Zinc in PDB 6tpq: Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna

All present enzymatic activity of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna:
3.1.26.8;

The structure of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna also contains other interesting chemical elements:

Magnesium

(Mg)

219 atoms

The binding sites of Zinc atom in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna (pdb code 6tpq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna, PDB code: 6tpq:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ p:Zn101 b:0.7 occ:1.00 SG p:CYS30 2.2 1.0 1.0 SG p:CYS33 2.2 0.8 1.0 SG p:CYS43 2.2 0.2 1.0 CB p:CYS46 2.2 0.7 1.0 CB p:CYS30 2.9 1.0 1.0 CB p:CYS43 3.1 0.2 1.0 OG p:SER32 3.2 0.4 1.0 N p:CYS46 3.3 0.7 1.0 CA p:CYS46 3.3 0.7 1.0 CB p:CYS33 3.4 0.8 1.0 SG p:CYS46 3.5 0.7 1.0 N p:CYS33 3.9 0.8 1.0 OG p:SER48 4.0 0.8 1.0 CA p:CYS33 4.3 0.8 1.0 CA p:CYS30 4.3 1.0 1.0 C p:CYS46 4.4 0.7 1.0 O p:CYS30 4.4 1.0 1.0 O p:CYS43 4.5 0.2 1.0 CA p:CYS43 4.5 0.2 1.0 CB p:SER32 4.6 0.4 1.0 C p:ALA45 4.6 0.5 1.0 C p:CYS30 4.6 1.0 1.0 O p:SER48 4.7 0.8 1.0 C p:SER32 4.7 0.4 1.0 C p:CYS43 4.8 0.2 1.0 N p:GLY47 4.8 0.8 1.0 CB p:ALA45 4.9 0.5 1.0 N p:SER32 4.9 0.4 1.0

Zinc binding site 2 out of 3 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ q:Zn101 b:0.3 occ:1.00 OD2 q:ASP39 1.9 0.7 1.0 SG q:CYS12 2.2 0.9 1.0 SG q:CYS9 2.3 0.1 1.0 SG q:CYS36 2.3 0.3 1.0 CB q:CYS12 2.5 0.9 1.0 CG q:ASP39 2.8 0.7 1.0 CB q:CYS9 3.2 0.1 1.0 OD1 q:ASP39 3.2 0.7 1.0 N q:CYS12 3.3 0.9 1.0 OE1 q:GLU11 3.3 0.4 1.0 CA q:CYS12 3.5 0.9 1.0 CB q:CYS36 3.6 0.3 1.0 CB q:ASP39 4.0 0.7 1.0 C q:CYS12 4.4 0.9 1.0 C q:GLU11 4.5 0.4 1.0 CD q:GLU11 4.6 0.4 1.0 OG1 q:THR43 4.6 0.2 1.0 CA q:CYS9 4.6 0.1 1.0 CB q:GLU11 4.6 0.4 1.0 N q:ASP39 4.7 0.7 1.0 N q:GLY13 4.8 0.8 1.0 OE2 q:GLU14 4.9 0.3 1.0 CA q:CYS36 4.9 0.3 1.0 CA q:GLU11 4.9 0.4 1.0 CA q:ASP39 5.0 0.7 1.0 N q:GLU11 5.0 0.4 1.0

Zinc binding site 3 out of 3 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ t:Zn101 b:0.4 occ:1.00 ND1 t:HIS32 2.0 0.2 1.0 SG t:CYS14 2.3 0.1 1.0 SG t:CYS11 2.4 0.1 1.0 SG t:CYS27 2.4 0.7 1.0 CE1 t:HIS32 2.7 0.2 1.0 CB t:CYS11 3.0 0.1 1.0 CG t:HIS32 3.0 0.2 1.0 CB t:CYS27 3.3 0.7 1.0 CB t:HIS32 3.6 0.2 1.0 NE2 t:HIS32 3.8 0.2 1.0 CB t:CYS14 3.8 0.1 1.0 N t:CYS11 3.9 0.1 1.0 N t:CYS14 3.9 0.1 1.0 CD2 t:HIS32 4.0 0.2 1.0 CA t:CYS11 4.0 0.1 1.0 CA t:CYS14 4.0 0.1 1.0 C t:LYS13 4.5 0.6 1.0 C t:CYS11 4.7 0.1 1.0 CA t:CYS27 4.7 0.7 1.0 O t:LYS13 4.9 0.6 1.0 N t:LYS13 4.9 0.6 1.0

S.Oerum, T.Dendooven, M.Catala, L.Gilet, C.Degut, A.Trinquier, M.Bourguet, P.Barraud, S.Cianferani, B.F.Luisi, C.Condon, C.Tisne. Structures of B. Subtilis Maturation Rnases Captured on 50S Ribosome with Pre-Rrnas. Mol.Cell V. 80 227 2020.
ISSN: ISSN 1097-2765
PubMed: 32991829
DOI: 10.1016/J.MOLCEL.2020.09.008