Zinc in PDB 7qh7: Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4

The structure of Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 also contains other interesting chemical elements:

Magnesium

(Mg)

50 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 (pdb code 7qh7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4, PDB code: 7qh7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn200 b:37.9 occ:1.00 SG 0:CYS123 2.3 6.7 1.0 SG 0:CYS126 2.3 8.7 1.0 SG 0:CYS110 2.3 11.8 1.0 CB 0:CYS123 2.6 6.7 1.0 CB 0:CYS110 3.4 11.8 1.0 CB 0:CYS113 3.4 13.4 1.0 SG 0:CYS113 3.4 13.4 1.0 CB 0:CYS126 3.8 8.7 1.0 ND1 0:HIS115 4.0 10.3 1.0 CA 0:CYS123 4.2 6.7 1.0 CA 0:CYS113 4.7 13.4 1.0 CE1 0:HIS115 4.8 10.3 1.0 CA 0:CYS110 4.8 11.8 1.0 N 0:CYS123 4.9 6.7 1.0 N 0:CYS126 4.9 8.7 1.0 C 0:CYS123 5.0 6.7 1.0 CG 0:HIS115 5.0 10.3 1.0 CA 0:CYS126 5.0 8.7 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ r:Zn301 b:34.1 occ:1.00 NZ r:LYS78 2.2 18.6 1.0 SG I:CYS64 2.3 21.4 1.0 SG r:CYS70 2.3 21.5 1.0 SG r:CYS108 2.3 20.2 1.0 OG I:SER63 2.5 22.2 1.0 CB r:CYS108 3.0 20.2 1.0 CB r:CYS70 3.1 21.5 1.0 CB I:SER63 3.4 22.2 1.0 CE r:LYS78 3.6 18.6 1.0 C I:SER63 3.7 22.2 1.0 N I:CYS64 3.7 21.4 1.0 CB I:CYS64 3.7 21.4 1.0 O I:SER63 3.9 22.2 1.0 CA I:CYS64 3.9 21.4 1.0 CG r:GLU111 4.0 18.2 1.0 CA I:SER63 4.2 22.2 1.0 CA r:CYS108 4.2 20.2 1.0 N r:CYS108 4.3 20.2 1.0 CA r:CYS70 4.5 21.5 1.0 CD r:LYS78 4.5 18.6 1.0 CB r:GLU111 4.7 18.2 1.0 N r:CYS70 4.8 21.5 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Human Mtlsu Assembly Intermediate Upon MRM2 Depletion - Class 4 within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn200 b:32.9 occ:1.00 NE2 4:HIS98 2.1 27.2 1.0 SG 4:CYS76 2.3 26.8 1.0 SG 4:CYS79 2.3 23.7 1.0 SG 4:CYS92 2.3 22.0 1.0 CD2 4:HIS98 2.6 27.2 1.0 CB 4:CYS79 3.1 23.7 1.0 CE1 4:HIS98 3.3 27.2 1.0 CB 4:CYS92 3.5 22.0 1.0 CB 4:CYS76 3.7 26.8 1.0 N 4:CYS79 3.7 23.7 1.0 N 4:CYS76 3.8 26.8 1.0 CG 4:HIS98 3.9 27.2 1.0 CA 4:CYS79 3.9 23.7 1.0 CA 4:CYS76 4.1 26.8 1.0 ND1 4:HIS98 4.2 27.2 1.0 O 4:THR94 4.3 23.5 1.0 O 4:CYS76 4.3 26.8 1.0 C 4:CYS76 4.3 26.8 1.0 O 4:HIS95 4.3 26.4 1.0 C 4:ASP78 4.5 25.7 1.0 CA 4:CYS92 4.7 22.0 1.0 CB 4:HIS95 4.7 26.4 1.0 N 4:ASP78 4.8 25.7 1.0 ND1 4:HIS95 5.0 26.4 1.0

P.Rebelo-Guiomar, S.Pellegrino, K.C.Dent, A.Sas-Chen, L.Miller-Fleming, C.Garone, L.Van Haute, J.F.Rogan, A.Dinan, A.E.Firth, B.Andrews, A.J.Whitworth, S.Schwartz, A.J.Warren, M.Minczuk. A Late-Stage Assembly Checkpoint of the Human Mitochondrial Ribosome Large Subunit. Nat Commun V. 13 929 2022.
ISSN: ESSN 2041-1723
PubMed: 35177605
DOI: 10.1038/S41467-022-28503-5