Barium in PDB 5fk1: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug, PDB code: 5fk1 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)	58.015 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.580, 62.580, 154.730, 90.00, 90.00, 90.00
R / Rfree (%)	23.85 / 28.9

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

Sodium

(Na)

3 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 Kt-7 Variant 3BN Is Ug (pdb code 5fk1). 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 Kt-7 Variant 3BN Is Ug, PDB code: 5fk1:
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 Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1096 b:0.2 occ:1.00 O6 A:G18 2.7 0.1 1.0 C6 A:G18 3.6 0.1 1.0 N1 A:G18 3.8 0.3 1.0 N7 A:G17 4.2 0.3 1.0 O2' A:G35 4.4 0.5 1.0 OP2 A:G16 4.5 0.8 1.0 OP1 A:A36 4.6 0.7 1.0 NA A:NA1108 4.7 94.7 1.0 OP2 A:G17 4.8 0.9 1.0 C8 A:G17 4.8 0.0 1.0 C5 A:G18 5.0 0.2 1.0

Barium binding site 2 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1097 b:0.6 occ:1.00 O A:HOH2010 2.6 56.1 1.0 O6 A:G74 2.7 0.0 1.0 O A:HOH2012 2.8 68.2 1.0 N7 A:G74 3.3 0.6 1.0 C6 A:G74 3.3 0.1 1.0 C5 A:G74 3.5 0.5 1.0 O A:HOH2011 4.0 69.6 1.0 C8 A:G74 4.4 0.3 1.0 N1 A:G74 4.5 0.8 1.0 OP1 A:A76 4.6 0.4 1.0 C4 A:G74 4.7 0.2 1.0

Barium binding site 3 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1098 b:91.3 occ:0.58 O6 A:G32 2.8 91.2 1.0 O A:HOH2005 2.8 51.3 1.0 N7 A:G32 3.1 0.1 1.0 O A:HOH2004 3.3 62.8 1.0 C6 A:G32 3.4 90.3 1.0 C5 A:G32 3.5 0.5 1.0 C8 A:G32 4.2 92.7 1.0 N4 A:C31 4.3 0.4 1.0 C5 A:C31 4.5 87.0 1.0 C4 A:C31 4.6 86.5 1.0 N1 A:G32 4.7 91.6 1.0 C4 A:G32 4.8 89.2 1.0 OP2 A:C31 4.9 0.1 1.0

Barium binding site 4 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1099 b:0.8 occ:1.00 O A:HOH2002 2.5 59.4 1.0 O6 A:G11 2.9 0.1 1.0 OP1 A:U64 3.8 0.9 1.0 O A:SAM1095 3.9 0.3 1.0 C6 A:G11 4.0 0.5 1.0 N1 A:G11 4.5 0.3 1.0 N6 A:A12 4.5 0.3 1.0 P A:U64 4.6 0.7 1.0 O2' A:C8 4.7 0.5 1.0 O5' A:U64 4.8 0.5 1.0 OP2 A:U64 4.9 0.9 1.0 O2' A:C59 4.9 93.3 1.0 CE A:SAM1095 5.0 0.6 1.0

Barium binding site 5 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1100 b:0.3 occ:1.00 N7 A:G50 2.7 0.2 1.0 C5 A:G50 3.6 0.9 1.0 C8 A:G50 3.6 0.5 1.0 O6 A:G50 3.6 0.8 1.0 C6 A:G50 4.0 0.4 1.0 OP1 A:A52 4.1 0.5 1.0 O A:HOH2008 4.8 68.4 1.0 N9 A:G50 4.8 0.5 1.0 C4 A:G50 4.8 0.9 1.0 OP2 A:A49 4.8 0.5 1.0 N7 A:A49 4.8 0.9 1.0

Barium binding site 6 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1101 b:0.2 occ:1.00 O A:HOH2006 2.6 62.5 1.0 O A:HOH2007 3.2 52.4 1.0 N7 A:G55 3.9 0.5 1.0 OP2 A:G55 3.9 0.9 1.0 C8 A:G55 4.2 0.4 1.0 O5' A:G55 4.5 0.0 1.0 C5 A:G55 4.5 0.1 1.0 N7 A:G56 4.6 0.5 1.0 N1 A:A45 4.8 0.5 1.0 P A:G55 4.9 1.0 1.0 N9 A:G55 4.9 0.2 1.0

Barium binding site 7 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1102 b:0.4 occ:1.00 O A:HOH2009 2.5 52.6 1.0 O2' A:U64 2.7 0.6 1.0 O4 A:U67 2.8 1.0 1.0 O2 A:U64 3.2 0.7 1.0 C4 A:U67 3.9 92.1 1.0 C2' A:U64 3.9 0.5 1.0 C1' A:U64 4.1 0.7 1.0 C2 A:U64 4.2 0.2 1.0 O3' A:U64 4.3 0.0 1.0 C5 A:U67 4.4 84.2 1.0 OP2 A:C66 4.4 87.1 1.0 N4 A:C25 4.5 96.2 1.0 N1 A:U64 4.6 0.9 1.0 C3' A:U64 4.8 0.7 1.0 N7 A:A24 5.0 0.6 1.0 O6 A:G68 5.0 92.3 1.0

Barium binding site 8 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1103 b:0.3 occ:1.00 O A:HOH2014 2.5 64.2 1.0 O A:HOH2013 2.6 63.2 1.0 O6 A:G86 2.9 0.9 1.0 N7 A:G86 3.0 0.8 1.0 C6 A:G86 3.5 0.2 1.0 C5 A:G86 3.6 0.9 1.0 N7 A:A85 3.8 0.8 1.0 C8 A:G86 4.1 94.5 1.0 N6 A:A85 4.2 0.3 1.0 C5 A:A85 4.3 0.1 1.0 OP2 A:A85 4.4 0.1 1.0 C8 A:A85 4.5 0.3 1.0 C6 A:A85 4.6 0.9 1.0 N6 A:A87 4.8 78.5 1.0 OP2 A:A84 4.8 91.1 1.0 N1 A:G86 4.9 95.9 1.0 C4 A:G86 4.9 0.7 1.0

Barium binding site 9 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1104 b:1.0 occ:1.00 OP2 A:G11 3.2 0.2 1.0 OP1 A:A62 3.6 0.7 1.0 OP1 A:A10 4.0 0.3 1.0 OP2 A:A10 4.1 0.0 1.0 N7 A:G11 4.3 98.9 1.0 P A:G11 4.6 96.3 1.0 C8 A:G11 4.6 97.7 1.0 P A:A10 4.6 0.0 1.0 O5' A:G11 4.9 95.6 1.0 N6 A:A12 4.9 0.3 1.0 OP2 A:U64 5.0 0.9 1.0 N7 A:A12 5.0 0.4 1.0

Barium binding site 10 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1105 b:0.3 occ:1.00 O6 A:G43 3.2 99.1 1.0 N7 A:G42 3.5 0.5 1.0 O6 A:G42 3.7 0.5 1.0 N7 A:G43 4.0 0.2 1.0 C6 A:G43 4.1 94.8 1.0 C5 A:G42 4.1 0.8 1.0 C6 A:G42 4.2 0.1 1.0 C5 A:G43 4.4 0.3 1.0 C8 A:G42 4.5 0.1 1.0 N4 A:C59 4.8 0.0 1.0 OP2 A:G42 4.9 0.7 1.0 OP2 A:C41 4.9 0.2 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