Zinc in PDB 2uub: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin.

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin., PDB code: 2uub was solved by A.Weixlbaumer, F.V.Murphy, A.Dziergowska, A.Malkiewicz, F.A.P.Vendeix, P.F.Agris, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.99 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.440, 400.440, 173.360, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24.3

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin. also contains other interesting chemical elements:

Magnesium	(Mg)	218 atoms
Potassium	(K)	35 atoms

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin. (pdb code 2uub). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin., PDB code: 2uub:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:81.9 occ:1.00 SG D:CYS31 1.9 72.1 1.0 SG D:CYS9 2.3 52.4 1.0 SG D:CYS26 2.3 71.5 1.0 SG D:CYS12 3.4 60.5 1.0 O D:LEU19 3.7 81.4 1.0 CB D:CYS31 3.7 77.3 1.0 O D:CYS31 3.7 85.1 1.0 CB D:CYS9 3.9 58.8 1.0 CB D:CYS26 4.0 75.3 1.0 CA D:CYS31 4.2 81.1 1.0 CA D:CYS9 4.2 60.0 1.0 C D:CYS31 4.4 82.5 1.0 CB D:CYS12 4.6 61.3 1.0 CA D:CYS26 4.6 76.3 1.0 N D:LEU21 4.9 77.1 1.0 C D:LEU19 4.9 79.4 1.0

Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn102 b:69.7 occ:1.00 SG N:CYS43 1.9 48.1 1.0 SG N:CYS27 2.0 56.9 1.0 SG N:CYS40 2.5 60.7 1.0 SG N:CYS24 2.7 64.8 1.0 CB N:CYS27 2.8 58.2 1.0 CB N:CYS40 3.5 59.5 1.0 N N:CYS27 3.5 59.5 1.0 CB N:CYS24 3.6 63.6 1.0 CB N:CYS43 3.6 49.5 1.0 CA N:CYS27 3.7 59.0 1.0 CB N:ARG29 4.0 66.6 1.0 N N:CYS40 4.2 61.5 1.0 N N:CYS43 4.3 53.2 1.0 C N:ARG26 4.4 59.1 1.0 CA N:CYS40 4.4 59.7 1.0 C N:CYS27 4.5 59.3 1.0 N2 A:G1202 4.5 62.4 1.0 CA N:CYS43 4.5 51.2 1.0 CB N:ARG26 4.5 58.4 1.0 N3 A:G1202 4.7 61.5 1.0 N N:ARG29 4.7 65.7 1.0 CG N:ARG26 4.8 56.0 1.0 N N:GLY28 4.8 60.9 1.0 CG N:ARG29 4.8 65.0 1.0 CA N:ARG26 4.9 59.5 1.0 O2' A:G1202 4.9 61.2 1.0 O N:CYS40 5.0 58.3 1.0

A.Weixlbaumer, F.V.Murphy, A.Dziergowska, A.Malkiewicz, F.A.P.Vendeix, P.F.Agris, V.Ramakrishnan. Mechanism For Expanding the Decoding Capacity of Transfer Rnas By Modification of Uridines Nat.Struct.Mol.Biol. V. 14 498 2007.
ISSN: ISSN 1545-9993
PubMed: 17496902
DOI: 10.1038/NSMB1242