Sodium in PDB 7eqj: Crystal Structure of E. Coli Valine Trna

The structure of Crystal Structure of E. Coli Valine Trna, PDB code: 7eqj was solved by J.Kim, H.Jeong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.49 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.541, 33.059, 131.797, 90, 98.15, 90
R / Rfree (%)	20.4 / 23.6

The structure of Crystal Structure of E. Coli Valine Trna also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of E. Coli Valine Trna (pdb code 7eqj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of E. Coli Valine Trna, PDB code: 7eqj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of E. Coli Valine Trna


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 E. Coli Valine Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:36.5 occ:1.00 O A:HOH262 2.2 37.3 1.0 O A:HOH260 2.2 35.5 1.0 O A:HOH236 2.2 35.1 1.0 O A:HOH259 2.3 42.6 1.0 O A:HOH213 2.4 31.6 1.0 O A:HOH206 2.4 31.3 1.0 OP2 A:U12 3.6 42.2 1.0 OP2 A:C11 4.0 41.0 1.0 O A:HOH216 4.0 34.1 1.0 OP2 A:A9 4.0 34.4 1.0 OP1 A:A9 4.1 36.2 1.0 OP2 A:U8 4.2 32.5 1.0 O A:HOH220 4.2 35.6 1.0 OP1 A:U8 4.2 31.0 1.0 C5 A:U12 4.5 32.5 1.0 O A:HOH235 4.5 34.4 1.0 P A:A9 4.6 33.4 1.0 O5' A:C11 4.7 41.3 1.0 P A:C11 4.7 38.7 1.0 P A:U8 4.7 35.7 1.0 OP1 A:C11 4.9 39.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of E. Coli Valine Trna


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 E. Coli Valine Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:46.2 occ:1.00 OP2 A:A21 2.4 35.5 1.0 OP1 A:G20 2.6 30.4 1.0 O A:HOH269 2.7 38.5 1.0 P A:A21 3.5 39.2 1.0 P A:G20 3.8 30.1 1.0 O5' A:A21 3.9 33.5 1.0 OP2 A:G20 4.1 29.1 1.0 OP1 A:A21 4.2 38.3 1.0 O5' A:G20 4.6 31.1 1.0 O A:HOH274 4.6 32.3 1.0 O3' A:G20 4.8 32.4 1.0 C5' A:G20 4.9 30.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of E. Coli Valine Trna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of E. Coli Valine Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:59.4 occ:1.00 OP2 A:A37 2.2 44.0 1.0 O A:HOH201 2.3 50.5 1.0 O A:HOH268 2.3 54.3 1.0 O A:HOH237 2.3 47.8 1.0 O A:HOH231 2.7 49.2 1.0 P A:A37 3.4 52.2 1.0 O5' A:A37 3.8 46.7 1.0 OP1 A:A37 4.1 49.7 1.0 O6 A:G39 4.1 59.5 1.0 OP2 A:A38 4.3 53.9 1.0 N7 A:A38 4.3 55.4 1.0 N4 A:C31 4.4 61.9 1.0 N7 A:A37 4.6 48.7 1.0 C8 A:A37 4.6 49.8 1.0 O3' A:C36 4.7 49.7 1.0 N6 A:A38 4.8 56.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of E. Coli Valine Trna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of E. Coli Valine Trna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:37.0 occ:1.00 OP2 B:A21 2.2 37.7 1.0 O B:HOH259 2.2 42.0 1.0 O B:HOH245 2.2 41.8 1.0 OP1 B:G20 2.6 31.9 1.0 P B:A21 3.3 37.4 1.0 P B:G20 3.8 30.3 1.0 OP1 B:A21 3.9 39.5 1.0 O5' B:A21 3.9 35.1 1.0 OP2 B:G20 4.2 29.0 1.0 O5' B:G20 4.5 32.9 1.0 O B:HOH271 4.5 35.1 1.0 O3' B:G20 4.6 33.1 1.0 C5' B:G20 4.7 33.5 1.0

H.Jeong, J.Kim. Unique Anticodon Loop Conformation with the Flipped-Out Wobble Nucleotide in the Crystal Structure of Unbound Trna Val . Rna V. 27 1330 2021.
ISSN: ESSN 1469-9001
PubMed: 34315814
DOI: 10.1261/RNA.078863.121