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Zinc in PDB 5c0w: Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates

Protein crystallography data

The structure of Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates, PDB code: 5c0w 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) 59.09 / 4.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 195.380, 195.380, 463.650, 90.00, 90.00, 120.00
R / Rfree (%) 27.1 / 28.4

Other elements in 5c0w:

The structure of Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates (pdb code 5c0w). 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 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates, PDB code: 5c0w:

Zinc binding site 1 out of 1 in 5c0w

Go back to Zinc Binding Sites List in 5c0w
Zinc binding site 1 out of 1 in the Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates


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 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1102

b:0.3
occ:1.00
NE2 J:HIS184 2.0 0.3 1.0
SG J:CYS52 2.3 0.1 1.0
SG J:CYS55 2.3 0.9 1.0
SG J:CYS47 2.3 0.5 1.0
CD2 J:HIS184 2.7 0.1 1.0
CB J:CYS47 3.2 1.0 1.0
CE1 J:HIS184 3.2 0.8 1.0
CB J:CYS52 3.3 0.5 1.0
CB J:CYS55 3.7 0.0 1.0
CG J:HIS184 4.0 0.7 1.0
ND1 J:HIS184 4.2 0.3 1.0
N J:CYS47 4.2 0.7 1.0
N J:CYS55 4.3 0.7 1.0
CA J:CYS47 4.3 0.0 1.0
CA J:CYS55 4.5 0.5 1.0
CA J:CYS52 4.6 1.0 1.0
CH2 J:TRP180 4.9 0.7 1.0

Reference:

D.L.Makino, B.Schuch, E.Stegmann, M.Baumgartner, C.Basquin, E.Conti. Rna Degradation Paths in A 12-Subunit Nuclear Exosome Complex. Nature V. 524 54 2015.
ISSN: ESSN 1476-4687
PubMed: 26222026
DOI: 10.1038/NATURE14865
Page generated: Wed Dec 16 06:05:39 2020

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