Magnesium in PDB 7oie: Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B

Enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B

All present enzymatic activity of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B:
3.1.1.29;

Other elements in 7oie:

The structure of Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 7oie

Go back to Magnesium Binding Sites List in 7oie
Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B


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 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
g:Mg201

b:7.5
occ:1.00
OD1 g:ASP99 4.2 9.0 1.0
N7 A:G224 4.2 7.5 1.0
CB g:ASP99 4.2 9.0 1.0
CG g:ASP99 4.2 9.0 1.0
O2' A:A223 4.6 7.5 1.0
OP2 A:G224 4.7 7.5 1.0
CA g:ASP99 4.8 9.0 1.0
OD2 g:ASP99 4.8 9.0 1.0
C8 A:G224 4.9 7.5 1.0
O g:ILE100 5.0 7.5 1.0
N4 A:C225 5.0 7.5 1.0

Magnesium binding site 2 out of 2 in 7oie

Go back to Magnesium Binding Sites List in 7oie
Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Late Human 39S Mitoribosome Assembly Intermediates, State 5B


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 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:7.5
occ:1.00
O W:SER46 4.0 7.5 1.0
N4 A:C1159 4.4 7.5 1.0
O W:GLY44 4.6 7.5 1.0
OG W:SER46 4.7 7.5 1.0
O6 A:G1158 4.7 24.3 1.0
N7 A:G1158 4.9 24.3 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 15:33:57 2021

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