Zinc in PDB 6cao: Structure of the Ribosomal Decoding Complex at Ambient Temperature

The structure of Structure of the Ribosomal Decoding Complex at Ambient Temperature, PDB code: 6cao was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.22 / 3.45
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.300, 402.300, 176.400, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.2

The structure of Structure of the Ribosomal Decoding Complex at Ambient Temperature also contains other interesting chemical elements:

Magnesium	(Mg)	303 atoms
Potassium	(K)	37 atoms

The binding sites of Zinc atom in the Structure of the Ribosomal Decoding Complex at Ambient Temperature (pdb code 6cao). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Ribosomal Decoding Complex at Ambient Temperature, PDB code: 6cao:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:70.0 occ:1.00 SG D:CYS31 2.3 0.3 1.0 SG D:CYS26 2.3 1.0 1.0 SG D:CYS9 2.3 98.7 1.0 SG D:CYS12 2.3 90.2 1.0 O D:LEU19 3.6 0.5 1.0 CB D:CYS12 3.6 85.2 1.0 O D:CYS31 3.7 0.1 1.0 CB D:CYS9 3.7 94.2 1.0 CB D:CYS31 3.8 0.9 1.0 CB D:CYS26 3.8 0.3 1.0 CA D:CYS9 4.2 95.2 1.0 CA D:CYS26 4.2 0.8 1.0 CA D:CYS31 4.3 0.8 1.0 C D:CYS31 4.4 0.4 1.0 NZ D:LYS18 4.5 0.5 1.0 C D:LEU19 4.7 0.2 1.0 CB D:MET33 4.8 99.4 1.0 N D:CYS9 5.0 90.9 1.0

Zinc binding site 2 out of 2 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:0.7 occ:1.00 SG N:CYS40 2.3 64.9 1.0 SG N:CYS27 2.3 75.1 1.0 SG N:CYS43 2.3 66.4 1.0 SG N:CYS24 2.3 75.1 1.0 CB N:CYS40 3.2 65.8 1.0 CB N:CYS27 3.2 76.0 1.0 CB N:CYS43 3.3 66.6 1.0 CB N:CYS24 3.3 73.4 1.0 N N:CYS27 3.7 85.8 1.0 N N:CYS40 3.7 74.2 1.0 N N:CYS43 3.9 64.7 1.0 CA N:CYS27 4.0 84.2 1.0 CA N:CYS40 4.0 73.1 1.0 CA N:CYS43 4.2 65.8 1.0 CB N:ARG29 4.5 74.4 1.0 N2 A:G1202 4.6 99.4 1.0 N N:GLY28 4.6 86.0 1.0 C N:CYS27 4.6 86.6 1.0 C N:CYS40 4.7 72.2 1.0 N N:ARG29 4.7 82.1 1.0 CA N:CYS24 4.7 75.3 1.0 CB N:ARG26 4.7 92.8 1.0 N3 A:G1202 4.8 89.4 1.0 C N:ARG26 4.8 90.4 1.0 C N:LEU39 4.9 69.4 1.0 N N:ARG26 5.0 0.1 1.0

E.H.Dao, F.Poitevin, R.G.Sierra, C.Gati, Y.Rao, H.I.Ciftci, F.Aksit, A.Mcgurk, T.Obrinski, P.Mgbam, B.Hayes, C.De Lichtenberg, F.Pardo-Avila, N.Corsepius, L.Zhang, M.H.Seaberg, M.S.Hunter, M.Liang, J.E.Koglin, S.Wakatsuki, H.Demirci. Structure of the 30S Ribosomal Decoding Complex at Ambient Temperature. Rna V. 24 1667 2018.
ISSN: ESSN 1469-9001
PubMed: 30139800
DOI: 10.1261/RNA.067660.118