Barium in PDB 7uq6: Trna T-Box Antiterminator Fusion, Construct #4

The structure of Trna T-Box Antiterminator Fusion, Construct #4, PDB code: 7uq6 was solved by J.C.Grigg, I.R.Price, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.21 / 2.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.576, 165.208, 57.047, 90, 90, 90
R / Rfree (%)	24.7 / 26.5

The structure of Trna T-Box Antiterminator Fusion, Construct #4 also contains other interesting chemical elements:

Potassium

(K)

11 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Barium atom in the Trna T-Box Antiterminator Fusion, Construct #4 (pdb code 7uq6). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 14 binding sites of Barium where determined in the Trna T-Box Antiterminator Fusion, Construct #4, PDB code: 7uq6:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba101 b:82.0 occ:1.00 O6 B:G42 2.6 59.9 1.0 O6 B:G41 3.5 39.1 1.0 H1 B:G42 3.5 42.7 1.0 C6 B:G42 3.5 45.3 1.0 N1 B:G42 3.9 35.5 1.0 H41 B:C46 4.0 49.5 1.0 H42 B:C46 4.4 49.5 1.0 C6 B:G41 4.5 38.2 1.0 H62 B:A40 4.5 49.5 1.0 BA B:BA111 4.5 63.1 1.0 N4 B:C46 4.6 41.2 1.0 N7 B:G41 4.7 42.9 1.0 C5 B:G42 4.8 39.8 1.0 N6 B:A40 4.9 41.1 1.0 C5 B:G41 4.9 37.5 1.0

Barium binding site 2 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba102 b:106.5 occ:1.00 O4 B:U66 2.9 70.8 1.0 C4 B:U66 4.0 63.4 1.0 BA B:BA110 4.0 234.6 1.0 H5 B:U66 4.3 73.4 1.0 C5 B:U66 4.6 61.0 1.0 OP2 B:U65 4.7 64.7 1.0 H5 B:U65 4.8 76.4 1.0 OP2 B:G64 4.9 74.4 1.0 OP1 B:G68 4.9 65.9 1.0

Barium binding site 3 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba103 b:97.8 occ:1.00 OP2 B:U16 2.7 70.3 1.0 O6 B:G70 3.3 60.3 1.0 HO2' B:G15 4.0 67.4 1.0 H1 B:G70 4.0 74.1 1.0 P B:U16 4.2 79.2 1.0 H3' B:G18 4.2 99.0 1.0 OP1 B:G18 4.3 75.3 1.0 C6 B:G70 4.3 51.4 1.0 H5'' B:G18 4.4 84.2 1.0 H3 B:U71 4.4 57.9 1.0 O2' B:G15 4.4 56.1 1.0 O5' B:G18 4.4 67.5 1.0 N1 B:G70 4.6 61.7 1.0 O5' B:U16 4.7 76.9 1.0 OP2 B:U19 4.8 90.9 1.0 H2' B:U16 4.9 74.8 1.0 C5' B:G18 4.9 70.0 1.0

Barium binding site 4 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba104 b:124.2 occ:1.00 OP1 B:U8 2.7 69.5 1.0 OP2 B:A9 2.8 64.3 1.0 OP2 B:U12 3.2 63.3 1.0 P B:U8 3.7 62.3 1.0 OP2 B:U8 3.7 61.1 1.0 BA B:BA105 3.9 96.9 1.0 P B:A9 4.0 59.6 1.0 OP1 B:A9 4.3 58.0 1.0 OP2 B:U11 4.4 66.9 1.0 H5' B:A9 4.5 84.9 1.0 OP1 B:U11 4.5 68.5 1.0 P B:U12 4.6 76.6 1.0 O5' B:U8 4.7 42.9 1.0 P B:U11 4.8 68.5 1.0 O5' B:A9 4.8 64.5 1.0 H3' B:U11 4.8 73.7 1.0 O3' B:G7 4.8 64.3 1.0 H5'' B:U8 4.8 61.4 1.0 O5' B:U11 4.9 48.3 1.0 H3' B:U8 4.9 70.7 1.0 H5 B:U12 5.0 66.1 1.0

Barium binding site 5 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba105 b:96.9 occ:1.00 OP1 B:A9 2.6 58.0 1.0 K B:K122 3.2 97.3 1.0 OP2 B:U11 3.3 66.9 1.0 OP2 B:G10 3.3 63.2 1.0 P B:A9 3.8 59.6 1.0 OP1 B:U11 3.9 68.5 1.0 H5' B:A9 3.9 84.9 1.0 BA B:BA104 3.9 124.2 1.0 OP2 B:A9 4.0 64.3 1.0 P B:U11 4.1 68.5 1.0 H4' B:A9 4.3 75.2 1.0 OP1 B:U8 4.5 69.5 1.0 C5' B:A9 4.6 70.7 1.0 O5' B:A9 4.7 64.5 1.0 P B:G10 4.8 58.8 1.0 C4' B:A9 4.9 62.6 1.0 O3' B:U8 4.9 65.4 1.0

Barium binding site 6 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba106 b:141.7 occ:1.00 HO2' B:A69 3.2 70.8 1.0 O6 B:G64 3.9 60.4 1.0 O2' B:A69 4.0 58.9 1.0 O6 B:G63 4.2 58.1 1.0 N7 B:G63 4.3 67.2 1.0 BA B:BA110 4.6 234.6 1.0 H2' B:A69 4.7 69.2 1.0 H41 B:C72 4.7 63.0 1.0 N7 B:G64 4.7 63.7 1.0 C6 B:G63 4.9 55.5 1.0 C5 B:G63 4.9 58.9 1.0 C6 B:G64 4.9 63.0 1.0 C2' B:A69 4.9 57.6 1.0

Barium binding site 7 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba107 b:88.4 occ:1.00 H21 B:G70 2.4 89.7 1.0 OP1 B:G70 2.7 75.2 1.0 N2 B:G70 2.8 74.6 1.0 H22 B:G70 2.9 89.7 1.0 OP1 B:U19 3.0 84.8 1.0 O4 B:U71 3.2 66.4 1.0 H4' B:G18 3.6 92.9 1.0 OP2 B:A20 3.6 116.4 1.0 C2 B:G70 3.8 64.4 1.0 H1 B:G70 3.8 74.1 1.0 H4' B:A69 4.0 71.8 1.0 H5'' B:U19 4.1 133.4 1.0 P B:G70 4.1 62.6 1.0 H3' B:U19 4.1 142.8 1.0 N1 B:G70 4.2 61.7 1.0 C4 B:U71 4.3 51.5 1.0 H5'' B:G18 4.3 84.2 1.0 P B:U19 4.4 78.8 1.0 H5 B:U71 4.5 55.6 1.0 C4' B:G18 4.5 77.3 1.0 OP2 B:G70 4.7 75.3 1.0 N3 B:G70 4.7 45.2 1.0 O5' B:G70 4.8 58.3 1.0 C5 B:U71 4.8 46.2 1.0 C5' B:G18 4.9 70.0 1.0 C5' B:U19 4.9 111.1 1.0 P B:A20 4.9 117.8 1.0 C4' B:A69 5.0 59.7 1.0

Barium binding site 8 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba108 b:81.4 occ:1.00 O6 B:G60 2.7 64.4 1.0 O4 B:U76 3.2 55.6 1.0 H41 B:C61 3.5 74.4 1.0 O6 B:G7 3.5 63.7 1.0 O6 B:G75 3.5 61.2 1.0 H42 B:C61 3.8 74.4 1.0 C6 B:G60 3.8 62.1 1.0 H3 B:U76 3.9 67.2 1.0 N4 B:C61 3.9 61.9 1.0 C6 B:G7 4.1 56.2 1.0 C4 B:U76 4.2 56.0 1.0 N7 B:G60 4.3 61.0 1.0 H41 B:C77 4.3 68.3 1.0 C5 B:G60 4.4 56.4 1.0 N3 B:U76 4.4 55.9 1.0 C6 B:G75 4.5 56.9 1.0 C5 B:G7 4.7 55.0 1.0 N4 B:C77 4.7 56.9 1.0 N7 B:G7 4.8 61.3 1.0 H42 B:C77 4.9 68.3 1.0 N1 B:G7 4.9 48.9 1.0 N1 B:G60 4.9 59.6 1.0 H1 B:G7 5.0 58.8 1.0 H1 B:G60 5.0 71.6 1.0

Barium binding site 9 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba109 b:70.0 occ:1.00 N7 B:G32 2.6 55.3 1.0 O6 B:G32 2.8 60.7 1.0 C5 B:G32 3.3 57.1 1.0 C6 B:G32 3.4 58.2 1.0 C8 B:G32 3.8 53.1 1.0 H8 B:G32 4.1 63.9 1.0 O6 B:G33 4.2 60.1 1.0 C4 B:G32 4.6 58.2 1.0 N1 B:G32 4.8 57.5 1.0 N9 B:G32 4.9 52.2 1.0 N7 B:G33 4.9 58.5 1.0

Barium binding site 10 out of 14 in the Trna T-Box Antiterminator Fusion, Construct #4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Trna T-Box Antiterminator Fusion, Construct #4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba110 b:234.6 occ:1.00 O4 B:U65 3.1 58.1 1.0 O4 B:U66 3.3 70.8 1.0 OP2 B:A69 3.6 64.8 1.0 H3 B:U66 3.8 68.6 1.0 BA B:BA102 4.0 106.5 1.0 C4 B:U65 4.1 60.1 1.0 C4 B:U66 4.1 63.4 1.0 OP1 B:A69 4.2 71.0 1.0 H5 B:U65 4.3 76.4 1.0 N3 B:U66 4.3 57.0 1.0 P B:A69 4.3 57.5 1.0 H8 B:A69 4.4 67.0 1.0 H2' B:A69 4.6 69.2 1.0 BA B:BA106 4.6 141.7 1.0 C5 B:U65 4.6 63.5 1.0

J.C.Grigg, I.R.Price, A.Ke. Trna Fusion to Streamline Rna Structure Determination: Case Studies in Probing Aminoacyl-Trna Sensing Mechanisms By the T-Box Riboswitch To Be Published.