Sodium in PDB 8z8u: Crystal Structure of Line-1 Ribozyme Mutant - C39U

The structure of Crystal Structure of Line-1 Ribozyme Mutant - C39U, PDB code: 8z8u was solved by Y.Ren, L.Huang, X.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.59 / 2.71
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.871, 94.871, 261.635, 90, 90, 120
R / Rfree (%)	21.9 / 24.6

The binding sites of Sodium atom in the Crystal Structure of Line-1 Ribozyme Mutant - C39U (pdb code 8z8u). 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 Line-1 Ribozyme Mutant - C39U, PDB code: 8z8u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Line-1 Ribozyme Mutant - C39U


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 Line-1 Ribozyme Mutant - C39U within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:44.8 occ:1.00 O A:HOH210 2.5 37.6 1.0 O2' B:C9 4.0 46.9 1.0 C1' A:C10 4.0 50.8 1.0 N2 B:G8 4.1 50.6 1.0 O4' A:C10 4.1 50.9 1.0 O2' A:C10 4.1 61.6 1.0 N6 A:A12 4.3 51.6 1.0 C6 A:A12 4.4 57.1 1.0 C1' B:C9 4.5 49.8 1.0 C5 A:A12 4.5 55.8 1.0 O4' B:C9 4.6 50.1 1.0 N7 A:A12 4.7 56.2 1.0 C2' A:C10 4.8 52.2 1.0 C4' A:C10 4.9 51.6 1.0 C2' B:C9 4.9 47.5 1.0 O2 A:C10 5.0 66.5 1.0 N1 A:A12 5.0 49.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Line-1 Ribozyme Mutant - C39U


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 Line-1 Ribozyme Mutant - C39U within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:62.7 occ:1.00 N4 B:C36 4.0 75.9 1.0 N4 B:C4 4.0 74.1 1.0 N6 B:A5 4.9 55.7 1.0

Y.Ren, X.Lin, W.Liao, X.Peng, J.Deng, Z.Zhang, J.Zhan, Y.Zhou, E.Westhof, D.M.J.Lilley, J.Wang, L.Huang. A General Strategy For Engineering Gu Base Pairs to Facilitate Rna Crystallization. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 39721592
DOI: 10.1093/NAR/GKAE1218