Sodium in PDB 4p43: Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2)

The structure of Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2), PDB code: 4p43 was solved by J.Kondo, M.Koganei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.30 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.450, 31.690, 49.410, 90.00, 116.34, 90.00
R / Rfree (%)	24.6 / 27

The structure of Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2) (pdb code 4p43). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2), PDB code: 4p43:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:38.4 occ:1.00 O2' A:C9 2.8 32.9 1.0 O B:HOH207 3.4 39.5 1.0 O2 A:C9 3.4 32.2 1.0 O4' A:G10 3.4 33.3 1.0 C2' A:C9 3.6 33.5 1.0 C1' A:C9 3.9 32.6 1.0 C4' A:G10 4.3 34.8 1.0 C1' A:G10 4.3 31.7 1.0 C2 A:C9 4.5 32.9 1.0 N2 B:G39 4.5 25.9 1.0 C5' A:G10 4.6 35.2 1.0 N1 A:C9 4.7 32.9 1.0 N9 A:G10 4.9 29.8 1.0 O4' A:C9 5.0 34.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:35.7 occ:1.00 O2' B:C32 2.7 31.4 1.0 O A:HOH214 3.0 31.8 1.0 O2 B:C32 3.2 34.4 1.0 O A:HOH204 3.4 40.0 1.0 O4' B:G33 3.4 30.3 1.0 C2' B:C32 3.5 34.3 1.0 C1' B:C32 3.8 33.6 1.0 O B:HOH209 3.9 34.8 1.0 C2 B:C32 4.3 32.7 1.0 C4' B:G33 4.3 33.8 1.0 C1' B:G33 4.3 31.1 1.0 N2 A:G16 4.4 24.6 1.0 C5' B:G33 4.6 36.1 1.0 N1 B:C32 4.6 32.7 1.0 O A:HOH223 4.6 36.4 1.0 O4' B:C32 4.9 35.4 1.0 C3' B:C32 5.0 34.8 1.0 N9 B:G33 5.0 28.1 1.0

J.Kondo, M.Koganei. Crystal Structure of the Bacterial A1408U-Mutant Ribosomal Decoding Site (C2 Form 2) To Be Published.