Sodium in PDB 7szu: Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6

The structure of Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6, PDB code: 7szu was solved by H.C.Rees, J.A.Piccirilli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.90 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.609, 96.992, 148.255, 90, 90, 90
R / Rfree (%)	21.9 / 26.3

The structure of Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6 (pdb code 7szu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6, PDB code: 7szu:

Sodium binding site 1 out of 1 in the Crystal Structure of Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6


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 Pepper Rna Aptamer in Complex with Hbc Ligand and Fab BL3-6 within 5.0Å range: probe atom residue distance (Å) B Occ R:Na104 b:61.3 occ:1.00 O R:HOH253 1.9 89.8 1.0 O R:HOH380 2.2 85.1 1.0 N7 R:G25 2.4 81.9 1.0 OP2 R:C24 2.5 92.4 1.0 O R:HOH323 2.6 86.6 1.0 C8 R:G25 3.2 86.1 1.0 H8 R:G25 3.2 101.4 1.0 H3' R:U23 3.3 97.6 1.0 P R:C24 3.4 110.2 1.0 OP1 R:C24 3.4 100.2 1.0 C5 R:G25 3.5 88.8 1.0 H2' R:U23 3.8 103.1 1.0 O6 R:G25 3.9 68.9 1.0 C6 R:G25 4.0 77.7 1.0 OP2 R:G25 4.0 102.8 1.0 C3' R:U23 4.1 82.7 1.0 O R:HOH315 4.2 67.6 1.0 O3' R:U23 4.2 95.0 1.0 N9 R:G25 4.4 89.7 1.0 C2' R:U23 4.4 87.3 1.0 H61 R:A26 4.4 84.7 1.0 N7 R:A26 4.5 83.3 1.0 C4 R:G25 4.5 84.2 1.0 O5' R:C24 4.7 101.7 1.0 H3' R:C24 4.8 116.2 1.0 O5' R:U23 4.8 81.8 1.0 O5' R:G25 4.9 100.4 1.0 N1 R:U23 5.0 76.0 1.0

H.C.Rees, W.Gogacz, N.S.Li, D.Koirala, J.A.Piccirilli. Structural Basis For Fluorescence Activation By Pepper Rna. Acs Chem.Biol. V. 17 1866 2022.
ISSN: ESSN 1554-8937
PubMed: 35759696
DOI: 10.1021/ACSCHEMBIO.2C00290