Calcium in PDB 9l6y: Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna

The structure of Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna, PDB code: 9l6y 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)	45.42 / 3.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.3, 55.28, 83.05, 90, 106.39, 90
R / Rfree (%)	22 / 25.7

The binding sites of Calcium atom in the Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna (pdb code 9l6y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna, PDB code: 9l6y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:75.4 occ:1.00 OP2 B:A11 2.5 67.5 1.0 P B:A11 4.0 70.6 1.0 N7 B:A11 4.5 69.9 1.0 O5' B:A11 4.5 67.9 1.0 C3' B:G10 4.7 63.4 1.0 C8 B:A11 4.7 70.3 1.0 O3' B:G10 4.8 60.0 1.0 OP1 B:A11 4.9 75.5 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:101.6 occ:1.00 N7 B:G14 3.1 93.5 1.0 C5 B:G14 3.6 88.3 1.0 O6 B:G14 3.6 93.8 1.0 C6 B:G14 3.8 88.7 1.0 C8 B:G14 4.0 91.1 1.0 OP2 B:A16 4.1 98.1 1.0 OP1 B:A16 4.5 96.5 1.0 C4 B:G14 4.6 83.8 1.0 P B:A16 4.7 96.2 1.0 N9 B:G14 4.8 90.8 1.0 N1 B:G14 4.9 83.2 1.0 O3' B:A15 5.0 93.2 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:95.3 occ:1.00 OP2 D:A11 2.5 80.2 1.0 N7 D:A11 3.8 64.9 1.0 P D:A11 3.9 76.4 1.0 C8 D:A11 4.0 68.9 1.0 O5' D:A11 4.1 60.5 1.0 C3' D:G10 4.8 66.7 1.0 O3' D:G10 4.9 70.0 1.0 OP1 D:A11 4.9 74.6 1.0 C5 D:A11 4.9 65.7 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:75.4 occ:1.00 OP2 D:G18 2.6 77.6 1.0 P D:G18 3.9 83.0 1.0 N7 D:G18 3.9 72.0 1.0 C8 D:G18 4.1 73.2 1.0 OP1 D:G18 4.2 69.4 1.0 OP2 D:A17 4.4 78.1 1.0 O3' D:A17 4.8 75.8 1.0 O5' D:A17 4.9 90.7 1.0 O5' D:G18 5.0 78.7 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the L7AE Derivative Protein LS12 in Complex with Its Co-Evolved Target CS2 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca103 b:107.5 occ:1.00 OP1 D:C32 3.6 130.3 1.0 P D:C32 4.7 139.7 1.0 OP2 D:C32 4.8 130.3 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