Chlorine in PDB 5jvg: The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin

The structure of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin, PDB code: 5jvg was solved by M.Krupkin, I.Wekselman, D.Matzov, Z.Eyal, Y.Diskin Posner, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.55 / 3.43
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	170.034, 412.632, 698.142, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.3

The structure of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin also contains other interesting chemical elements:

Magnesium

(Mg)

446 atoms

The binding sites of Chlorine atom in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin (pdb code 5jvg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin, PDB code: 5jvg:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Cl2901 b:0.1 occ:1.00 CL2 X:6NO2901 0.0 0.1 1.0 C02 X:6NO2901 1.8 0.1 1.0 C01 X:6NO2901 2.7 0.1 1.0 C03 X:6NO2901 2.8 0.1 1.0 O01 X:6NO2901 3.0 0.1 1.0 O03 X:6NO2901 3.0 0.1 1.0 C07 X:6NO2901 3.3 0.1 1.0 C06 X:6NO2901 4.0 0.1 1.0 C04 X:6NO2901 4.1 0.1 1.0 C05 X:6NO2901 4.6 0.1 1.0 CD1 J:ILE53 4.9 72.8 1.0 NH1 J:ARG52 4.9 0.4 1.0

Chlorine binding site 2 out of 2 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Cl2901 b:0.1 occ:1.00 CL1 X:6NO2901 0.0 0.1 1.0 C06 X:6NO2901 1.7 0.1 1.0 C01 X:6NO2901 2.7 0.1 1.0 OG J:SER56 2.7 98.1 1.0 C05 X:6NO2901 2.7 0.1 1.0 O01 X:6NO2901 2.9 0.1 1.0 C08 X:6NO2901 2.9 0.1 1.0 CB J:SER56 3.3 93.8 1.0 NH1 J:ARG61 3.8 0.1 1.0 C02 X:6NO2901 4.0 0.1 1.0 C04 X:6NO2901 4.0 0.1 1.0 C J:SER56 4.3 95.8 1.0 N J:ARG57 4.3 0.9 1.0 CZ J:ARG61 4.3 0.7 1.0 O J:ILE53 4.3 72.1 1.0 CA J:ILE53 4.4 71.3 1.0 CA J:SER56 4.4 92.9 1.0 CG J:ARG61 4.4 0.8 1.0 C03 X:6NO2901 4.5 0.1 1.0 O J:SER56 4.7 99.1 1.0 NE J:ARG61 4.8 0.6 1.0 NH2 J:ARG61 4.8 0.3 1.0 CG2 J:ILE53 4.8 72.6 1.0 C J:ILE53 4.8 71.2 1.0 CA J:ARG57 4.9 0.4 1.0 CD J:ARG61 4.9 0.8 1.0

M.Krupkin, I.Wekselman, D.Matzov, Z.Eyal, Y.Diskin Posner, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath. Avilamycin and Evernimicin Induce Structural Changes in Rproteins UL16 and Ctc That Enhance the Inhibition of A-Site Trna Binding. Proc.Natl.Acad.Sci.Usa V. 113 E6796 2016.
ISSN: ESSN 1091-6490
PubMed: 27791159
DOI: 10.1073/PNAS.1614297113