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Zinc in PDB 4ifd: Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna

Protein crystallography data

The structure of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna, PDB code: 4ifd was solved by D.L.Makino, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.64 / 2.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 154.090, 107.440, 150.460, 90.00, 110.63, 90.00
R / Rfree (%) 18.3 / 22.4

Other elements in 4ifd:

The structure of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna also contains other interesting chemical elements:

Bromine (Br) 10 atoms
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna (pdb code 4ifd). 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 Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna, PDB code: 4ifd:

Zinc binding site 1 out of 1 in 4ifd

Go back to Zinc Binding Sites List in 4ifd
Zinc binding site 1 out of 1 in the Crystal Structure of An 11-Subunit Eukaryotic 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 Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1106

b:62.5
occ:1.00
NE2 J:HIS184 2.0 53.9 1.0
SG J:CYS55 2.3 64.4 1.0
SG J:CYS52 2.3 61.7 1.0
SG J:CYS47 2.3 53.1 1.0
CD2 J:HIS184 2.7 58.5 1.0
CB J:CYS47 3.2 52.3 1.0
CE1 J:HIS184 3.2 61.5 1.0
CB J:CYS52 3.3 66.9 1.0
CB J:CYS55 3.6 70.2 1.0
CG J:HIS184 4.0 62.4 1.0
ND1 J:HIS184 4.2 62.9 1.0
N J:CYS47 4.2 53.2 1.0
N J:CYS55 4.2 68.1 1.0
CA J:CYS47 4.3 57.6 1.0
CA J:CYS55 4.5 67.3 1.0
CA J:CYS52 4.6 67.9 1.0
CH2 J:TRP180 4.9 51.9 1.0

Reference:

D.L.Makino, M.Baumgartner, E.Conti. Crystal Structure of An Rna-Bound 11-Subunit Eukaryotic Exosome Complex. Nature V. 495 70 2013.
ISSN: ISSN 0028-0836
PubMed: 23376952
DOI: 10.1038/NATURE11870
Page generated: Wed Dec 16 05:23:56 2020

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