Magnesium in PDB 9l6x: Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna

The structure of Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna, PDB code: 9l6x was solved by T.Teramoto, M.Nakashima, K.Fukunaga, Y.Yokobayashi, Y.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.94 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.87, 91.88, 61.21, 90, 106.11, 90
R / Rfree (%)	19.9 / 23.9

The binding sites of Magnesium atom in the Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna (pdb code 9l6x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna, PDB code: 9l6x:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:41.1 occ:1.00 OP2 B:G4 3.2 37.0 1.0 OP2 B:U3 4.0 45.0 1.0 OP1 B:U3 4.0 47.5 1.0 P B:U3 4.2 44.3 1.0 O5' B:U3 4.3 45.2 1.0 O B:HOH226 4.5 34.7 1.0 P B:G4 4.5 44.0 1.0 O B:HOH271 4.8 41.0 1.0 O B:HOH206 4.8 32.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:46.7 occ:1.00 OP1 B:G2 2.1 49.0 1.0 OP2 B:U3 2.8 45.0 1.0 P B:G2 2.9 56.3 1.0 O5' B:G2 3.3 44.3 1.0 OP2 B:G2 3.3 54.5 1.0 C5' B:G2 3.7 45.8 1.0 P B:U3 3.8 44.3 1.0 O B:HOH248 3.9 43.4 1.0 O3' B:G2 4.1 45.8 1.0 OP1 B:U3 4.3 47.5 1.0 O3' B:G1 4.4 50.7 1.0 C3' B:G2 4.4 45.9 1.0 C4' B:G2 4.6 44.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the L7AE Derivative Protein LS4 in Complex with Its Co-Evolved Target CS1 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:42.3 occ:1.00 O B:HOH271 2.0 41.0 1.0 O C:HOH243 2.2 43.8 1.0 O B:HOH263 2.4 52.9 1.0 OP2 B:G5 2.5 35.0 1.0 O B:HOH226 2.6 34.7 1.0 O B:HOH202 3.6 37.5 1.0 P B:G5 3.9 37.9 1.0 CE C:LYS77 4.2 33.6 1.0 O5' B:G5 4.4 35.6 1.0 NZ C:LYS77 4.4 36.0 1.0 OP1 B:G5 4.6 40.9 1.0 N7 B:G5 4.7 35.8 1.0 C8 B:G5 4.7 38.5 1.0 CD C:LYS77 4.8 36.2 1.0 OE1 C:GLU9 4.9 39.2 1.0

K.Fukunaga, T.Teramoto, M.Nakashima, T.Ohtani, R.Katsuki, T.Matsuura, Y.Yokobayashi, Y.Kakuta. Structural Insights Into Lab-Coevolved Rna-Rbp Pairs and Applications of Synthetic Riboswitches in Cell-Free System. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40119732
DOI: 10.1093/NAR/GKAF212