Barium in PDB 5fkd: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua, PDB code: 5fkd 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)	57.326 / 3.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.770, 61.770, 153.928, 90.00, 90.00, 90.00
R / Rfree (%)	23.27 / 29.34

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua also contains other interesting chemical elements:

Potassium

(K)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Barium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua (pdb code 5fkd). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 13 binding sites of Barium where determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua, PDB code: 5fkd:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1096 b:0.9 occ:0.97 O6 A:G11 2.8 0.5 1.0 O A:SAM1095 3.5 0.3 1.0 OP1 A:U64 3.6 0.2 1.0 C6 A:G11 4.0 0.3 1.0 OP2 A:U64 4.2 0.0 1.0 O2' A:C8 4.2 0.7 1.0 P A:U64 4.3 99.1 1.0 C A:SAM1095 4.5 0.3 1.0 N1 A:G11 4.6 0.0 1.0 OXT A:SAM1095 4.7 0.7 1.0 O5' A:U64 4.8 90.3 1.0 BA A:BA1105 5.0 0.1 1.0

Barium binding site 2 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1097 b:0.5 occ:1.00 N7 A:G86 3.0 0.5 1.0 O6 A:G86 3.3 0.2 1.0 C5 A:G86 3.8 0.5 1.0 C6 A:G86 3.9 0.7 1.0 N7 A:A85 4.1 0.5 1.0 C8 A:G86 4.1 95.0 1.0 N6 A:A87 4.4 81.7 1.0 OP2 A:A85 4.5 0.4 1.0 N6 A:A85 4.6 0.8 1.0 C5 A:A85 4.6 0.9 1.0 C8 A:A85 4.8 0.2 1.0 C6 A:A85 4.8 0.5 1.0

Barium binding site 3 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1098 b:0.3 occ:1.00 O6 A:G16 3.4 0.5 1.0 O6 A:G17 3.6 0.0 1.0 N7 A:G16 3.8 0.7 1.0 OP2 A:G15 4.0 0.9 1.0 N7 A:G17 4.1 0.7 1.0 C6 A:G16 4.1 0.7 1.0 N6 A:A18 4.3 0.5 1.0 C5 A:G16 4.3 0.1 1.0 C6 A:G17 4.5 0.9 1.0 OP1 A:A36 4.7 0.3 1.0 N1 A:A18 4.7 0.5 1.0 C5 A:G17 4.7 1.0 1.0 C6 A:A18 4.8 0.4 1.0 N7 A:G15 4.8 0.5 1.0 C8 A:G16 5.0 0.3 1.0 O6 A:G15 5.0 0.7 1.0

Barium binding site 4 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1099 b:0.8 occ:1.00 OP1 A:G1 2.7 0.8 1.0 OP2 A:G1 2.8 0.0 1.0 P A:G1 3.0 0.7 1.0 OP3 A:G1 3.1 0.2 1.0 O5' A:G1 4.5 0.6 1.0

Barium binding site 5 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1100 b:0.4 occ:1.00 N7 A:G55 3.8 0.4 1.0 N1 A:A45 3.9 0.2 1.0 N6 A:A45 4.0 0.1 1.0 OP2 A:G55 4.0 0.1 1.0 C6 A:A45 4.4 0.6 1.0 C5 A:G55 4.5 0.5 1.0 O6 A:G55 4.5 0.9 1.0 C8 A:G55 4.5 0.7 1.0 N1 A:A46 4.5 99.8 1.0 C6 A:G55 4.7 0.4 1.0 C2 A:A45 4.9 0.8 1.0

Barium binding site 6 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1101 b:0.5 occ:1.00 O2' A:U64 2.8 84.2 1.0 O4 A:U67 3.0 0.3 1.0 O2 A:U64 3.6 0.8 1.0 C4 A:U67 3.9 0.7 1.0 C2' A:U64 4.1 0.2 1.0 OP2 A:C66 4.1 94.0 1.0 C5 A:U67 4.3 0.2 1.0 C2 A:U64 4.4 0.4 1.0 C1' A:U64 4.5 0.4 1.0 O3' A:U64 4.7 1.0 1.0 N4 A:C25 4.7 0.9 1.0 O6 A:G68 4.8 88.4 1.0 N1 A:U64 4.9 0.4 1.0

Barium binding site 7 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1102 b:0.8 occ:1.00 O6 A:G50 2.8 0.3 1.0 N7 A:G50 3.1 0.1 1.0 C6 A:G50 3.4 0.9 1.0 C5 A:G50 3.6 0.0 1.0 OP1 A:A52 3.6 0.5 1.0 C8 A:G50 4.3 0.1 1.0 N7 A:A49 4.6 0.6 1.0 N1 A:G50 4.8 0.8 1.0 C4 A:G50 4.9 0.2 1.0 P A:A52 4.9 0.6 1.0

Barium binding site 8 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1103 b:0.7 occ:1.00 O6 A:G74 2.6 0.5 1.0 C6 A:G74 2.8 0.1 1.0 N7 A:G74 2.9 0.5 1.0 C5 A:G74 3.0 0.8 1.0 C8 A:G74 3.9 0.4 1.0 N1 A:G74 4.0 0.8 1.0 C4 A:G74 4.1 0.1 1.0 N9 A:G74 4.6 0.0 1.0 OP1 A:A76 4.7 0.2 1.0 C2 A:G74 4.9 0.8 1.0 OP2 A:G73 4.9 0.4 1.0 N3 A:G74 5.0 0.6 1.0

Barium binding site 9 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1104 b:0.7 occ:0.83 O6 A:G32 2.6 94.2 1.0 N7 A:G32 3.1 0.6 1.0 C6 A:G32 3.4 92.9 1.0 C5 A:G32 3.6 0.5 1.0 N4 A:C31 4.1 89.4 1.0 C8 A:G32 4.4 0.8 1.0 C5 A:C31 4.5 87.7 1.0 C4 A:C31 4.6 87.9 1.0 N1 A:G32 4.7 93.2 1.0 OP2 A:C31 4.7 91.5 1.0 C4 A:G32 4.9 90.4 1.0

Barium binding site 10 out of 13 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ua


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 3BN Is Ua within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1105 b:0.1 occ:1.00 OP2 A:A10 3.0 0.1 1.0 OP2 A:U64 3.2 0.0 1.0 N7 A:G11 3.8 0.5 1.0 P A:A10 3.8 0.1 1.0 OP1 A:A10 3.8 0.8 1.0 OP1 A:A62 3.9 92.5 1.0 O5' A:A10 4.2 0.1 1.0 OP2 A:G11 4.4 0.8 1.0 O6 A:G11 4.4 0.5 1.0 P A:U64 4.5 99.1 1.0 C8 A:G11 4.6 0.2 1.0 C5 A:G11 4.6 0.2 1.0 OP1 A:U64 4.9 0.2 1.0 N6 A:A12 4.9 0.5 1.0 C6 A:G11 4.9 0.3 1.0 P A:A62 4.9 0.1 1.0 BA A:BA1096 5.0 0.9 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