Chlorine in PDB 5jvh: The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin

The structure of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin, PDB code: 5jvh was solved by A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 3.58
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.475, 407.380, 692.552, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.7

The structure of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin also contains other interesting chemical elements:

Magnesium

(Mg)

123 atoms

The binding sites of Chlorine atom in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin (pdb code 5jvh). 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 Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin, PDB code: 5jvh:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Cl2901 b:0.8 occ:1.00 CL1 X:6O12901 0.0 0.8 1.0 C02 X:6O12901 1.7 0.4 1.0 C01 X:6O12901 2.7 0.8 1.0 C03 X:6O12901 2.8 0.5 1.0 O01 X:6O12901 2.9 0.6 1.0 O03 X:6O12901 3.0 0.2 1.0 C07 X:6O12901 3.3 0.4 1.0 CG S:GLU179 3.5 0.7 1.0 OE2 S:GLU179 3.7 0.7 1.0 C06 X:6O12901 4.0 0.4 1.0 CD S:GLU179 4.0 0.5 1.0 C04 X:6O12901 4.1 0.1 1.0 C05 X:6O12901 4.6 0.6 1.0 NH1 J:ARG52 4.6 0.6 1.0 CD1 J:ILE53 4.8 82.0 1.0 CB S:GLU179 4.8 0.7 1.0

Chlorine binding site 2 out of 2 in the The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure Large Ribosomal Subunit (50S) of Deinococcus Radiodurans in Complex with Evernimicin within 5.0Å range: probe atom residue distance (Å) B Occ X:Cl2901 b:0.2 occ:1.00 CL2 X:6O12901 0.0 0.2 1.0 C06 X:6O12901 1.7 0.4 1.0 C01 X:6O12901 2.7 0.8 1.0 C05 X:6O12901 2.7 0.6 1.0 OG J:SER56 2.7 0.1 1.0 O01 X:6O12901 2.9 0.6 1.0 C08 X:6O12901 2.9 0.3 1.0 CB J:SER56 3.4 0.8 1.0 NH1 J:ARG60 3.7 0.4 1.0 C02 X:6O12901 4.0 0.4 1.0 C04 X:6O12901 4.0 0.1 1.0 CZ J:ARG60 4.1 0.8 1.0 NH2 J:ARG60 4.4 0.8 1.0 C03 X:6O12901 4.5 0.5 1.0 O S:GLU179 4.6 0.4 1.0 NE J:ARG60 4.6 0.2 1.0 CA J:SER56 4.6 0.4 1.0 C J:SER56 4.6 0.4 1.0 CA J:ILE53 4.8 85.0 1.0 O J:ILE53 4.8 86.2 1.0 N J:ARG57 4.8 0.7 1.0 NH1 J:ARG52 4.9 0.6 1.0 CD J:ARG60 5.0 0.2 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