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:

Zinc (Zn) 1 atom

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

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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

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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

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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

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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

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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

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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

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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

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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 Dec 15 00:06:41 2020

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