Barium in PDB 4b5r: Sam-I Riboswitch Bearing the H. Marismortui K-T-7

The structure of Sam-I Riboswitch Bearing the H. Marismortui K-T-7, PDB code: 4b5r was solved by P.Daldrop, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.90 / 2.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.720, 58.720, 154.710, 90.00, 90.00, 90.00
R / Rfree (%)	21.913 / 25.195

The structure of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 also contains other interesting chemical elements:

Potassium

(K)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Barium atom in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7 (pdb code 4b5r). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 12 binding sites of Barium where determined in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7, PDB code: 4b5r:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1096 b:48.4 occ:1.00 O6 A:G27 3.0 34.9 1.0 O6 A:G28 3.1 33.5 1.0 N7 A:G27 3.3 40.1 1.0 C6 A:G27 3.8 37.0 1.0 C6 A:G28 3.8 32.5 1.0 N7 A:G28 3.8 35.8 1.0 C5 A:G27 3.9 39.0 1.0 C5 A:U26 3.9 33.7 1.0 C5 A:G28 4.1 33.8 1.0 C4 A:U26 4.3 33.7 1.0 O4 A:U26 4.4 34.4 1.0 C8 A:G27 4.5 39.7 1.0 C6 A:U26 4.5 34.3 1.0 N4 A:C65 4.7 31.2 1.0 OP2 A:U26 4.8 33.2 1.0 O6 A:G23 4.9 24.4 1.0 C8 A:G28 4.9 35.6 1.0 N1 A:G28 4.9 31.0 1.0

Barium binding site 2 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1099 b:85.1 occ:1.00 O2' A:U64 3.0 31.2 1.0 O2 A:U64 3.1 31.4 1.0 O4 A:U67 3.4 22.3 1.0 C2 A:U64 4.1 31.0 1.0 C2' A:U64 4.2 28.8 1.0 OP2 A:C66 4.3 27.1 1.0 C1' A:U64 4.4 29.6 1.0 N7 A:A24 4.4 24.3 1.0 C4 A:U67 4.4 23.5 1.0 N4 A:C25 4.5 29.7 1.0 C2 A:A85 4.5 31.8 1.0 O3' A:U64 4.6 25.1 1.0 N1 A:U64 4.7 29.8 1.0 C5 A:U67 4.9 23.9 1.0

Barium binding site 3 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1101 b:82.4 occ:1.00 O6 A:G11 2.7 31.9 1.0 OP1 A:U64 3.4 37.1 1.0 C6 A:G11 3.9 29.8 1.0 P A:U64 4.1 37.0 1.0 OP2 A:U64 4.1 34.6 1.0 O A:SAM1095 4.2 32.0 1.0 C5' A:U64 4.3 33.5 1.0 O2' A:C8 4.3 33.5 1.0 O5' A:U64 4.6 34.4 1.0 N6 A:A10 4.6 32.5 1.0 N7 A:A10 4.8 33.6 1.0 N1 A:G11 4.8 28.4 1.0 N6 A:A12 4.9 30.6 1.0 C5 A:G11 4.9 29.4 1.0

Barium binding site 4 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1104 b:63.9 occ:1.00 O6 A:G16 2.9 38.5 1.0 N7 A:G16 3.0 38.8 1.0 O6 A:G15 3.4 38.8 1.0 C6 A:G16 3.6 39.0 1.0 C5 A:G16 3.6 39.2 1.0 N7 A:G15 3.8 37.3 1.0 C6 A:G15 3.8 37.9 1.0 C5 A:G15 4.0 37.9 1.0 C8 A:G16 4.2 38.5 1.0 N4 A:C40 4.7 29.2 1.0 C8 A:G15 4.7 38.8 1.0 N7 A:G17 4.8 35.0 1.0 O6 A:G17 4.8 35.0 1.0 N1 A:G15 4.9 37.6 1.0 OP2 A:G15 4.9 58.7 1.0 C4 A:G16 4.9 38.9 1.0 N1 A:G16 4.9 40.0 1.0

Barium binding site 5 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1105 b:35.4 occ:1.00 C4' A:G42 4.5 34.1 1.0 O3' A:G42 4.8 34.8 1.0 C5' A:G42 4.8 34.8 1.0

Barium binding site 6 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1106 b:0.3 occ:1.00 BA A:BA1112 4.7 0.5 1.0

Barium binding site 7 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1107 b:49.7 occ:1.00 O6 A:G18 3.0 37.0 1.0 C6 A:G18 4.0 35.7 1.0 O6 A:G19 4.2 40.4 1.0 N7 A:G18 4.4 35.7 1.0 C5 A:G18 4.6 36.0 1.0 OP2 A:G17 4.7 36.0 1.0 OP2 A:G16 4.9 36.7 1.0 C5' A:G35 5.0 35.0 1.0 N7 A:G17 5.0 35.0 1.0

Barium binding site 8 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1108 b:98.4 occ:1.00 O4 A:U88 3.4 35.3 1.0 C4 A:U88 4.3 33.6 1.0 O4 A:U4 4.3 43.0 1.0 O4 A:U5 4.4 41.6 1.0 C5 A:U88 4.5 33.5 1.0 O6 A:G89 4.7 45.4 1.0 N6 A:A6 4.9 38.9 1.0 N7 A:A87 5.0 28.0 1.0

Barium binding site 9 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1109 b:75.6 occ:1.00 OP2 A:C31 4.6 24.1 1.0 N7 A:G32 4.7 27.5 1.0 OP1 A:G32 4.8 24.6 1.0

Barium binding site 10 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1110 b:0.3 occ:1.00 N7 A:G1 3.2 62.9 1.0 C8 A:G1 3.8 65.6 1.0 OP2 A:G1 3.8 72.9 1.0 C5 A:G1 4.2 60.5 1.0 OP3 A:G1 4.3 83.4 1.0 O6 A:G1 4.6 59.0 1.0 P A:G1 4.6 82.7 1.0 C6 A:G1 4.8 58.8 1.0 O5' A:G1 4.8 75.8 1.0 N7 A:G2 5.0 38.3 1.0

P.Daldrop, D.M.J.Lilley. The Plasticity of A Structural Motif in Rna: Structural Polymorphism of A Kink Turn As A Function of Its Environment. Rna V. 19 357 2013.
ISSN: ISSN 1355-8382
PubMed: 23325110
DOI: 10.1261/RNA.036657.112