Zinc in PDB 4jv5: Crystal Structures of Pseudouridinilated Stop Codons with Asls

The structure of Crystal Structures of Pseudouridinilated Stop Codons with Asls, PDB code: 4jv5 was solved by I.S.Fernandez, C.L.Ng, A.C.Kelley, W.Guowei, Y.T.Yu, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 3.16
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.000, 401.000, 176.000, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.9

The structure of Crystal Structures of Pseudouridinilated Stop Codons with Asls also contains other interesting chemical elements:

Magnesium

(Mg)

17 atoms

The binding sites of Zinc atom in the Crystal Structures of Pseudouridinilated Stop Codons with Asls (pdb code 4jv5). 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 Structures of Pseudouridinilated Stop Codons with Asls, PDB code: 4jv5:

Zinc binding site 1 out of 1 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.3 occ:1.00 SG D:CYS9 0.5 0.9 1.0 CB D:CYS9 2.1 0.9 1.0 SG D:CYS12 2.3 0.4 1.0 SG D:CYS31 2.4 90.7 1.0 SG D:CYS26 2.4 0.5 1.0 CA D:CYS31 2.5 0.0 1.0 CB D:CYS12 2.6 0.2 1.0 CB D:CYS31 2.6 93.4 1.0 C D:CYS31 2.9 0.8 1.0 CA D:CYS9 3.2 0.9 1.0 O D:CYS31 3.3 0.9 1.0 N D:ALA32 3.5 0.8 1.0 CB D:CYS26 3.7 1.0 1.0 N D:CYS31 4.0 0.1 1.0 C D:CYS9 4.1 0.9 1.0 CA D:CYS12 4.2 0.4 1.0 CA D:CYS26 4.2 0.5 1.0 N D:CYS9 4.5 0.4 1.0 O D:LYS30 4.5 0.3 1.0 C D:LYS30 4.6 0.2 1.0 O D:CYS9 4.6 0.5 1.0 CA D:ALA32 4.7 0.2 1.0 CB D:ALA32 4.8 0.5 1.0 O D:CYS12 4.8 0.7 1.0 C D:CYS12 4.9 0.1 1.0 N D:ARG10 4.9 99.0 1.0 O D:LEU19 5.0 0.5 1.0 CB D:LYS22 5.0 0.4 1.0 N D:CYS12 5.0 0.8 1.0

I.S.Fernandez, C.L.Ng, A.C.Kelley, G.Wu, Y.T.Yu, V.Ramakrishnan. Unusual Base Pairing During the Decoding of A Stop Codon By the Ribosome. Nature V. 500 107 2013.
ISSN: ISSN 0028-0836
PubMed: 23812587
DOI: 10.1038/NATURE12302