Zinc in PDB 4b3m: Crystal Structure of the 30S Ribosome in Complex with Compound 1

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 1, PDB code: 4b3m 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 / 2.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.650, 401.650, 175.260, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.1

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 1 also contains other interesting chemical elements:

Magnesium	(Mg)	240 atoms
Potassium	(K)	17 atoms

The binding sites of Zinc atom in the Crystal Structure of the 30S Ribosome in Complex with Compound 1 (pdb code 4b3m). 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 1, PDB code: 4b3m:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1209 b:0.9 occ:1.00 SG D:CYS30 2.0 78.0 1.0 SG D:CYS8 2.1 76.9 1.0 SG D:CYS25 2.4 90.5 1.0 SG D:CYS11 3.0 94.0 1.0 CB D:CYS30 3.5 78.0 1.0 O D:LEU18 3.5 0.9 1.0 CB D:CYS8 3.7 76.9 1.0 O D:CYS30 3.7 0.1 1.0 CA D:CYS30 3.9 0.1 1.0 CA D:CYS8 4.0 0.1 1.0 CB D:CYS25 4.1 90.5 1.0 C D:CYS30 4.2 0.1 1.0 CD D:LYS21 4.3 88.1 1.0 CB D:CYS11 4.5 94.0 1.0 C D:LEU18 4.7 0.9 1.0 CA D:CYS25 4.8 0.1 1.0 N D:LEU20 4.8 0.2 1.0 N D:CYS8 4.9 0.1 1.0 CB D:LYS21 4.9 88.1 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn1061 b:98.0 occ:1.00 SG N:CYS42 2.0 63.2 1.0 SG N:CYS26 2.1 48.4 1.0 CB N:CYS26 2.5 48.4 1.0 CB N:CYS42 2.8 63.2 1.0 N N:CYS26 3.2 92.2 1.0 CA N:CYS26 3.3 92.2 1.0 SG N:CYS39 3.4 77.2 1.0 N2 A:G1202 3.5 88.6 1.0 SG N:CYS23 3.6 88.7 1.0 CA N:CYS42 3.9 74.4 1.0 C N:ARG25 3.9 86.2 1.0 N N:CYS42 3.9 74.4 1.0 CB N:ARG25 4.0 78.5 1.0 CD N:ARG25 4.1 78.5 1.0 CG N:ARG25 4.2 78.5 1.0 N3 A:G1202 4.3 88.9 1.0 C2 A:G1202 4.4 88.9 1.0 CA N:ARG25 4.5 86.2 1.0 CB N:CYS39 4.5 77.2 1.0 O N:ARG25 4.6 86.2 1.0 C N:CYS26 4.7 92.2 1.0 CB N:CYS23 4.8 88.7 1.0 OE1 N:GLU45 4.8 81.8 1.0 N N:CYS39 4.9 83.4 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