Barium in PDB 4frn: Crystal Structure of the Cobalamin Riboswitch Regulatory Element

The structure of Crystal Structure of the Cobalamin Riboswitch Regulatory Element, PDB code: 4frn was solved by F.E.Reyes, J.E.Johnson, J.T.Polaski, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.83 / 3.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.605, 81.833, 147.722, 90.00, 90.00, 90.00
R / Rfree (%)	25.1 / 27.3

The structure of Crystal Structure of the Cobalamin Riboswitch Regulatory Element also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

Pages:

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

Binding sites:

The binding sites of Barium atom in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element (pdb code 4frn). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 12 binding sites of Barium where determined in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element, PDB code: 4frn:
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 Crystal Structure of the Cobalamin Riboswitch Regulatory Element


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 the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba202 b:0.7 occ:1.00 O4 A:U49 3.4 73.6 1.0 O6 A:G50 3.8 68.6 1.0 O4 A:U44 3.9 66.7 1.0 C4 A:U49 4.2 75.0 1.0 C5 A:U49 4.3 76.3 1.0 N7 A:G50 4.4 71.6 1.0 N4 A:C91 4.6 89.1 1.0 C6 A:G50 4.7 69.2 1.0 C4 A:U44 4.7 66.1 1.0 N6 A:A51 4.8 67.7 1.0 C5 A:G50 5.0 70.6 1.0

Barium binding site 2 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


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 the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba203 b:0.9 occ:1.00 OP2 A:A92 2.7 89.6 1.0 OP1 A:C91 3.3 93.3 1.0 N6 A:A87 3.5 0.7 1.0 OP2 A:G90 3.9 0.8 1.0 P A:A92 4.0 88.5 1.0 OP1 A:G90 4.2 0.2 1.0 OP2 A:A93 4.2 93.7 1.0 P A:G90 4.3 0.4 1.0 OP1 A:A92 4.5 89.0 1.0 O5' A:G90 4.5 0.9 1.0 O5' A:A92 4.7 88.7 1.0 P A:C91 4.7 92.7 1.0 C6 A:A87 4.8 0.1 1.0

Barium binding site 3 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


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 the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba204 b:0.0 occ:1.00 OP1 A:A53 2.7 70.0 1.0 OP2 A:C62 2.7 75.2 1.0 OP1 A:U52 3.9 74.4 1.0 OP2 A:U52 3.9 72.9 1.0 P A:C62 4.0 74.6 1.0 O5' A:U52 4.1 69.7 1.0 P A:U52 4.1 72.3 1.0 P A:A53 4.1 68.8 1.0 OP1 A:C62 4.6 75.5 1.0 C5' A:A53 4.6 71.0 1.0 O5' A:A53 4.7 70.1 1.0 C5' A:U52 4.8 68.8 1.0 O5' A:C62 4.8 72.2 1.0

Barium binding site 4 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


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 the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba205 b:0.5 occ:1.00 OP2 A:A53 3.6 68.5 1.0 O6 A:G55 4.0 76.3 1.0 O6 A:G56 4.0 85.2 1.0 O2' A:A61 4.1 76.2 1.0 C5 A:C54 4.2 69.9 1.0 C2' A:A61 4.4 78.4 1.0 N4 A:C54 4.4 69.0 1.0 OP1 A:A61 4.5 87.4 1.0 O5' A:A53 4.6 70.1 1.0 OP2 A:A61 4.6 87.9 1.0 P A:A53 4.7 68.8 1.0 C4 A:C54 4.7 69.4 1.0 N7 A:G55 4.7 78.0 1.0 OP2 A:C54 4.7 76.3 1.0 C6 A:G55 4.9 77.8 1.0 P A:A61 4.9 88.0 1.0

Barium binding site 5 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


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 the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba206 b:0.9 occ:1.00 OP1 A:U13 2.7 76.0 1.0 OP2 A:G14 2.7 76.8 1.0 OP2 A:A6 2.9 86.5 1.0 OP2 A:U5 3.5 85.6 1.0 O5' A:U5 3.8 89.0 1.0 P A:G14 3.8 76.3 1.0 P A:U5 3.9 87.8 1.0 P A:U13 3.9 74.7 1.0 OP1 A:U5 4.0 87.9 1.0 OP1 A:G14 4.1 75.5 1.0 O5' A:U13 4.1 73.2 1.0 P A:A6 4.3 89.1 1.0 C5' A:U5 4.6 91.1 1.0 C3' A:U5 4.7 90.9 1.0 O5' A:G14 4.8 78.5 1.0 O3' A:U5 4.9 91.2 1.0 OP2 A:U13 4.9 76.0 1.0 O3' A:A12 5.0 73.5 1.0

Barium binding site 6 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


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 the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba207 b:0.5 occ:1.00 OP2 A:A8 2.7 91.1 1.0 O6 A:G10 3.8 83.5 1.0 P A:A8 4.0 94.6 1.0 N7 A:A8 4.2 87.3 1.0 OP1 A:A7 4.3 86.8 1.0 OP1 A:A6 4.3 90.5 1.0 O5' A:A8 4.3 95.3 1.0 C8 A:A8 4.4 90.2 1.0 N6 A:A9 4.5 80.3 1.0 N7 A:A9 4.7 86.6 1.0 C6 A:G10 4.7 82.0 1.0 O5' A:A7 4.9 90.6 1.0 C3' A:A7 5.0 94.0 1.0

Barium binding site 7 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba202 b:0.9 occ:1.00 O4 B:U49 3.7 69.4 1.0 O4 B:U44 3.8 63.8 1.0 O6 B:G50 4.1 62.3 1.0 C4 B:U49 4.5 71.2 1.0 C5 B:U49 4.6 73.4 1.0 C4 B:U44 4.6 62.8 1.0 N7 B:G50 4.8 66.2 1.0 N4 B:C91 4.8 92.6 1.0

Barium binding site 8 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba203 b:1.0 occ:1.00 OP2 B:C62 2.7 64.3 1.0 OP1 B:A53 2.7 59.5 1.0 OP1 B:U52 3.8 63.1 1.0 OP2 B:U52 3.8 62.2 1.0 O5' B:U52 4.0 59.4 1.0 P B:U52 4.0 61.7 1.0 P B:C62 4.0 63.8 1.0 P B:A53 4.1 58.6 1.0 OP1 B:C62 4.5 64.6 1.0 C5' B:A53 4.7 61.5 1.0 O5' B:A53 4.7 60.2 1.0 C5' B:U52 4.7 58.7 1.0 O5' B:C62 4.7 62.4 1.0 C3' B:U52 5.0 56.6 1.0

Barium binding site 9 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba204 b:0.9 occ:1.00 O6 B:G56 3.7 70.7 1.0 OP2 B:A53 3.9 58.2 1.0 O2' B:A61 3.9 64.1 1.0 O6 B:G55 4.0 67.3 1.0 C2' B:A61 4.1 65.4 1.0 OP2 B:A61 4.2 70.8 1.0 OP1 B:A61 4.3 71.1 1.0 C5 B:C54 4.6 62.9 1.0 P B:A61 4.6 71.0 1.0 N4 B:C54 4.7 62.0 1.0 C3' B:A61 4.8 65.4 1.0 C6 B:G56 4.8 72.2 1.0 N7 B:G55 4.9 69.4 1.0 C6 B:G55 4.9 68.9 1.0 P B:A53 4.9 58.6 1.0 O5' B:A53 4.9 60.2 1.0 O5' B:A61 5.0 69.1 1.0

Barium binding site 10 out of 12 in the Crystal Structure of the Cobalamin Riboswitch Regulatory Element


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Crystal Structure of the Cobalamin Riboswitch Regulatory Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba205 b:0.8 occ:1.00 OP2 B:A92 2.7 91.2 1.0 OP1 B:C91 2.9 90.6 1.0 OP2 B:G90 4.1 94.5 1.0 P B:A92 4.1 90.3 1.0 P B:C91 4.3 90.4 1.0 OP1 B:G90 4.4 91.0 1.0 OP2 B:A93 4.5 99.2 1.0 O5' B:G90 4.5 92.4 1.0 P B:G90 4.5 92.5 1.0 N1 B:A87 4.5 0.7 1.0 OP1 B:A92 4.8 90.4 1.0 O5' B:A92 4.8 91.7 1.0 OP2 B:C91 4.8 91.8 1.0 N6 B:A87 4.9 99.8 1.0

J.E.Johnson, F.E.Reyes, J.T.Polaski, R.T.Batey. B12 Cofactors Directly Stabilize An Mrna Regulatory Switch. Nature V. 492 133 2012.
ISSN: ISSN 0028-0836
PubMed: 23064232
DOI: 10.1038/NATURE11607