Zinc in PDB 1xnr: Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center

The structure of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center, PDB code: 1xnr was solved by F.V.Murphy, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.00 / 3.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.122, 401.122, 175.899, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 27.3

The structure of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center also contains other interesting chemical elements:

Magnesium

(Mg)

108 atoms

The binding sites of Zinc atom in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center (pdb code 1xnr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center, PDB code: 1xnr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


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 Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn306 b:65.5 occ:1.00 SG D:CYS31 2.3 56.2 1.0 SG D:CYS26 2.3 52.4 1.0 SG D:CYS9 2.4 29.6 1.0 SG D:CYS12 2.8 78.4 1.0 O D:LEU19 3.2 0.1 1.0 CB D:CYS26 3.6 52.4 1.0 CB D:CYS9 3.7 29.6 1.0 O D:CYS31 4.0 99.3 1.0 CB D:CYS12 4.0 78.4 1.0 CB D:CYS31 4.0 56.2 1.0 CA D:CYS9 4.1 0.1 1.0 CA D:CYS26 4.3 0.3 1.0 C D:LEU19 4.4 0.1 1.0 CA D:CYS31 4.7 99.3 1.0 C D:CYS31 4.7 99.3 1.0 N D:LEU19 4.9 0.1 1.0 N D:CYS9 5.0 0.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn307 b:65.5 occ:1.00 SG N:CYS43 2.1 55.0 1.0 SG N:CYS27 2.3 43.7 1.0 SG N:CYS40 2.6 46.7 1.0 SG N:CYS24 2.7 68.6 1.0 CB N:CYS27 2.7 43.7 1.0 CB N:CYS43 3.1 55.0 1.0 N N:CYS27 3.5 65.8 1.0 CA N:CYS27 3.7 65.8 1.0 N N:CYS43 3.9 58.3 1.0 CB N:CYS40 4.0 46.7 1.0 N2 A:G1202 4.0 65.2 1.0 CB N:CYS24 4.0 68.6 1.0 CA N:CYS43 4.1 58.3 1.0 N N:CYS40 4.4 79.2 1.0 C N:ARG26 4.5 95.1 1.0 N3 A:G1202 4.5 65.2 1.0 CG N:ARG26 4.6 57.8 1.0 CB N:ARG26 4.6 57.8 1.0 O N:CYS40 4.6 79.2 1.0 CA N:CYS40 4.7 79.2 1.0 C2 A:G1202 4.7 65.2 1.0 C N:CYS27 4.7 65.8 1.0 N N:GLY28 4.9 89.1 1.0 CB N:ARG29 4.9 84.9 1.0 NE N:ARG26 4.9 57.8 1.0 CB N:ILE42 5.0 50.3 1.0 CD2 N:LEU39 5.0 28.1 1.0 CA N:ARG26 5.0 95.1 1.0

F.V.Murphy, V.Ramakrishnan. Structure of A Purine-Purine Wobble Base Pair in the Decoding Center of the Ribosome. Nat.Struct.Mol.Biol. V. 11 1251 2004.
ISSN: ISSN 1545-9993
PubMed: 15558050
DOI: 10.1038/NSMB866