Magnesium in PDB 7oi7: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2

Enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2

All present enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2:
3.1.1.29;

Other elements in 7oi7:

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 49;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2 (pdb code 7oi7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 49 binding sites of Magnesium where determined in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2, PDB code: 7oi7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 49 in 7oi7

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Magnesium binding site 1 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg201

b:47.9
occ:1.00
O W:GLY44 4.0 70.0 1.0
O W:SER46 4.4 75.6 1.0

Magnesium binding site 2 out of 49 in 7oi7

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Magnesium binding site 2 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
g:Mg201

b:10.6
occ:1.00
OD1 g:ASP99 2.7 25.8 1.0
CG g:ASP99 3.8 25.8 1.0
N7 A:G224 4.1 44.5 1.0
OD2 g:ASP99 4.3 25.8 1.0
OP2 A:G224 4.5 44.5 1.0
O2' A:A223 4.7 44.5 1.0
O g:ILE100 4.7 26.1 1.0
O6 A:G224 4.8 44.5 1.0
C8 A:G224 4.8 44.5 1.0
N4 A:C225 4.9 44.5 1.0

Magnesium binding site 3 out of 49 in 7oi7

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Magnesium binding site 3 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1631

b:59.7
occ:1.00
OP1 A:A1196 2.1 87.1 1.0
OP2 A:U1194 2.6 96.8 1.0
P A:A1196 3.1 87.1 1.0
OP2 A:A1196 3.2 87.1 1.0
OP2 A:C1197 3.6 74.0 1.0
O5' A:A1196 4.1 87.1 1.0
P A:U1194 4.1 96.8 1.0
C5' A:U1194 4.1 96.8 1.0
O3' A:C1195 4.3 101.5 1.0
C2' A:U1193 4.3 81.5 1.0
O5' A:U1194 4.6 96.8 1.0
C3' A:U1193 4.6 81.5 1.0
O3' A:U1193 4.7 81.5 1.0
C5' A:A1196 4.7 87.1 1.0
N6 A:A1199 4.8 66.2 1.0
P A:C1197 5.0 74.0 1.0

Magnesium binding site 4 out of 49 in 7oi7

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Magnesium binding site 4 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1632

b:24.9
occ:1.00
O4 A:U88 2.1 35.8 1.0
OP2 A:A87 2.7 31.5 1.0
C4 A:U88 3.2 35.8 1.0
O4 A:U89 3.2 34.6 1.0
N6 A:A69 3.7 23.6 1.0
C5 A:U88 3.9 35.8 1.0
P A:A87 4.1 31.5 1.0
C4 A:U89 4.2 34.6 1.0
N3 A:U88 4.2 35.8 1.0
N1 A:A70 4.3 4.4 1.0
OP1 A:A87 4.6 31.5 1.0
C2 A:A70 4.7 4.4 1.0
O5' A:A86 4.7 44.5 1.0
C5 A:U89 4.8 34.6 1.0
C6 A:A69 4.8 23.6 1.0

Magnesium binding site 5 out of 49 in 7oi7

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Magnesium binding site 5 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1633

b:72.5
occ:1.00
OP2 A:C56 2.7 100.3 1.0
OP1 A:C55 2.7 102.3 1.0
OP2 A:A52 2.9 79.8 1.0
N7 A:A53 3.1 89.4 1.0
O5' A:A52 3.6 79.8 1.0
C8 A:A52 3.6 79.8 1.0
N7 A:A52 3.8 79.8 1.0
OP2 A:A53 3.8 89.4 1.0
P A:A52 3.8 79.8 1.0
C8 A:A53 4.0 89.4 1.0
P A:C56 4.1 100.3 1.0
C5 A:A53 4.1 89.4 1.0
N6 A:A53 4.2 89.4 1.0
P A:C55 4.2 102.3 1.0
C3' A:A52 4.5 79.8 1.0
N9 A:A52 4.5 79.8 1.0
C6 A:A53 4.6 89.4 1.0
OP1 A:C56 4.6 100.3 1.0
C5 A:A52 4.8 79.8 1.0
C5' A:A52 4.9 79.8 1.0
OP1 A:A52 4.9 79.8 1.0
O3' A:A54 4.9 102.1 1.0
O3' A:C51 4.9 81.5 1.0
C3' A:C51 4.9 81.5 1.0
OP2 A:C55 5.0 102.3 1.0
O5' A:C56 5.0 100.3 1.0
C5' A:C55 5.0 102.3 1.0

Magnesium binding site 6 out of 49 in 7oi7

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Magnesium binding site 6 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1634

b:16.4
occ:1.00
OP2 A:G106 2.0 44.5 1.0
P A:G106 3.4 44.5 1.0
O F:GLY149 3.7 44.5 1.0
OP2 A:U108 3.9 44.5 1.0
O5' A:G106 4.1 44.5 1.0
OP1 A:G106 4.2 44.5 1.0
OP1 A:A105 4.2 44.5 1.0
OP2 A:A107 4.3 44.5 1.0
O F:GLY148 4.3 70.5 1.0
OP2 A:A105 4.5 44.5 1.0
C F:GLY148 4.5 70.5 1.0
O3' A:A105 4.5 44.5 1.0
CA F:GLY148 4.6 70.5 1.0
P A:A105 4.7 44.5 1.0
C3' A:A105 4.8 44.5 1.0
C F:GLY149 4.8 44.5 1.0
O5' A:A105 4.9 44.5 1.0
C8 A:G106 5.0 44.5 1.0

Magnesium binding site 7 out of 49 in 7oi7

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Magnesium binding site 7 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1635

b:28.6
occ:1.00
OP1 A:A144 2.1 15.8 1.0
OP2 A:A145 2.8 44.5 1.0
O6 A:G146 3.2 44.5 1.0
P A:A144 3.4 15.8 1.0
N7 A:G146 3.7 44.5 1.0
C6 A:G146 4.0 44.5 1.0
OP2 A:A144 4.1 15.8 1.0
N7 A:A145 4.1 44.5 1.0
O5' A:A144 4.2 15.8 1.0
N4 A:C147 4.2 44.5 1.0
C5 A:G146 4.2 44.5 1.0
P A:A145 4.3 44.5 1.0
C8 A:A145 4.5 44.5 1.0
O3' A:C143 4.6 63.9 1.0
O5' A:A145 4.8 44.5 1.0
C5' A:A144 4.9 15.8 1.0
C8 A:G146 4.9 44.5 1.0
C3' A:A144 4.9 15.8 1.0

Magnesium binding site 8 out of 49 in 7oi7

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Magnesium binding site 8 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1636

b:7.8
occ:1.00
O6 A:G106 2.5 44.5 1.0
OP1 A:A109 2.6 44.5 1.0
C6 A:G106 3.5 44.5 1.0
P A:A109 4.0 44.5 1.0
N7 A:A105 4.0 44.5 1.0
N7 A:G106 4.2 44.5 1.0
MG A:MG1669 4.2 43.2 1.0
C5 A:G106 4.2 44.5 1.0
OP2 A:A105 4.5 44.5 1.0
OP2 A:A109 4.5 44.5 1.0
N1 A:G106 4.6 44.5 1.0
N6 A:A105 4.6 44.5 1.0
OP1 A:A125 4.8 44.5 1.0
C5' A:U104 4.8 44.5 1.0
C5' A:A109 4.8 44.5 1.0
O5' A:A109 4.9 44.5 1.0
C8 A:A105 4.9 44.5 1.0
C5 A:A105 4.9 44.5 1.0

Magnesium binding site 9 out of 49 in 7oi7

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Magnesium binding site 9 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1637

b:19.6
occ:1.00
O5' A:G248 3.3 44.5 1.0
OP2 A:G248 3.3 44.5 1.0
P A:G248 3.7 44.5 1.0
OP2 A:C249 3.8 34.0 1.0
O3' A:A247 3.9 21.2 1.0
O4 A:U250 4.0 11.5 1.0
O6 A:G311 4.4 47.3 1.0
C5' A:G248 4.5 44.5 1.0
NZ 2:LYS59 4.5 29.0 1.0
O6 A:G312 4.6 8.0 1.0
C5 A:U250 4.7 11.5 1.0
C4 A:U250 4.7 11.5 1.0
N4 A:C252 4.7 30.2 1.0
C4' A:G248 4.9 44.5 1.0

Magnesium binding site 10 out of 49 in 7oi7

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Magnesium binding site 10 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 2


Mono view


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1638

b:10.2
occ:1.00
OP2 A:G341 2.1 44.5 1.0
P A:G341 3.5 44.5 1.0
O F:GLY123 4.1 17.6 1.0
O3' A:U340 4.2 44.5 1.0
OP1 A:G341 4.3 44.5 1.0
OP2 A:G339 4.3 35.3 1.0
OP1 A:G338 4.4 44.5 1.0
O F:ALA118 4.4 36.5 1.0
O5' A:G341 4.5 44.5 1.0
O F:GLY122 4.6 26.1 1.0
C5' A:G341 4.8 44.5 1.0
NZ i:LYS112 4.9 24.9 1.0
C F:GLY123 4.9 17.6 1.0
CA F:ALA118 4.9 36.5 1.0
CA F:GLY124 5.0 19.2 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 15:34:01 2021

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