Zinc in PDB 2zjp: Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans

The structure of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans, PDB code: 2zjp was solved by J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.T.Spahn, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.900, 408.900, 694.500, 90.00, 90.00, 90.00
R / Rfree (%)	30 / 34

The structure of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans also contains other interesting chemical elements:

Magnesium

(Mg)

35 atoms

The binding sites of Zinc atom in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans (pdb code 2zjp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans, PDB code: 2zjp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn38 b:0.3 occ:1.00 ND1 4:HIS32 1.7 0.9 1.0 SG 4:CYS14 2.2 0.3 1.0 CE1 4:HIS32 2.5 0.4 1.0 SG 4:CYS11 2.6 0.4 1.0 CG 4:HIS32 2.7 0.8 1.0 N 4:CYS11 3.1 0.7 1.0 CB 4:MET10 3.2 0.3 1.0 CB 4:HIS32 3.3 0.5 1.0 SG 4:CYS27 3.4 0.7 1.0 C 4:MET10 3.4 0.7 1.0 NE2 4:HIS32 3.5 0.7 1.0 CB 4:CYS11 3.5 0.1 1.0 CA 4:MET10 3.6 0.9 1.0 CD2 4:HIS32 3.6 0.8 1.0 N 4:MET10 3.8 0.7 1.0 CA 4:CYS11 3.8 0.7 1.0 CB 4:CYS27 3.9 0.1 1.0 CB 4:CYS14 4.0 0.4 1.0 O 4:MET10 4.2 0.2 1.0 N 4:CYS14 4.3 0.3 1.0 C 4:CYS11 4.4 0.3 1.0 CG 4:MET10 4.4 0.1 1.0 O 4:CYS11 4.5 0.5 1.0 CA 4:CYS14 4.6 1.0 1.0 CA 4:HIS32 4.7 0.4 1.0 C 4:LYS9 5.0 98.0 1.0

Zinc binding site 2 out of 2 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ Y:Zn61 b:0.9 occ:1.00 SG Y:CYS46 2.2 51.7 1.0 SG Y:CYS33 2.2 90.6 1.0 SG Y:CYS36 2.3 0.0 1.0 CB Y:CYS33 2.4 86.0 1.0 SG Y:CYS49 2.5 31.2 1.0 CB Y:CYS46 3.1 40.5 1.0 N Y:CYS36 3.7 0.5 1.0 N Y:GLY38 3.7 71.0 1.0 CB Y:CYS36 3.7 0.3 1.0 O Y:GLY38 3.8 63.7 1.0 CB Y:CYS49 3.9 29.9 1.0 CA Y:CYS33 3.9 83.3 1.0 N Y:HIS37 4.0 0.2 1.0 CA Y:CYS36 4.0 0.7 1.0 C Y:CYS36 4.1 0.5 1.0 N Y:CYS49 4.1 28.0 1.0 CA Y:GLY38 4.3 67.0 1.0 C Y:GLN35 4.4 0.5 1.0 CB Y:GLN35 4.5 0.1 1.0 C Y:GLY38 4.5 63.8 1.0 C Y:CYS33 4.5 83.6 1.0 CA Y:CYS46 4.5 39.2 1.0 N Y:GLN35 4.6 0.2 1.0 C Y:HIS37 4.6 0.4 1.0 CA Y:CYS49 4.7 27.5 1.0 N Y:CYS33 4.7 81.5 1.0 CA Y:HIS37 4.7 1.0 1.0 CA Y:GLN35 4.7 0.8 1.0 O Y:CYS36 4.8 0.6 1.0 CB Y:ASN48 4.9 46.9 1.0 O Y:CYS33 4.9 83.9 1.0

J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, P.Fucini. Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off By Thiostrepton and Micrococcin. Mol.Cell V. 30 26 2008.
ISSN: ISSN 1097-2765
PubMed: 18406324
DOI: 10.1016/J.MOLCEL.2008.01.009