Sodium in PDB 9l6z: Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State

The structure of Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State, PDB code: 9l6z 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)	38.54 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.8, 54.27, 54.866, 90, 93.97, 90
R / Rfree (%)	17.1 / 21.4

The binding sites of Sodium atom in the Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State (pdb code 9l6z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State, PDB code: 9l6z:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State


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 L7AE Derivative Protein LS12 in Rna-Free State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:9.6 occ:1.00 O A:HOH413 3.1 25.3 1.0 O A:HOH411 3.1 27.7 1.0 O A:HOH357 3.1 15.3 1.0 NH1 A:ARG41 3.5 19.6 1.0 CA A:ALA38 3.7 8.7 1.0 CD1 A:LEU43 3.7 15.9 1.0 CD A:ARG41 3.9 10.6 1.0 CB A:ALA38 4.0 7.4 1.0 N A:ALA38 4.0 7.4 1.0 CE A:LYS29 4.2 19.5 1.0 O A:HOH309 4.3 36.2 1.0 C A:LEU37 4.5 11.3 1.0 CZ A:ARG41 4.6 19.7 1.0 CB A:LEU43 4.6 13.1 1.0 O A:LEU37 4.7 7.8 1.0 NE A:ARG41 4.7 12.8 1.0 CG A:LEU43 4.7 15.7 1.0 NZ A:LYS29 4.9 23.1 1.0 CB A:LEU37 4.9 9.3 1.0 O A:SER34 4.9 7.5 1.0 CB A:ARG41 5.0 9.4 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State


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 L7AE Derivative Protein LS12 in Rna-Free State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:7.0 occ:1.00 O A:HOH392 2.6 28.7 1.0 OG A:SER40 2.9 17.8 1.0 OG B:SER40 3.0 12.5 1.0 CB A:SER40 3.4 14.0 1.0 CB B:SER40 3.6 12.5 1.0 CA A:SER40 3.6 9.8 1.0 CA B:SER40 3.8 12.6 1.0 CD1 B:LEU65 3.9 9.0 1.0 CD A:LYS69 4.1 20.9 1.0 CD2 A:LEU65 4.2 12.2 1.0 O A:SER40 4.4 12.6 1.0 C A:SER40 4.5 12.6 1.0 CD B:LYS69 4.6 15.5 1.0 CD1 A:LEU65 4.6 12.6 1.0 O B:SER40 4.6 12.3 1.0 CD2 B:LEU65 4.6 11.7 1.0 N A:SER40 4.6 7.2 1.0 CG B:LEU65 4.6 11.6 1.0 C B:SER40 4.7 12.5 1.0 CE B:LYS69 4.7 20.9 1.0 CG A:LYS69 4.8 17.9 1.0 CE A:LYS69 4.8 25.7 1.0 CG B:LYS69 4.8 10.2 1.0 N B:SER40 4.8 7.8 1.0 NZ A:LYS69 4.9 27.0 1.0 CG A:LEU65 5.0 17.7 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State


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 the L7AE Derivative Protein LS12 in Rna-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:7.6 occ:1.00 NH2 B:ARG88 3.5 20.7 1.0 N B:ALA93 3.5 7.8 1.0 CA B:GLY31 3.8 7.8 1.0 CA B:GLY92 4.0 10.7 1.0 CB B:ALA93 4.2 8.5 1.0 C B:GLY92 4.3 9.4 1.0 CA B:ALA93 4.5 7.2 1.0 N B:GLY31 4.5 8.7 1.0 O B:PRO91 4.5 9.2 1.0 CZ B:ARG88 4.7 23.2 1.0 N B:THR32 4.8 6.3 1.0 N B:SER94 4.9 6.8 1.0 C B:GLY31 4.9 6.5 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State


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 the L7AE Derivative Protein LS12 in Rna-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:15.4 occ:1.00 O B:HOH381 3.2 15.9 1.0 O B:HOH366 3.2 16.2 1.0 O B:HOH302 3.7 30.0 1.0 N B:ASP10 4.0 13.8 1.0 CB B:ASP10 4.2 15.2 1.0 CA B:ASP10 4.2 14.0 1.0 CB B:GLU9 4.4 19.3 1.0 CD B:GLU9 4.4 30.8 1.0 C B:GLU9 4.5 15.4 1.0 CG B:GLU9 4.5 24.2 1.0 OE1 B:GLU9 4.5 21.6 1.0 OE2 B:GLU9 4.6 25.7 1.0 ND2 B:ASN13 4.7 23.2 1.0 CA B:GLU9 5.0 15.2 1.0 CG B:ASP10 5.0 15.3 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the L7AE Derivative Protein LS12 in Rna-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:15.7 occ:1.00 O B:HOH328 3.1 10.9 1.0 NH1 B:ARG41 3.5 14.9 1.0 CD B:ARG41 3.7 15.7 1.0 CA B:ALA38 3.7 8.1 1.0 CD1 B:LEU43 3.8 16.0 1.0 CB B:ALA38 4.0 8.0 1.0 N B:ALA38 4.1 7.3 1.0 CZ B:ARG41 4.4 12.4 1.0 C B:LEU37 4.4 7.2 1.0 NE B:ARG41 4.5 13.9 1.0 O B:LEU37 4.6 9.0 1.0 CB B:LEU43 4.7 11.8 1.0 CE B:LYS29 4.8 14.8 1.0 CG B:LEU43 4.8 16.1 1.0 CB B:ARG41 4.8 12.2 1.0 CG B:ARG41 4.8 11.7 1.0 CG B:LYS29 4.9 13.5 1.0 CB B:LEU37 5.0 7.0 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