Zinc in PDB 5ool: Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna

All present enzymatic activity of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna:
3.1.1.29;

The structure of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna also contains other interesting chemical elements:

Magnesium

(Mg)

92 atoms

The binding sites of Zinc atom in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna (pdb code 5ool). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna, PDB code: 5ool:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn301 b:1.0 occ:1.00 SG r:CYS70 2.1 61.9 1.0 CB r:CYS73 2.3 63.8 1.0 SG I:CYS64 2.4 26.6 1.0 SG r:CYS108 2.6 54.3 1.0 SG r:CYS73 3.1 63.8 1.0 CB r:CYS70 3.3 61.9 1.0 N r:CYS70 3.4 61.9 1.0 CA r:CYS73 3.6 63.8 1.0 CB I:CYS64 3.7 26.6 1.0 N r:CYS73 3.9 63.8 1.0 CA r:CYS70 3.9 61.9 1.0 CA I:CYS64 4.2 26.6 1.0 CB r:CYS108 4.4 54.3 1.0 C r:GLN69 4.5 66.9 1.0 CB r:GLN69 4.5 66.9 1.0 N r:GLN69 4.5 66.9 1.0 O r:CYS70 4.6 61.9 1.0 C r:CYS70 4.7 61.9 1.0 CA r:GLN69 4.7 66.9 1.0 C r:CYS73 4.8 63.8 1.0 CE r:LYS78 5.0 56.9 1.0

Zinc binding site 2 out of 3 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn200 b:63.6 occ:1.00 SG 0:CYS113 2.2 59.1 1.0 SG 0:CYS110 2.2 58.0 1.0 SG 0:CYS123 2.2 57.1 1.0 SG 0:CYS126 2.3 60.8 1.0 CB 0:CYS123 2.6 57.1 1.0 CB 0:CYS110 2.9 58.0 1.0 CB 0:CYS126 3.4 60.8 1.0 CB 0:CYS113 3.5 59.1 1.0 N 0:CYS126 4.0 60.8 1.0 CA 0:CYS123 4.1 57.1 1.0 N 0:CYS113 4.3 59.1 1.0 CA 0:CYS126 4.3 60.8 1.0 CA 0:CYS110 4.4 58.0 1.0 CA 0:CYS113 4.5 59.1 1.0 C 0:CYS123 4.6 57.1 1.0 CB 0:TYR125 4.8 60.6 1.0 O 0:CYS123 4.8 57.1 1.0 N 0:CYS123 4.9 57.1 1.0 O 0:HIS115 4.9 57.5 1.0 C 0:CYS110 5.0 58.0 1.0 C 0:TYR125 5.0 60.6 1.0

Zinc binding site 3 out of 3 in the Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Native Assembly Intermediate of the Human Mitochondrial Ribosome with Unfolded Interfacial Rrna within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn200 b:0.5 occ:1.00 ND1 4:HIS98 1.5 66.4 1.0 SG 4:CYS79 2.2 70.8 1.0 SG 4:CYS76 2.2 72.9 1.0 SG 4:CYS92 2.3 69.6 1.0 CE1 4:HIS98 2.3 66.4 1.0 CB 4:CYS76 2.4 72.9 1.0 CG 4:HIS98 2.7 66.4 1.0 CB 4:CYS92 3.1 69.6 1.0 CB 4:HIS98 3.4 66.4 1.0 NE2 4:HIS98 3.5 66.4 1.0 CA 4:CYS76 3.6 72.9 1.0 N 4:CYS76 3.6 72.9 1.0 CD2 4:HIS98 3.7 66.4 1.0 CB 4:CYS79 3.9 70.8 1.0 O 4:HIS95 4.0 68.7 1.0 CB 4:HIS95 4.0 68.7 1.0 N 4:CYS79 4.1 70.8 1.0 CA 4:CYS79 4.3 70.8 1.0 CA 4:CYS92 4.5 69.6 1.0 C 4:CYS76 4.6 72.9 1.0 C 4:ARG75 4.6 71.8 1.0 CG 4:HIS95 4.8 68.7 1.0 CD2 4:HIS95 4.8 68.7 1.0 CA 4:HIS95 4.8 68.7 1.0 C 4:ASP78 4.8 74.2 1.0 C 4:HIS95 4.8 68.7 1.0 N 4:HIS95 4.8 68.7 1.0 CA 4:HIS98 4.9 66.4 1.0

A.Brown, S.Rathore, D.Kimanius, S.Aibara, X.C.Bai, J.Rorbach, A.Amunts, V.Ramakrishnan. Structures of the Human Mitochondrial Ribosome in Native States of Assembly. Nat. Struct. Mol. Biol. V. 24 866 2017.
ISSN: ESSN 1545-9985
PubMed: 28892042
DOI: 10.1038/NSMB.3464