Barium in PDB 5fjc: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc 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)	41.134 / 1.71
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.398, 60.398, 152.950, 90.00, 90.00, 90.00
R / Rfree (%)	20.09 / 24.05

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	4 atoms
Sodium	(Na)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Barium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU (pdb code 5fjc). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 21 binding sites of Barium where determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba102 b:54.2 occ:0.51 O6 A:G50 2.8 62.6 1.0 O A:HOH2097 2.9 38.7 1.0 C6 A:G50 3.7 49.8 1.0 N1 A:G50 3.9 52.2 1.0 OP1 A:A52 4.4 67.5 1.0 BA A:BA118 4.7 45.9 0.9 O A:HOH2099 4.9 43.0 1.0 O A:HOH2090 5.0 39.5 1.0 N6 A:A49 5.0 37.4 1.0

Barium binding site 2 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba103 b:52.7 occ:0.64 O A:HOH2159 2.7 44.1 1.0 O6 A:G82 2.8 29.4 1.0 O4 A:U81 3.4 31.4 1.0 C6 A:G82 3.8 29.7 1.0 N7 A:G82 4.1 26.9 1.0 C4 A:U81 4.1 29.5 1.0 N4 A:C69 4.3 28.0 1.0 OP1 A:U67 4.3 37.5 1.0 C5 A:G82 4.3 30.9 1.0 N6 A:A83 4.4 52.4 1.0 OP2 A:G68 4.5 31.2 1.0 C5 A:U81 4.6 24.8 1.0 N7 A:A83 5.0 37.0 1.0 OP2 A:U67 5.0 32.6 1.0

Barium binding site 3 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba104 b:37.4 occ:0.57 BA A:BA116 2.3 53.7 0.5 O A:HOH2028 2.4 35.9 1.0 O A:HOH2021 2.5 43.5 1.0 O A:HOH2025 2.7 46.8 1.0 O6 A:G11 2.7 30.4 1.0 O A:HOH2180 2.9 41.5 1.0 O A:SAM101 2.9 39.6 1.0 C6 A:G11 3.8 39.0 1.0 C A:SAM101 4.0 50.1 1.0 N1 A:G11 4.1 30.8 1.0 CB A:SAM101 4.3 44.6 1.0 O2' A:C59 4.4 35.3 1.0 CA A:SAM101 4.4 37.9 1.0 N6 A:A10 4.6 36.1 1.0 OP1 A:U64 4.6 45.5 1.0 N6 A:A12 4.7 35.1 1.0 CE A:SAM101 4.7 52.6 1.0 BA A:BA122 4.8 0.8 0.7 O2' A:C8 4.9 35.4 1.0

Barium binding site 4 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba105 b:33.2 occ:0.47 O4 A:U80 2.8 34.8 1.0 O A:HOH2124 2.9 32.3 1.0 O6 A:G79 2.9 31.7 1.0 O A:HOH2134 2.9 36.0 1.0 O6 A:G71 3.0 25.3 1.0 N6 A:A70 3.2 28.3 1.0 O A:HOH2149 3.4 44.5 1.0 N4 A:C72 3.7 30.0 1.0 C4 A:U80 3.8 37.1 1.0 N3 A:U80 4.0 34.4 1.0 C6 A:A70 4.0 25.6 1.0 C6 A:G79 4.0 33.4 1.0 C6 A:G71 4.2 25.2 1.0 O A:HOH2150 4.3 44.3 1.0 N7 A:G71 4.6 29.3 1.0 C5 A:A70 4.6 26.3 1.0 O4 A:U81 4.8 31.4 1.0 C5 A:G71 4.8 26.2 1.0 N7 A:A70 4.8 30.3 1.0 N1 A:A70 4.8 28.4 1.0 C4 A:C72 4.8 26.7 1.0 O A:HOH2135 4.8 37.5 1.0 C5 A:G79 4.9 37.0 1.0 N1 A:G79 5.0 28.8 1.0 N7 A:G79 5.0 31.9 1.0

Barium binding site 5 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba106 b:39.0 occ:0.74 O A:HOH2163 2.3 39.6 1.0 O A:HOH2162 2.5 41.1 1.0 O A:HOH2161 2.7 34.7 1.0 O A:HOH2168 2.8 53.5 1.0 O6 A:G86 2.9 27.2 1.0 N7 A:G86 3.2 28.1 1.0 N7 A:A85 3.3 35.9 1.0 C6 A:G86 3.7 31.4 1.0 C5 A:G86 3.8 28.5 1.0 C8 A:A85 4.1 42.7 1.0 C5 A:A85 4.1 30.3 1.0 N6 A:A85 4.3 27.6 1.0 OP2 A:A85 4.3 35.4 1.0 C8 A:G86 4.4 32.3 1.0 N6 A:A87 4.5 27.4 1.0 C6 A:A85 4.6 31.1 1.0 O A:HOH2165 4.9 41.0 1.0 N4 A:C8 4.9 34.3 1.0 OP2 A:A84 4.9 40.1 1.0 O4 A:U7 5.0 32.5 1.0

Barium binding site 6 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba107 b:38.2 occ:0.76 O A:HOH2037 2.3 41.3 1.0 O A:HOH2039 2.5 31.3 1.0 O A:HOH2036 2.5 36.4 1.0 O6 A:G18 2.7 31.5 1.0 O A:HOH2040 3.0 38.9 1.0 C6 A:G18 3.9 37.1 1.0 O2' A:G35 4.2 32.4 1.0 O6 A:G19 4.5 37.0 1.0 N7 A:G17 4.6 41.0 1.0 OP2 A:G17 4.6 52.1 1.0 C5 A:G18 4.7 35.6 1.0 OP2 A:G16 4.7 68.9 1.0 N7 A:G18 4.7 37.1 1.0 N1 A:G18 4.9 33.3 1.0 C2' A:G35 5.0 30.7 1.0

Barium binding site 7 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba108 b:42.3 occ:0.55 O A:HOH2074 2.4 43.0 1.0 O A:HOH2070 2.6 41.4 1.0 O A:HOH2073 2.6 39.2 1.0 BA A:BA121 3.2 0.5 0.6 OP1 A:G32 3.9 35.4 1.0 OP2 A:C31 4.8 34.8 1.0

Barium binding site 8 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba109 b:34.2 occ:0.61 O A:HOH2001 2.7 52.3 1.0 N7 A:GTP1 2.9 54.3 1.0 O6 A:GTP1 3.1 38.5 1.0 O3B A:GTP1 3.1 69.8 1.0 O A:HOH2003 3.2 51.0 1.0 C5 A:GTP1 3.5 54.1 1.0 O A:HOH2179 3.7 47.0 1.0 C6 A:GTP1 3.7 51.0 1.0 C8 A:GTP1 4.0 63.2 1.0 O1A A:GTP1 4.3 72.5 1.0 H8 A:GTP1 4.4 75.8 1.0 PB A:GTP1 4.5 69.4 1.0 O2B A:GTP1 4.6 68.0 1.0 N1 A:G94 4.7 46.9 1.0 O A:HOH2002 4.7 55.1 1.0 O6 A:G2 4.9 35.9 1.0 C4 A:GTP1 4.9 59.7 1.0 O6 A:G94 4.9 40.6 1.0

Barium binding site 9 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba110 b:69.7 occ:1.00 O A:HOH2181 2.5 45.1 1.0 O A:HOH2083 2.7 38.4 1.0 O A:HOH2082 2.7 43.0 1.0 O6 A:G43 2.8 32.3 1.0 O A:HOH2086 2.9 40.8 1.0 N7 A:G43 3.0 36.2 1.0 O A:HOH2085 3.0 36.3 1.0 C6 A:G43 3.5 35.1 1.0 C5 A:G43 3.5 36.8 1.0 N7 A:G42 3.6 39.2 1.0 C5 A:G42 4.1 35.8 1.0 O6 A:G42 4.2 39.0 1.0 C8 A:G43 4.2 36.5 1.0 C8 A:G42 4.3 38.4 1.0 C6 A:G42 4.3 39.6 1.0 N4 A:C44 4.6 41.1 1.0 N1 A:G43 4.8 35.5 1.0 C4 A:G43 4.9 33.4 1.0 O6 A:G58 4.9 31.3 1.0 OP2 A:G42 4.9 44.4 1.0

Barium binding site 10 out of 21 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba111 b:49.3 occ:0.45 O6 A:G94 2.7 40.6 1.0 O A:HOH2176 2.8 34.2 1.0 O A:HOH2178 2.9 45.8 1.0 O A:HOH2179 3.1 47.0 1.0 C6 A:G94 3.8 47.2 1.0 N4 A:C93 4.3 42.3 1.0 C5 A:G94 4.6 44.5 1.0 N7 A:G94 4.7 44.5 1.0 N1 A:G94 4.8 46.9 1.0

L.Huang, J.Wang, D.M.J.Lilley. A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function. Nucleic Acids Res. V. 44 5390 2016.
ISSN: ISSN 0305-1048
PubMed: 27016741
DOI: 10.1093/NAR/GKW201