
Magnesium binding site 9 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 9 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1609
b:15.8
occ:1.00
|
OP1
|
2:G1474
|
2.0
|
40.2
|
1.0
|
OP1
|
2:G1477
|
2.3
|
21.7
|
1.0
|
O1P
|
2:6MZ1469
|
2.4
|
23.4
|
1.0
|
P
|
2:G1474
|
3.5
|
40.2
|
1.0
|
P
|
2:G1477
|
3.5
|
21.7
|
1.0
|
O3'
|
2:A1476
|
3.6
|
21.7
|
1.0
|
P
|
2:6MZ1469
|
3.8
|
23.4
|
1.0
|
O2'
|
2:U1475
|
4.0
|
23.2
|
1.0
|
O5'
|
2:G1477
|
4.1
|
21.7
|
1.0
|
C3'
|
2:G1473
|
4.3
|
38.3
|
1.0
|
OP2
|
2:G1474
|
4.3
|
40.2
|
1.0
|
C5'
|
2:G1474
|
4.3
|
40.2
|
1.0
|
O3'
|
2:G1473
|
4.3
|
38.3
|
1.0
|
OP1
|
2:G1473
|
4.4
|
38.3
|
1.0
|
O5'
|
2:G1474
|
4.4
|
40.2
|
1.0
|
O5'
|
2:6MZ1469
|
4.4
|
23.4
|
1.0
|
O2P
|
2:6MZ1469
|
4.6
|
23.4
|
1.0
|
OP2
|
2:C1470
|
4.6
|
32.9
|
1.0
|
C5'
|
2:G1477
|
4.7
|
21.7
|
1.0
|
C2'
|
2:U1475
|
4.7
|
23.2
|
1.0
|
OP2
|
2:G1477
|
4.7
|
21.7
|
1.0
|
O3'
|
2:A1468
|
4.9
|
21.7
|
1.0
|
C3'
|
2:A1476
|
5.0
|
21.7
|
1.0
|
|
Magnesium binding site 10 out
of 25 in 6swd
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Magnesium Binding Sites List in 6swd
Magnesium binding site 10 out
of 25 in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1610
b:9.8
occ:1.00
|
OP2
|
2:C106
|
2.4
|
15.6
|
1.0
|
P
|
2:C106
|
3.8
|
15.6
|
1.0
|
O6
|
2:G107
|
4.1
|
18.1
|
1.0
|
OP1
|
2:C339
|
4.2
|
18.9
|
1.0
|
O6
|
2:G108
|
4.3
|
21.7
|
1.0
|
OP1
|
2:C106
|
4.3
|
15.6
|
1.0
|
C5
|
2:C339
|
4.4
|
18.9
|
1.0
|
OP2
|
2:A105
|
4.5
|
21.7
|
1.0
|
O5'
|
2:C106
|
4.7
|
15.6
|
1.0
|
O3'
|
2:A105
|
4.8
|
21.7
|
1.0
|
C4'
|
2:A105
|
4.8
|
21.7
|
1.0
|
N7
|
2:G107
|
4.8
|
18.1
|
1.0
|
N6
|
2:A324
|
4.9
|
21.7
|
1.0
|
C6
|
2:C339
|
5.0
|
18.9
|
1.0
|
|
Reference:
P.D.Coureux,
C.Lazennec-Schurdevin,
S.Bourcier,
Y.Mechulam,
E.Schmitt.
Cryo-Em Study of An Archaeal 30S Initiation Complex Gives Insights Into Evolution of Translation Initiation. Commun Biol V. 3 58 2020.
ISSN: ESSN 2399-3642
PubMed: 32029867
DOI: 10.1038/S42003-020-0780-0
Page generated: Tue Oct 1 18:26:52 2024
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