Zinc in PDB 5vzj: Structure of A Twelve Component MPP6-Nuclear Rna Exosome Complex Bound to Rna

The structure of Structure of A Twelve Component MPP6-Nuclear Rna Exosome Complex Bound to Rna, PDB code: 5vzj was solved by C.D.Lima, E.V.Wasmuth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.25 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	141.090, 213.592, 225.909, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.6

The binding sites of Zinc atom in the Structure of A Twelve Component MPP6-Nuclear Rna Exosome Complex Bound to Rna (pdb code 5vzj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of A Twelve Component MPP6-Nuclear Rna Exosome Complex Bound to Rna, PDB code: 5vzj:

Zinc binding site 1 out of 1 in the Structure of A Twelve Component MPP6-Nuclear Rna Exosome Complex Bound to Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Twelve Component MPP6-Nuclear Rna Exosome Complex Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn2001 b:0.1 occ:1.00 NE2 K:HIS184 2.0 0.7 1.0 SG K:CYS52 2.3 78.5 1.0 SG K:CYS47 2.3 77.7 1.0 SG K:CYS55 2.3 76.5 1.0 CD2 K:HIS184 2.4 0.5 1.0 CB K:CYS47 3.0 76.9 1.0 CE1 K:HIS184 3.3 0.5 1.0 CB K:CYS52 3.3 79.3 1.0 CB K:CYS55 3.4 76.9 1.0 N K:CYS47 3.7 76.0 1.0 CG K:HIS184 3.7 0.0 1.0 CA K:CYS47 4.0 76.3 1.0 ND1 K:HIS184 4.1 0.9 1.0 N K:CYS55 4.3 0.1 1.0 CA K:CYS55 4.5 83.3 1.0 CA K:CYS52 4.6 80.4 1.0 CH2 K:TRP180 4.7 97.5 1.0 C K:PRO46 4.9 75.4 1.0 C K:CYS47 5.0 76.7 1.0

E.V.Wasmuth, J.C.Zinder, D.Zattas, M.Das, C.D.Lima. Structure and Reconstitution of Yeast MPP6-Nuclear Exosome Complexes Reveals That MPP6 Stimulates Rna Decay and Recruits the MTR4 Helicase. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28742025
DOI: 10.7554/ELIFE.29062