Zinc in PDB 4b3t: Crystal Structure of the 30S Ribosome in Complex with Compound 39

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 39, PDB code: 4b3t was solved by C.L.Ng, K.Lang, D.Shcherbakov, T.Matt, D.Perez-Fernandez, R.Patak, M.Meyer, S.Duscha, R.Akbergenov, H.Boukari, P.Freihofer, I.Kudyba, M.S.K.Reddy, R.S.Nandurikar, V.Ramakrishnan, A.Vasella, E.C.Bottger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.730, 401.730, 173.910, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.3

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 39 also contains other interesting chemical elements:

Magnesium	(Mg)	219 atoms
Potassium	(K)	17 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of the 30S Ribosome in Complex with Compound 39 (pdb code 4b3t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the 30S Ribosome in Complex with Compound 39, PDB code: 4b3t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1209 b:0.0 occ:1.00 SG D:CYS30 2.1 80.3 1.0 SG D:CYS25 2.1 90.8 1.0 SG D:CYS8 2.2 82.2 1.0 SG D:CYS11 3.0 93.9 1.0 O D:LEU18 3.3 0.4 1.0 CB D:CYS30 3.5 80.3 1.0 CB D:CYS8 3.7 82.2 1.0 CB D:CYS25 3.8 90.8 1.0 O D:CYS30 3.9 0.3 1.0 CA D:CYS8 3.9 0.9 1.0 CA D:CYS30 4.1 0.3 1.0 CG D:LYS21 4.2 0.0 1.0 CB D:CYS11 4.4 93.9 1.0 C D:LEU18 4.5 0.4 1.0 CB D:LYS21 4.5 0.0 1.0 C D:CYS30 4.5 0.3 1.0 N D:LYS21 4.5 0.8 1.0 N D:LEU20 4.5 0.4 1.0 N D:CYS8 4.7 0.9 1.0 CA D:CYS25 4.7 0.4 1.0 CG1 D:VAL7 4.8 76.1 1.0 CA D:TYR19 5.0 0.8 1.0 CB D:LEU20 5.0 74.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn1061 b:0.2 occ:1.00 SG N:CYS42 1.9 45.8 1.0 SG N:CYS26 2.1 46.3 1.0 SG N:CYS23 2.2 80.5 1.0 SG N:CYS39 2.2 84.5 1.0 CB N:CYS39 2.8 84.5 1.0 CB N:CYS42 3.0 45.8 1.0 CB N:CYS23 3.1 80.5 1.0 N N:CYS39 3.2 75.1 1.0 CA N:CYS39 3.5 75.1 1.0 CB N:CYS26 3.5 46.3 1.0 CB N:ARG28 3.6 82.1 1.0 N N:CYS26 3.9 70.7 1.0 N N:CYS42 3.9 78.8 1.0 CA N:CYS42 4.1 78.8 1.0 C N:CYS39 4.2 75.1 1.0 O N:CYS39 4.2 75.1 1.0 CA N:CYS26 4.3 70.7 1.0 C N:LEU38 4.3 0.1 1.0 CG N:ARG28 4.4 82.1 1.0 CA N:CYS23 4.5 85.8 1.0 N N:ARG28 4.7 0.1 1.0 CA N:LEU38 4.7 0.1 1.0 CA N:ARG28 4.8 0.1 1.0 CB N:ARG25 4.9 71.7 1.0 C N:CYS26 4.9 70.7 1.0 C N:ARG25 4.9 67.1 1.0 CD2 N:LEU38 5.0 79.1 1.0

D.Perez-Fernandez, D.Shcherbakov, T.Matt, N.C.Leong, I.Kudyba, S.Duscha, H.Boukari, R.Patak, S.R.Dubakka, K.Lang, M.Meyer, R.Akbergenov, P.Freihofer, S.Vaddi, P.Thommes, V.Ramakrishnan, A.Vasella, E.C.Bottger. 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics Nat.Commun. V. 5 3112 2014.
ISSN: ESSN 2041-1723
PubMed: 24473108
DOI: 10.1038/NCOMMS4112