Zinc in PDB 2e5l: A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine- Dalgarno Interaction

The structure of A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine- Dalgarno Interaction, PDB code: 2e5l was solved by T.Kaminishi, D.N.Wilson, C.Takemoto, J.M.Harms, M.Kawazoe, F.Schluenzen, K.Hanawa-Suetsugu, M.Shirouzu, P.Fucini, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	148.83 / 3.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	411.790, 411.790, 173.160, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 30.1

The binding sites of Zinc atom in the A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine- Dalgarno Interaction (pdb code 2e5l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine- Dalgarno Interaction, PDB code: 2e5l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine- Dalgarno Interaction


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine- Dalgarno Interaction within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn210 b:85.7 occ:1.00 SG D:CYS26 1.7 36.7 1.0 SG D:CYS9 1.8 57.0 1.0 SG D:CYS31 1.9 55.3 1.0 SG D:CYS12 2.0 51.9 1.0 CB D:CYS31 3.1 55.3 1.0 CA D:CYS31 3.4 0.1 1.0 CB D:CYS9 3.4 57.0 1.0 O D:CYS31 3.4 0.1 1.0 CB D:CYS26 3.5 36.7 1.0 C D:CYS31 3.8 0.1 1.0 CB D:CYS12 3.9 51.9 1.0 O D:LEU19 4.0 0.3 1.0 CA D:CYS9 4.2 75.7 1.0 CA D:CYS26 4.3 0.8 1.0 CB D:LYS22 4.8 0.7 1.0 N D:CYS9 4.8 75.7 1.0 N D:LYS22 4.8 89.9 1.0 N D:CYS31 4.9 0.1 1.0 N D:LEU21 4.9 0.4 1.0

Zinc binding site 2 out of 2 in the A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine- Dalgarno Interaction


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine- Dalgarno Interaction within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn62 b:87.4 occ:1.00 SG N:CYS40 2.0 71.9 1.0 SG N:CYS27 2.1 49.7 1.0 SG N:CYS43 2.2 56.5 1.0 SG N:CYS24 2.5 0.4 1.0 CB N:CYS27 2.5 49.7 1.0 CB N:CYS43 2.9 56.5 1.0 CB N:CYS24 3.0 0.4 1.0 N N:CYS27 3.1 76.6 1.0 CB N:CYS40 3.2 71.9 1.0 CA N:CYS27 3.3 76.6 1.0 N N:CYS40 3.4 72.8 1.0 CA N:CYS40 3.9 72.8 1.0 CA N:CYS43 4.1 58.3 1.0 N N:CYS43 4.2 58.3 1.0 CB N:ARG26 4.2 0.7 1.0 C N:ARG26 4.3 94.2 1.0 C N:CYS27 4.3 76.6 1.0 N N:GLY28 4.4 0.6 1.0 C N:LEU39 4.5 56.0 1.0 CA N:CYS24 4.5 85.4 1.0 O N:CYS40 4.6 72.8 1.0 CA N:LEU39 4.6 56.0 1.0 CA N:ARG26 4.7 94.2 1.0 C N:CYS40 4.7 72.8 1.0 CG N:ARG26 4.7 0.7 1.0 CB N:ARG29 4.7 0.8 1.0 CD N:ARG26 4.7 0.7 1.0 CB N:LEU39 4.7 0.3 1.0 N N:ARG26 4.8 94.2 1.0 N N:ARG29 4.9 76.3 1.0 C N:CYS24 5.0 85.4 1.0

T.Kaminishi, D.N.Wilson, C.Takemoto, J.M.Harms, M.Kawazoe, F.Schluenzen, K.Hanawa-Suetsugu, M.Shirouzu, P.Fucini, S.Yokoyama. A Snapshot of the 30S Ribosomal Subunit Capturing Mrna Via the Shine-Dalgarno Interaction Structure V. 15 289 2007.
ISSN: ISSN 0969-2126
PubMed: 17355865
DOI: 10.1016/J.STR.2006.12.008