Magnesium in PDB 7oi8: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A

Enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A

All present enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A:
3.1.1.29;

Other elements in 7oi8:

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A 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 3A (pdb code 7oi8). 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 3A, PDB code: 7oi8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 49 in 7oi8

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Magnesium binding site 1 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:41.4
occ:1.00
O E:GLN233 3.3 62.2 1.0
O E:THR234 3.7 56.8 1.0
NE2 E:HIS237 4.0 58.3 1.0
OP1 A:A792 4.2 37.0 1.0
CE1 E:HIS237 4.2 58.3 1.0
O E:ALA229 4.2 60.8 1.0
C E:GLN233 4.4 62.2 1.0
CA E:THR234 4.4 56.8 1.0
C E:THR234 4.4 56.8 1.0
OP1 A:A793 4.8 34.7 1.0
N E:THR234 4.8 56.8 1.0

Magnesium binding site 2 out of 49 in 7oi8

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


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:23.9
occ:1.00
O W:GLY44 3.4 28.4 1.0
N6 A:A1157 3.4 31.6 1.0
O6 A:G1158 3.6 22.8 1.0
N7 A:A1157 3.8 31.6 1.0
N7 A:G1158 3.8 22.8 1.0
C6 A:A1157 4.0 31.6 1.0
C5 A:A1157 4.1 31.6 1.0
C W:GLY44 4.3 28.4 1.0
N4 A:C1159 4.3 29.2 1.0
C6 A:G1158 4.4 22.8 1.0
CA W:GLY44 4.5 28.4 1.0
C5 A:G1158 4.5 22.8 1.0
C8 A:A1157 4.8 31.6 1.0
OG W:SER46 4.8 24.1 1.0
C8 A:G1158 5.0 22.8 1.0
O W:SER46 5.0 24.1 1.0

Magnesium binding site 3 out of 49 in 7oi8

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


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:24.6
occ:1.00
OD2 g:ASP99 2.7 24.6 1.0
OP2 A:G224 3.4 24.6 1.0
CG g:ASP99 3.8 24.6 1.0
N7 A:G224 4.0 24.6 1.0
O g:ILE100 4.3 23.0 1.0
OD1 g:ASP99 4.4 24.6 1.0
O2' A:A223 4.5 24.6 1.0
O3' A:A223 4.5 24.6 1.0
N g:ILE100 4.6 23.0 1.0
C8 A:G224 4.6 24.6 1.0
P A:G224 4.6 24.6 1.0
CA g:ASP99 4.8 24.6 1.0
CB g:ASP99 4.9 24.6 1.0

Magnesium binding site 4 out of 49 in 7oi8

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Magnesium binding site 4 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:17.6
occ:1.00
OP1 A:A1196 2.6 24.6 1.0
OP2 A:U1194 3.1 10.2 1.0
OP2 A:C1197 3.4 24.6 1.0
P A:A1196 4.0 24.6 1.0
C2 A:U1193 4.2 24.6 1.0
N3 A:U1193 4.3 24.6 1.0
C2' A:U1193 4.3 24.6 1.0
P A:C1197 4.4 24.6 1.0
P A:U1194 4.5 10.2 1.0
N1 A:U1193 4.5 24.6 1.0
O2 A:U1193 4.5 24.6 1.0
C3' A:U1193 4.6 24.6 1.0
C4 A:U1193 4.6 24.6 1.0
OP1 A:C1197 4.7 24.6 1.0
OP2 A:A1196 4.7 24.6 1.0
C6 A:U1193 4.8 24.6 1.0
O5' A:A1196 4.8 24.6 1.0
C5 A:U1193 4.9 24.6 1.0
C5' A:A1196 4.9 24.6 1.0
O5' A:U1194 4.9 10.2 1.0
O3' A:A1196 4.9 24.6 1.0
O3' A:C1195 4.9 2.6 1.0
C5' A:U1194 4.9 10.2 1.0
O3' A:U1193 5.0 24.6 1.0

Magnesium binding site 5 out of 49 in 7oi8

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Magnesium binding site 5 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:11.7
occ:1.00
O4 A:U88 2.4 24.6 1.0
OP2 A:A87 2.6 24.6 1.0
C4 A:U88 3.5 24.6 1.0
O4 A:U89 3.7 24.6 1.0
N6 A:A69 3.8 24.6 1.0
P A:A87 4.0 24.6 1.0
C5 A:U88 4.1 24.6 1.0
O5' A:A86 4.2 24.6 1.0
N1 A:A70 4.4 24.6 1.0
NH1 H:ARG69 4.5 20.4 1.0
N3 A:U88 4.6 24.6 1.0
OP1 A:A87 4.6 24.6 1.0
O3' A:A86 4.7 24.6 1.0
C4 A:U89 4.7 24.6 1.0
C3' A:A86 4.7 24.6 1.0
C2 A:A70 4.7 24.6 1.0
OP1 A:A86 4.8 24.6 1.0
OP2 A:A86 4.8 24.6 1.0
P A:A86 4.8 24.6 1.0
C5' A:A86 5.0 24.6 1.0

Magnesium binding site 6 out of 49 in 7oi8

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Magnesium binding site 6 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:16.1
occ:1.00
OP2 A:C56 2.1 24.6 1.0
OP1 A:C55 2.5 24.6 1.0
N7 A:A53 3.0 24.6 1.0
P A:C56 3.5 24.6 1.0
OP2 A:A52 3.6 24.6 1.0
C8 A:A53 3.9 24.6 1.0
P A:C55 4.0 24.6 1.0
N6 A:A53 4.0 24.6 1.0
N7 A:A52 4.0 24.6 1.0
C5 A:A53 4.1 24.6 1.0
O3' A:C55 4.1 24.6 1.0
OP1 A:C56 4.2 24.6 1.0
OP2 A:A53 4.3 24.6 1.0
C8 A:A52 4.3 24.6 1.0
C6 A:A53 4.5 24.6 1.0
C5' A:C55 4.5 24.6 1.0
O5' A:C56 4.6 24.6 1.0
O5' A:C55 4.7 24.6 1.0
O5' A:A52 4.7 24.6 1.0
C3' A:C55 4.7 24.6 1.0
P A:A52 4.8 24.6 1.0
OP2 A:C55 4.8 24.6 1.0
O3' A:A54 4.8 24.6 1.0
C5 A:A52 4.9 24.6 1.0

Magnesium binding site 7 out of 49 in 7oi8

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Magnesium binding site 7 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:24.6
occ:1.00
OP2 A:G106 2.1 24.6 1.0
P A:G106 3.4 24.6 1.0
O F:GLY149 3.4 6.6 1.0
OP1 A:G106 3.9 24.6 1.0
O F:GLY148 3.9 22.0 1.0
OP2 A:U108 4.0 24.6 1.0
O5' A:G106 4.2 24.6 1.0
C F:GLY148 4.2 22.0 1.0
OP2 A:A107 4.3 24.6 1.0
C F:GLY149 4.4 6.6 1.0
OP1 A:A105 4.4 24.6 1.0
O3' A:A105 4.5 24.6 1.0
CA F:GLY148 4.6 22.0 1.0
CG2 F:VAL120 4.6 17.7 1.0
N F:GLY149 4.8 6.6 1.0

Magnesium binding site 8 out of 49 in 7oi8

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Magnesium binding site 8 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:15.6
occ:1.00
OP2 A:A145 2.2 24.6 1.0
OP1 A:A144 2.2 24.6 1.0
P A:A145 3.5 24.6 1.0
P A:A144 3.6 24.6 1.0
O6 A:G146 4.1 24.6 1.0
OP1 A:A145 4.1 24.6 1.0
N7 A:G146 4.1 24.6 1.0
O5' A:A144 4.3 24.6 1.0
O5' A:A145 4.3 24.6 1.0
N4 A:C147 4.3 24.6 1.0
OP2 A:A144 4.5 24.6 1.0
O3' A:C143 4.6 44.1 1.0
O3' A:A144 4.6 24.6 1.0
C6 A:G146 4.8 24.6 1.0
C3' A:A144 4.8 24.6 1.0
C5 A:G146 4.9 24.6 1.0
C5' A:A144 4.9 24.6 1.0
N7 A:A145 4.9 24.6 1.0

Magnesium binding site 9 out of 49 in 7oi8

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Magnesium binding site 9 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:18.9
occ:1.00
O6 A:G106 2.1 24.6 1.0
OP1 A:A109 2.2 24.6 1.0
C6 A:G106 3.2 24.6 1.0
P A:A109 3.5 24.6 1.0
N7 A:G106 3.9 24.6 1.0
C5 A:G106 3.9 24.6 1.0
OP2 A:A109 4.0 24.6 1.0
N7 A:A105 4.1 24.6 1.0
OP2 A:A105 4.2 24.6 1.0
N1 A:G106 4.3 24.6 1.0
O5' A:A109 4.4 24.6 1.0
C5' A:A109 4.5 24.6 1.0
O3' A:U108 4.6 24.6 1.0
MG A:MG1641 4.6 16.5 1.0
N6 A:A105 4.7 24.6 1.0
OP1 A:A125 4.8 24.6 1.0
C8 A:A105 4.8 24.6 1.0
C5 A:A105 4.9 24.6 1.0

Magnesium binding site 10 out of 49 in 7oi8

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Magnesium binding site 10 out of 49 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 3A


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 3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:10.1
occ:1.00
OP2 A:G248 2.4 24.6 1.0
P A:G248 3.5 24.6 1.0
O5' A:G248 3.7 24.6 1.0
OP2 A:C249 3.7 24.6 1.0
O3' A:A247 3.8 24.6 1.0
O4 A:U250 4.1 38.8 1.0
O6 A:G311 4.4 24.6 1.0
O6 A:G312 4.5 14.4 1.0
OP1 A:G248 4.8 24.6 1.0
C5' A:G248 4.9 24.6 1.0
N4 A:C252 5.0 27.6 1.0
C4 A:U250 5.0 38.8 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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