Magnesium in PDB 7oi6: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1

All present enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1:
3.1.1.29; 3.6.4.13;

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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 - 48;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1 (pdb code 7oi6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 48 binding sites of Magnesium where determined in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1, PDB code: 7oi6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:5.0 occ:1.00 O F:GLY148 2.0 5.0 1.0 OP1 A:G106 2.1 5.0 1.0 OP2 A:G106 2.2 5.0 1.0 O F:GLY149 2.3 5.0 1.0 P A:G106 2.5 5.0 1.0 C F:GLY148 2.9 5.0 1.0 C F:GLY149 3.3 5.0 1.0 N F:GLY149 3.6 5.0 1.0 O5' A:G106 3.6 5.0 1.0 O3' A:A105 3.8 5.0 1.0 CA F:GLY148 3.8 5.0 1.0 CA F:GLY149 3.8 5.0 1.0 OP1 A:A105 4.2 5.0 1.0 OP2 A:A107 4.3 5.0 1.0 N F:GLY150 4.5 5.0 1.0 OP2 A:U108 4.7 5.0 1.0 C5' A:G106 4.7 5.0 1.0 C3' A:A105 4.7 5.0 1.0 N F:GLY148 4.9 5.0 1.0 CA F:GLY150 4.9 5.0 1.0 OP2 A:A105 5.0 5.0 1.0

Magnesium binding site 2 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ g:Mg201 b:5.0 occ:1.00 N g:ILE100 2.1 7.1 1.0 CA g:ASP99 2.5 5.0 1.0 C g:ASP99 2.7 5.0 1.0 CB g:ASP99 3.2 5.0 1.0 O g:ILE100 3.3 7.1 1.0 CA g:ILE100 3.3 7.1 1.0 C g:ILE100 3.6 7.1 1.0 N g:ASP99 3.7 5.0 1.0 OP2 A:G224 3.8 3.1 1.0 O g:ASP99 3.8 5.0 1.0 O2' A:A223 4.0 2.4 1.0 CB g:ILE100 4.1 7.1 1.0 O g:LYS98 4.2 11.4 1.0 C g:LYS98 4.4 11.4 1.0 N g:THR101 4.7 5.0 1.0 O3' A:A223 4.9 2.4 1.0 N7 A:G224 5.0 3.1 1.0 P A:G224 5.0 3.1 1.0

Magnesium binding site 3 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:5.0 occ:1.00 OP1 A:A86 2.1 5.0 1.0 O5' A:A86 2.1 5.0 1.0 P A:A86 2.5 5.0 1.0 C5' A:A86 2.5 5.0 1.0 OP2 A:A86 3.2 5.0 1.0 OP2 A:A87 3.6 5.0 1.0 C4' A:A86 3.8 5.0 1.0 O3' A:A85 3.9 6.3 1.0 C3' A:A86 4.2 5.0 1.0 O3' A:A86 4.5 5.0 1.0 O4' A:A86 4.6 5.0 1.0 O4 A:U88 4.7 53.3 1.0 P A:A87 4.7 5.0 1.0

Magnesium binding site 4 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:67.8 occ:1.00 OP2 A:C56 2.1 120.7 1.0 OP2 A:C55 2.1 117.5 1.0 OP1 A:C55 2.2 117.5 1.0 P A:C55 2.4 117.5 1.0 N7 A:A53 2.7 99.4 1.0 C8 A:A53 2.8 99.4 1.0 OP2 A:A53 3.1 99.4 1.0 P A:C56 3.5 120.7 1.0 O3' A:A54 3.5 97.0 1.0 O5' A:C55 3.7 117.5 1.0 O5' A:A53 3.8 99.4 1.0 P A:A53 4.1 99.4 1.0 C5 A:A53 4.1 99.4 1.0 O3' A:C55 4.1 117.5 1.0 N9 A:A53 4.2 99.4 1.0 OP1 A:C56 4.4 120.7 1.0 O5' A:C56 4.5 120.7 1.0 C5' A:C55 4.5 117.5 1.0 C3' A:C55 4.5 117.5 1.0 C4 A:A53 4.8 99.4 1.0 C3' A:A54 4.8 97.0 1.0 C3' A:A53 4.9 99.4 1.0

Magnesium binding site 5 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:5.0 occ:1.00 OP1 A:A144 2.0 5.0 1.0 OP2 A:A145 3.1 5.0 1.0 P A:A144 3.5 5.0 1.0 O3' A:C143 4.0 5.0 1.0 O5' A:A144 4.3 5.0 1.0 P A:A145 4.4 5.0 1.0 N4 A:C147 4.4 5.0 1.0 OP2 A:A144 4.6 5.0 1.0 O5' A:A145 4.8 5.0 1.0 O6 A:G146 4.8 5.0 1.0

Magnesium binding site 6 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:5.0 occ:1.00 O6 A:G106 2.0 5.0 1.0 OP1 A:A109 2.0 5.0 1.0 OP2 A:A109 2.1 5.0 1.0 P A:A109 2.3 5.0 1.0 O5' A:A109 3.2 5.0 1.0 C6 A:G106 3.2 5.0 1.0 C5' A:A109 3.4 5.0 1.0 O3' A:U108 3.8 5.0 1.0 MG A:MG1636 3.9 6.1 1.0 N6 A:A105 3.9 5.0 1.0 C5 A:G106 4.1 5.0 1.0 N1 A:G106 4.2 5.0 1.0 N7 A:G106 4.2 5.0 1.0 N7 A:A105 4.6 5.0 1.0 C6 A:A105 4.6 5.0 1.0 C4' A:A109 4.8 5.0 1.0 C5 A:A105 4.8 5.0 1.0 C3' A:U108 4.9 5.0 1.0

Magnesium binding site 7 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:5.0 occ:1.00 OP2 A:G248 2.0 4.7 1.0 O5' A:G248 2.2 4.7 1.0 C5' A:G248 2.4 4.7 1.0 P A:G248 2.4 4.7 1.0 O3' A:A247 2.8 24.7 1.0 C4' A:G248 2.9 4.7 1.0 C3' A:G248 3.7 4.7 1.0 OP2 A:C249 3.7 17.3 1.0 OP1 A:G248 3.9 4.7 1.0 O3' A:G248 4.1 4.7 1.0 O4' A:G248 4.2 4.7 1.0 C3' A:A247 4.2 24.7 1.0 P A:C249 4.6 17.3 1.0 O4 A:U250 4.9 29.4 1.0 C4' A:A247 4.9 24.7 1.0 O2' A:A247 4.9 24.7 1.0 O6 A:G312 5.0 28.2 1.0

Magnesium binding site 8 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:10.3 occ:1.00 OP2 A:G341 2.0 5.0 1.0 O3' A:U340 2.1 5.0 1.0 P A:G341 2.5 5.0 1.0 O2' A:U340 2.9 5.0 1.0 C3' A:U340 3.1 5.0 1.0 OP1 A:G341 3.5 5.0 1.0 C2' A:U340 3.5 5.0 1.0 OP2 A:A342 3.6 5.0 1.0 O5' A:G341 3.6 5.0 1.0 C5' A:G341 4.2 5.0 1.0 C4' A:U340 4.4 5.0 1.0 O F:GLY123 4.4 17.8 1.0 C1' A:U340 4.4 5.0 1.0 OP2 A:G339 4.8 5.0 1.0 C4' A:G341 4.9 5.0 1.0

Magnesium binding site 9 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:23.5 occ:1.00 OP2 A:C593 2.6 59.5 1.0 O6 A:G358 2.9 59.4 1.0 C6 A:C593 3.2 59.5 1.0 O4' A:C593 3.5 59.5 1.0 C5' A:C593 3.6 59.5 1.0 C5 A:C593 3.7 59.5 1.0 P A:C593 3.8 59.5 1.0 C6 A:G358 4.0 59.4 1.0 N1 A:C593 4.2 59.5 1.0 C4' A:C593 4.2 59.5 1.0 O5' A:C593 4.2 59.5 1.0 OP1 A:C593 4.3 59.5 1.0 C1' A:C593 4.5 59.5 1.0 N1 A:G358 4.7 59.4 1.0 C5 A:G358 5.0 59.4 1.0

Magnesium binding site 10 out of 48 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:12.1 occ:1.00 OP1 A:U583 2.1 5.0 1.0 OP2 A:C582 2.1 5.0 1.0 OP1 A:C582 2.1 5.0 1.0 P A:C582 2.4 5.0 1.0 OP2 A:U583 2.6 5.0 1.0 P A:U583 2.7 5.0 1.0 O5' A:C582 3.3 5.0 1.0 O5' A:U583 3.8 5.0 1.0 O3' A:A581 3.8 5.0 1.0 O3' A:C582 4.0 5.0 1.0 C5' A:C582 4.2 5.0 1.0 O5' A:U471 4.3 32.5 1.0 OP1 A:U471 4.4 32.5 1.0 O5' A:A472 4.5 17.9 1.0 C3' A:C582 4.5 5.0 1.0 C4' A:C582 4.9 5.0 1.0 C3' A:A581 4.9 5.0 1.0

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