Zinc in PDB 4aqy: Structure of Ribosome-Apramycin Complexes

The structure of Structure of Ribosome-Apramycin Complexes, PDB code: 4aqy was solved by T.Matt, C.L.Ng, K.Lang, S.H.Sha, R.Akbergenov, D.Shcherbakov, M.Meyer, S.Duscha, J.Xie, S.R.Dubbaka, D.Perez-Fernandez, A.Vasella, V.Ramakrishnan, J.Schacht, E.C.Bottger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.180, 402.180, 175.000, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.5

The structure of Structure of Ribosome-Apramycin Complexes also contains other interesting chemical elements:

Magnesium	(Mg)	203 atoms
Potassium	(K)	15 atoms

The binding sites of Zinc atom in the Structure of Ribosome-Apramycin Complexes (pdb code 4aqy). 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 Ribosome-Apramycin Complexes, PDB code: 4aqy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1210 b:0.1 occ:1.00 SG D:CYS26 2.1 0.6 1.0 SG D:CYS31 2.2 0.4 1.0 SG D:CYS9 2.3 86.0 1.0 SG D:CYS12 2.3 0.6 1.0 O D:CYS31 3.2 0.7 1.0 O D:LEU19 3.6 0.0 1.0 CB D:CYS12 3.6 0.6 1.0 CB D:CYS26 3.7 0.6 1.0 CB D:CYS9 3.7 86.0 1.0 CB D:CYS31 3.7 0.4 1.0 CA D:CYS9 3.9 0.6 1.0 C D:CYS31 4.0 0.7 1.0 CA D:CYS31 4.1 0.7 1.0 CA D:CYS26 4.2 0.6 1.0 CG D:LYS22 4.5 0.6 1.0 N D:LEU21 4.5 0.0 1.0 C D:LEU19 4.6 0.0 1.0 CG D:LYS18 4.7 0.9 1.0 CD D:LYS22 4.8 0.6 1.0 N D:CYS9 4.9 0.6 1.0 CA D:TYR20 5.0 0.5 1.0

Zinc binding site 2 out of 2 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn1062 b:0.0 occ:1.00 SG N:CYS27 2.1 81.4 1.0 SG N:CYS43 2.1 66.6 1.0 SG N:CYS40 2.3 0.7 1.0 SG N:CYS24 2.6 1.0 1.0 CB N:CYS43 3.1 66.6 1.0 CB N:CYS40 3.2 0.7 1.0 CB N:CYS27 3.3 81.4 1.0 CB N:CYS24 3.6 1.0 1.0 N N:CYS40 3.7 0.1 1.0 CB N:ARG29 3.9 0.6 1.0 CA N:CYS40 4.0 0.1 1.0 N N:CYS43 4.1 0.1 1.0 CA N:CYS43 4.2 0.1 1.0 N N:CYS27 4.4 0.5 1.0 CA N:CYS27 4.4 0.5 1.0 N2 A:G1202 4.6 0.9 1.0 C N:CYS40 4.6 0.1 1.0 CG N:ARG26 4.6 1.0 1.0 O N:CYS40 4.7 0.1 1.0 N N:ARG29 4.7 0.8 1.0 CD2 N:LEU39 4.8 0.0 1.0 C N:LEU39 4.8 0.6 1.0 CG N:ARG29 4.9 0.6 1.0 CA N:CYS24 4.9 0.4 1.0 N3 A:G1202 4.9 0.6 1.0 CA N:ARG29 5.0 0.8 1.0 C N:CYS27 5.0 0.5 1.0 N N:GLY28 5.0 0.7 1.0

T.Matt, C.L.Ng, K.Lang, S.H.Sha, R.Akbergenov, D.Shcherbakov, M.Meyer, S.Duscha, J.Xie, S.R.Dubbaka, D.Perez-Fernandez, A.Vasella, V.Ramakrishnan, J.Schacht, E.C.Bottger. Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin. Proc.Natl.Acad.Sci.Usa V. 109 10984 2012.
ISSN: ISSN 0027-8424
PubMed: 22699498
DOI: 10.1073/PNAS.1204073109