Zinc in PDB 6tnn: Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna

The structure of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna also contains other interesting chemical elements:

Magnesium

(Mg)

221 atoms

The binding sites of Zinc atom in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna (pdb code 6tnn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna, PDB code: 6tnn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ p:Zn101 b:88.0 occ:1.00 SG p:CYS33 2.3 56.1 1.0 SG p:CYS30 2.4 51.4 1.0 CB p:CYS46 2.4 54.0 1.0 SG p:CYS43 2.7 45.9 1.0 CB p:CYS30 3.3 51.4 1.0 CB p:CYS43 3.3 45.9 1.0 N p:CYS46 3.6 54.0 1.0 CA p:CYS46 3.6 54.0 1.0 SG p:CYS46 3.6 54.0 1.0 CB p:CYS33 3.6 56.1 1.0 N p:CYS33 4.2 56.1 1.0 C p:CYS46 4.5 54.0 1.0 CA p:CYS33 4.6 56.1 1.0 CB p:SER32 4.6 56.3 1.0 OG p:SER48 4.7 43.6 1.0 C p:ALA45 4.7 51.4 1.0 CA p:CYS30 4.7 51.4 1.0 N p:GLY47 4.8 48.9 1.0 CA p:CYS43 4.8 45.9 1.0 C p:SER32 4.9 56.3 1.0 O p:CYS30 5.0 51.4 1.0 O p:CYS43 5.0 45.9 1.0

Zinc binding site 2 out of 3 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ q:Zn101 b:71.5 occ:1.00 OD2 q:ASP39 2.0 50.3 1.0 SG q:CYS12 2.3 57.0 1.0 SG q:CYS36 2.3 42.6 1.0 SG q:CYS9 2.5 49.9 1.0 CG q:ASP39 3.1 50.3 1.0 CB q:CYS12 3.3 57.0 1.0 CB q:CYS9 3.4 49.9 1.0 CB q:CYS36 3.5 42.6 1.0 N q:CYS12 3.8 57.0 1.0 OD1 q:ASP39 3.9 50.3 1.0 CB q:ASP39 4.0 50.3 1.0 OE1 q:GLU11 4.1 59.2 1.0 CA q:CYS12 4.2 57.0 1.0 OG1 q:THR43 4.2 41.5 1.0 CG2 q:THR43 4.7 41.5 1.0 OE2 q:GLU14 4.8 50.4 1.0 N q:ASP39 4.8 50.3 1.0 CA q:CYS9 4.9 49.9 1.0 C q:GLU11 4.9 59.2 1.0 CA q:CYS36 4.9 42.6 1.0 CB q:GLU11 4.9 59.2 1.0 C q:CYS12 4.9 57.0 1.0 OD1 q:ASN16 4.9 39.9 1.0 N q:GLU11 5.0 59.2 1.0

Zinc binding site 3 out of 3 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ t:Zn101 b:91.1 occ:1.00 ND1 t:HIS32 2.1 44.0 1.0 SG t:CYS11 2.3 59.3 1.0 SG t:CYS27 2.4 55.4 1.0 SG t:CYS14 2.4 56.1 1.0 CG t:HIS32 3.0 44.0 1.0 CE1 t:HIS32 3.1 44.0 1.0 CB t:HIS32 3.3 44.0 1.0 CB t:CYS27 3.3 55.4 1.0 NZ t:LYS13 3.9 61.3 1.0 CB t:CYS11 4.0 59.3 1.0 CB t:CYS14 4.1 56.1 1.0 CD2 t:HIS32 4.2 44.0 1.0 NE2 t:HIS32 4.2 44.0 1.0 N t:CYS14 4.5 56.1 1.0 N t:CYS11 4.5 59.3 1.0 CA t:CYS14 4.5 56.1 1.0 CG t:LYS13 4.5 61.3 1.0 O t:ASN29 4.7 50.5 1.0 CE t:LYS13 4.7 61.3 1.0 CA t:CYS27 4.8 55.4 1.0 CA t:CYS11 4.8 59.3 1.0 CB t:ASN29 4.8 50.5 1.0 CA t:HIS32 4.8 44.0 1.0 C t:LYS13 4.9 61.3 1.0 N t:ASN29 5.0 50.5 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