Zinc in PDB 6c0f: Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2)

All present enzymatic activity of Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2):
3.6.4.13;

The binding sites of Zinc atom in the Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2) (pdb code 6c0f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2), PDB code: 6c0f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:40.6 occ:1.00 SG D:CYS38 2.1 41.0 1.0 SG D:CYS28 2.1 49.0 1.0 SG D:CYS43 2.1 41.3 1.0 SG D:CYS15 2.1 48.8 1.0 CB D:CYS38 3.4 41.0 1.0 CB D:CYS15 3.6 48.8 1.0 CG2 D:ILE10 3.9 44.5 1.0 CB D:CYS28 3.9 49.0 1.0 ND2 D:ASN30 3.9 53.0 1.0 CB D:CYS43 3.9 41.3 1.0 CA D:CYS38 4.3 43.8 1.0 CB D:ARG18 4.3 51.3 1.0 N D:ARG18 4.7 51.3 1.0 CA D:CYS28 4.7 46.8 1.0 CA D:CYS43 4.7 41.5 1.0 CA D:ARG18 4.8 51.3 1.0 CD D:ARG18 4.9 51.3 1.0 CG D:ARG18 4.9 51.3 1.0 C D:CYS38 5.0 43.8 1.0

Zinc binding site 2 out of 3 in the Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2) within 5.0Å range: probe atom residue distance (Å) B Occ j:Zn101 b:77.6 occ:1.00 SG j:CYS37 2.1 76.1 1.0 SG j:CYS34 2.2 77.2 1.0 SG j:CYS22 2.2 80.7 1.0 SG j:CYS19 2.4 76.2 1.0 CB j:CYS34 3.0 77.2 1.0 CB j:CYS37 3.1 76.1 1.0 CB j:CYS19 3.1 76.2 1.0 CB j:CYS22 3.5 80.7 1.0 N j:CYS37 3.5 75.8 1.0 N j:CYS22 3.7 78.2 1.0 CA j:CYS37 3.8 75.8 1.0 CA j:CYS22 4.2 78.2 1.0 CB j:TYR39 4.3 74.2 1.0 CB j:ARG21 4.4 78.3 1.0 N j:GLY38 4.5 74.9 1.0 CA j:CYS34 4.5 79.9 1.0 C j:CYS37 4.5 75.8 1.0 CB j:SER36 4.5 74.7 1.0 N j:TYR39 4.5 73.3 1.0 CA j:CYS19 4.6 78.6 1.0 C j:SER36 4.7 83.8 1.0 C j:ARG21 4.8 79.1 1.0 N j:GLY23 4.8 75.2 1.0 C j:CYS22 4.9 78.2 1.0 N j:ARG21 4.9 79.1 1.0 CA j:ARG21 5.0 79.1 1.0 CA j:SER36 5.0 83.8 1.0

Zinc binding site 3 out of 3 in the Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Nucleolar Pre-60S Ribosomal Subunit (State 2) within 5.0Å range: probe atom residue distance (Å) B Occ u:Zn300 b:0.7 occ:1.00 SG u:CYS36 2.1 0.4 1.0 SG u:CYS9 2.1 0.9 1.0 SG u:CYS32 2.1 0.5 1.0 SG u:CYS6 2.1 0.2 1.0 CB u:CYS9 2.8 0.9 1.0 CB u:CYS36 3.3 0.4 1.0 CB u:CYS6 3.4 0.2 1.0 CB u:CYS32 3.4 0.5 1.0 N u:CYS32 3.5 0.5 1.0 N u:CYS9 3.5 0.8 1.0 CA u:CYS9 3.7 0.8 1.0 OG u:SER11 3.7 0.9 1.0 CA u:CYS32 3.9 0.5 1.0 N u:ARG33 4.3 0.4 1.0 NH2 u:ARG33 4.4 0.8 1.0 C u:PHE8 4.4 0.8 1.0 CG u:ARG33 4.5 0.8 1.0 C u:CYS32 4.5 0.5 1.0 C u:PHE31 4.6 0.2 1.0 CZ u:ARG33 4.6 0.8 1.0 CA u:CYS36 4.7 0.9 1.0 CB u:PHE8 4.7 0.6 1.0 CA u:CYS6 4.8 0.5 1.0 CA u:PHE31 4.8 0.2 1.0 N u:PHE8 4.9 0.8 1.0 CA u:PHE8 4.9 0.8 1.0 CB u:SER11 4.9 0.9 1.0 C u:CYS9 4.9 0.8 1.0

Z.A.Sanghai, L.Miller, K.R.Molloy, J.Barandun, M.Hunziker, M.Chaker-Margot, J.Wang, B.T.Chait, S.Klinge. Modular Assembly of the Nucleolar Pre-60S Ribosomal Subunit. Nature V. 556 126 2018.
ISSN: ESSN 1476-4687
PubMed: 29512650
DOI: 10.1038/NATURE26156