Magnesium in PDB 6swe: IC2 Head of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
Other elements in 6swe:
The structure of IC2 Head 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:
The binding sites of Magnesium atom in the IC2 Head of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi
(pdb code 6swe). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
IC2 Head of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi, PDB code: 6swe:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 6swe
Go back to
Magnesium Binding Sites List in 6swe
Magnesium binding site 1 out
of 8 in the IC2 Head 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 Head 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:Mg1401
b:19.7
occ:1.00
|
O2'
|
2:G1033
|
3.9
|
35.9
|
1.0
|
O6
|
2:G1029
|
4.3
|
32.5
|
1.0
|
N6
|
2:A1165
|
4.5
|
34.6
|
1.0
|
N7
|
2:G1029
|
4.8
|
32.5
|
1.0
|
N2
|
2:G1167
|
5.0
|
38.7
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 6swe
Go back to
Magnesium Binding Sites List in 6swe
Magnesium binding site 2 out
of 8 in the IC2 Head 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 Head 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:Mg1402
b:28.5
occ:1.00
|
OP2
|
2:G1172
|
1.9
|
27.1
|
1.0
|
OP1
|
2:G1171
|
2.1
|
30.2
|
1.0
|
OP1
|
2:C1019
|
2.5
|
29.7
|
1.0
|
P
|
2:G1172
|
3.1
|
27.1
|
1.0
|
P
|
2:G1171
|
3.4
|
30.2
|
1.0
|
OP1
|
2:G1172
|
3.5
|
27.1
|
1.0
|
P
|
2:C1019
|
3.7
|
29.7
|
1.0
|
OP2
|
2:G1171
|
3.8
|
30.2
|
1.0
|
O3'
|
2:G1171
|
3.9
|
30.2
|
1.0
|
OP2
|
2:C1019
|
4.0
|
29.7
|
1.0
|
C5'
|
2:G1171
|
4.0
|
30.2
|
1.0
|
O2'
|
2:A1170
|
4.2
|
31.2
|
1.0
|
O5'
|
2:G1171
|
4.2
|
30.2
|
1.0
|
C3'
|
2:G1171
|
4.3
|
30.2
|
1.0
|
O5'
|
2:G1172
|
4.4
|
27.1
|
1.0
|
O3'
|
2:A1170
|
4.6
|
31.2
|
1.0
|
O5'
|
2:C1019
|
4.6
|
29.7
|
1.0
|
C4'
|
2:G1171
|
4.7
|
30.2
|
1.0
|
O3'
|
2:G1018
|
4.9
|
28.0
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 6swe
Go back to
Magnesium Binding Sites List in 6swe
Magnesium binding site 3 out
of 8 in the IC2 Head 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 Head 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:Mg1403
b:27.2
occ:1.00
|
O6
|
2:G1196
|
2.0
|
32.7
|
1.0
|
O4
|
2:U953
|
2.2
|
23.9
|
1.0
|
OP2
|
2:C952
|
2.3
|
26.6
|
1.0
|
OP1
|
2:C951
|
2.7
|
30.0
|
1.0
|
C6
|
2:G1196
|
3.2
|
32.7
|
1.0
|
C4
|
2:U953
|
3.3
|
23.9
|
1.0
|
P
|
2:C952
|
3.7
|
26.6
|
1.0
|
C5
|
2:U953
|
3.9
|
23.9
|
1.0
|
P
|
2:C951
|
3.9
|
30.0
|
1.0
|
N1
|
2:G1196
|
4.0
|
32.7
|
1.0
|
O2
|
2:C954
|
4.1
|
26.7
|
1.0
|
O6
|
2:G1195
|
4.1
|
33.2
|
1.0
|
C5
|
2:G1196
|
4.2
|
32.7
|
1.0
|
N3
|
2:C954
|
4.3
|
26.7
|
1.0
|
OP1
|
2:C952
|
4.3
|
26.6
|
1.0
|
OP2
|
2:C951
|
4.4
|
30.0
|
1.0
|
N3
|
2:U953
|
4.4
|
23.9
|
1.0
|
C2
|
2:C954
|
4.5
|
26.7
|
1.0
|
N4
|
2:C1197
|
4.5
|
30.5
|
1.0
|
O3'
|
2:C951
|
4.5
|
30.0
|
1.0
|
O5'
|
2:C951
|
4.6
|
30.0
|
1.0
|
N7
|
2:G1196
|
4.6
|
32.7
|
1.0
|
C5'
|
2:C951
|
4.7
|
30.0
|
1.0
|
O5'
|
2:C952
|
4.7
|
26.6
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 6swe
Go back to
Magnesium Binding Sites List in 6swe
Magnesium binding site 4 out
of 8 in the IC2 Head 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 Head 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:Mg1404
b:21.3
occ:1.00
|
OP2
|
2:G1171
|
2.2
|
30.2
|
1.0
|
OP2
|
2:C1019
|
2.4
|
29.7
|
1.0
|
P
|
2:G1171
|
3.6
|
30.2
|
1.0
|
P
|
2:C1019
|
3.7
|
29.7
|
1.0
|
O3'
|
2:A1170
|
4.1
|
31.2
|
1.0
|
O3'
|
2:G1018
|
4.2
|
28.0
|
1.0
|
N7
|
2:G1172
|
4.3
|
27.1
|
1.0
|
OP1
|
2:G1171
|
4.4
|
30.2
|
1.0
|
OP1
|
2:C1019
|
4.4
|
29.7
|
1.0
|
O2'
|
2:G1018
|
4.5
|
28.0
|
1.0
|
O4
|
2:U1173
|
4.6
|
29.8
|
1.0
|
O5'
|
2:G1171
|
4.6
|
30.2
|
1.0
|
OP2
|
2:G1172
|
4.6
|
27.1
|
1.0
|
O5'
|
2:C1019
|
4.8
|
29.7
|
1.0
|
N7
|
2:G1171
|
4.9
|
30.2
|
1.0
|
C8
|
2:G1172
|
4.9
|
27.1
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 6swe
Go back to
Magnesium Binding Sites List in 6swe
Magnesium binding site 5 out
of 8 in the IC2 Head 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 Head 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:Mg1405
b:33.2
occ:1.00
|
OP1
|
2:U1198
|
2.3
|
24.4
|
1.0
|
P
|
2:U1198
|
3.8
|
24.4
|
1.0
|
OP1
|
2:G923
|
4.2
|
33.2
|
1.0
|
OP2
|
2:C924
|
4.4
|
33.2
|
1.0
|
O3'
|
2:C1197
|
4.4
|
30.5
|
1.0
|
OP2
|
2:U1198
|
4.5
|
24.4
|
1.0
|
N2
|
2:G947
|
4.5
|
23.2
|
1.0
|
O2'
|
2:C1197
|
4.6
|
30.5
|
1.0
|
N7
|
2:A949
|
4.6
|
24.8
|
1.0
|
C2'
|
2:C1197
|
4.6
|
30.5
|
1.0
|
N6
|
2:A949
|
4.7
|
24.8
|
1.0
|
O5'
|
2:U1198
|
4.8
|
24.4
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 6swe
Go back to
Magnesium Binding Sites List in 6swe
Magnesium binding site 6 out
of 8 in the IC2 Head 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 Head 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:Mg1406
b:23.9
occ:1.00
|
OP1
|
2:C1277
|
2.1
|
27.0
|
1.0
|
OP2
|
2:G1278
|
2.3
|
26.0
|
1.0
|
P
|
2:C1277
|
3.4
|
27.0
|
1.0
|
P
|
2:G1278
|
3.8
|
26.0
|
1.0
|
OP2
|
2:C1277
|
4.0
|
27.0
|
1.0
|
O5'
|
2:C1277
|
4.1
|
27.0
|
1.0
|
NH2
|
U:ARG43
|
4.1
|
23.2
|
1.0
|
N7
|
2:G1279
|
4.4
|
25.9
|
1.0
|
O5'
|
2:G1278
|
4.4
|
26.0
|
1.0
|
O3'
|
2:C1277
|
4.5
|
27.0
|
1.0
|
O2'
|
2:G1216
|
4.5
|
33.2
|
1.0
|
C5'
|
2:C1277
|
4.5
|
27.0
|
1.0
|
O3'
|
2:U1276
|
4.6
|
29.9
|
1.0
|
OE2
|
U:GLU42
|
4.7
|
25.3
|
1.0
|
C3'
|
2:C1277
|
4.7
|
27.0
|
1.0
|
OP1
|
2:G1278
|
4.8
|
26.0
|
1.0
|
OE1
|
U:GLU42
|
5.0
|
25.3
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 6swe
Go back to
Magnesium Binding Sites List in 6swe
Magnesium binding site 7 out
of 8 in the IC2 Head 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 Head 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:Mg1407
b:26.5
occ:1.00
|
OP2
|
2:C1294
|
2.3
|
24.5
|
1.0
|
O3'
|
2:A1293
|
2.9
|
30.0
|
1.0
|
O2'
|
2:C1296
|
3.0
|
31.6
|
1.0
|
OP2
|
2:U1295
|
3.0
|
28.5
|
1.0
|
OP2
|
2:G1297
|
3.1
|
33.2
|
1.0
|
P
|
2:C1294
|
3.2
|
24.5
|
1.0
|
O2'
|
2:A1293
|
3.5
|
30.0
|
1.0
|
O3'
|
2:C1296
|
3.7
|
31.6
|
1.0
|
C1'
|
2:A1293
|
3.8
|
30.0
|
1.0
|
P
|
2:G1297
|
3.9
|
33.2
|
1.0
|
C2'
|
2:A1293
|
4.0
|
30.0
|
1.0
|
C3'
|
2:A1293
|
4.0
|
30.0
|
1.0
|
O5'
|
2:C1294
|
4.1
|
24.5
|
1.0
|
C2'
|
2:C1296
|
4.1
|
31.6
|
1.0
|
N3
|
2:A1293
|
4.3
|
30.0
|
1.0
|
OP1
|
2:C1294
|
4.4
|
24.5
|
1.0
|
C3'
|
2:C1296
|
4.4
|
31.6
|
1.0
|
C8
|
2:G1297
|
4.4
|
33.2
|
1.0
|
O5'
|
2:G1297
|
4.4
|
33.2
|
1.0
|
P
|
2:U1295
|
4.4
|
28.5
|
1.0
|
N7
|
2:G1297
|
4.5
|
33.2
|
1.0
|
O4'
|
2:A1293
|
4.6
|
30.0
|
1.0
|
N9
|
2:A1293
|
4.7
|
30.0
|
1.0
|
C4'
|
2:A1293
|
4.7
|
30.0
|
1.0
|
C3'
|
2:C1294
|
4.8
|
24.5
|
1.0
|
C4
|
2:A1293
|
4.9
|
30.0
|
1.0
|
C5'
|
2:C1294
|
5.0
|
24.5
|
1.0
|
C1'
|
2:C1296
|
5.0
|
31.6
|
1.0
|
O3'
|
2:C1294
|
5.0
|
24.5
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 6swe
Go back to
Magnesium Binding Sites List in 6swe
Magnesium binding site 8 out
of 8 in the IC2 Head 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 Head 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
|
4:Mg101
b:47.7
occ:1.00
|
OP2
|
4:A38
|
2.3
|
55.5
|
1.0
|
P
|
4:A38
|
3.6
|
55.5
|
1.0
|
O6
|
4:G32
|
4.0
|
39.8
|
1.0
|
O5'
|
4:A38
|
4.1
|
55.5
|
1.0
|
N4
|
4:C40
|
4.1
|
56.0
|
1.0
|
N7
|
4:A39
|
4.2
|
54.6
|
1.0
|
OP1
|
4:A38
|
4.3
|
55.5
|
1.0
|
N6
|
4:A39
|
4.4
|
54.6
|
1.0
|
N4
|
4:OMC33
|
4.5
|
40.1
|
1.0
|
O3'
|
4:U37
|
4.7
|
48.5
|
1.0
|
N7
|
4:A38
|
4.8
|
55.5
|
1.0
|
C8
|
4:A38
|
4.8
|
55.5
|
1.0
|
C4
|
4:C40
|
5.0
|
56.0
|
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 18:26:49 2024
|