Barium in PDB 7eaf: Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn

The structure of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn, PDB code: 7eaf was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.22 / 2.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.46, 61.46, 157.91, 90, 90, 90
R / Rfree (%)	26.2 / 29.8

The structure of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Barium atom in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn (pdb code 7eaf). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 6 binding sites of Barium where determined in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn, PDB code: 7eaf:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6;

Barium binding site 1 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba102 b:101.8 occ:0.50 OP2 A:G32 4.7 72.5 1.0 N7 A:G32 4.9 69.6 1.0

Barium binding site 2 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba103 b:84.4 occ:0.83 O6 A:G27 2.9 68.6 1.0 N7 A:G27 3.2 71.1 1.0 C6 A:G27 3.6 65.1 1.0 C5 A:G27 3.7 67.7 1.0 O6 A:G28 3.7 67.5 1.0 N7 A:G28 3.8 69.6 1.0 C5 A:U26 3.9 63.2 1.0 C4 A:U26 4.2 63.4 1.0 O4 A:U26 4.2 61.5 1.0 C6 A:G28 4.3 67.8 1.0 C8 A:G27 4.4 73.8 1.0 C5 A:G28 4.4 68.0 1.0 C6 A:U26 4.6 64.7 1.0 OP2 A:U26 4.7 64.2 1.0 C8 A:G28 4.9 71.9 1.0 N1 A:G27 4.9 65.0 1.0 O6 A:G23 4.9 73.0 1.0

Barium binding site 3 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba104 b:117.4 occ:1.00 N7 A:G16 2.7 75.8 1.0 O6 A:G16 3.0 79.3 1.0 O6 A:G15 3.4 78.7 1.0 C5 A:G16 3.5 74.9 1.0 N7 A:G15 3.5 82.6 1.0 C6 A:G15 3.5 79.6 1.0 C6 A:G16 3.5 77.3 1.0 C5 A:G15 3.6 80.3 1.0 C8 A:G16 3.9 78.9 1.0 C8 A:G15 4.3 86.1 1.0 N1 A:G15 4.5 78.2 1.0 C4 A:G15 4.5 80.4 1.0 O6 A:G17 4.6 75.4 1.0 C4 A:G16 4.8 75.5 1.0 N7 A:G17 4.9 70.6 1.0 N1 A:G16 4.9 75.6 1.0 N9 A:G15 4.9 81.3 1.0 N4 A:C40 5.0 78.2 1.0 N9 A:G16 5.0 76.8 1.0

Barium binding site 4 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba105 b:194.1 occ:1.00 O6 A:G22 2.7 74.6 1.0 C6 A:G22 3.8 71.5 1.0 N7 A:G22 4.1 68.4 1.0 O6 A:G23 4.2 73.0 1.0 N4 A:C30 4.2 76.3 1.0 C5 A:G22 4.3 68.8 1.0 O6 A:G21 4.6 72.7 1.0 N4 A:C29 4.9 70.6 1.0 N1 A:G22 5.0 72.9 1.0

Barium binding site 5 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba106 b:112.3 occ:0.97 N7 A:G50 2.7 82.7 1.0 O6 A:G50 3.1 96.9 1.0 C5 A:G50 3.3 81.7 1.0 OP1 A:A52 3.4 82.9 1.0 C6 A:G50 3.5 89.5 1.0 C8 A:G50 3.8 85.0 1.0 C4 A:G50 4.6 83.8 1.0 P A:A52 4.7 96.2 1.0 N7 A:A49 4.7 72.6 1.0 N9 A:G50 4.8 86.7 1.0 N1 A:G50 4.8 88.2 1.0 OP2 A:A49 4.9 79.7 1.0

Barium binding site 6 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba107 b:101.7 occ:1.00 N7 A:G74 2.6 80.8 1.0 O6 A:G74 3.2 86.1 1.0 C5 A:G74 3.4 74.2 1.0 C6 A:G74 3.6 77.8 1.0 C8 A:G74 3.6 76.8 1.0 OP1 A:A76 4.5 78.9 1.0 C4 A:G74 4.6 73.9 1.0 N7 A:G73 4.6 73.8 1.0 N9 A:G74 4.7 75.2 1.0 OP2 A:G73 4.9 81.6 1.0 N1 A:G74 5.0 72.2 1.0

L.Huang, X.Liao, M.Li, J.Wang, X.Peng, T.J.Wilson, D.M.J.Lilley. Structure and Folding of Four Putative Kink Turns Identified in Structured Rna Species in A Test of Structural Prediction Rules. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33978763
DOI: 10.1093/NAR/GKAB333