Barium in PDB 4aob: Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine

The structure of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine, PDB code: 4aob was solved by K.T.Schroeder, P.Daldrop, S.A.Mcphee, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50 / 2.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.300, 61.300, 157.538, 90.00, 90.00, 90.00
R / Rfree (%)	18.906 / 23.943

The structure of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine also contains other interesting chemical elements:

Potassium	(K)	8 atoms
Sodium	(Na)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Barium atom in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine (pdb code 4aob). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 15 binding sites of Barium where determined in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine, PDB code: 4aob:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1095 b:0.5 occ:1.00 N7 A:G86 2.8 55.4 1.0 O6 A:G86 3.6 62.8 1.0 C5 A:G86 3.7 55.4 1.0 N7 A:A85 3.8 72.8 1.0 C8 A:G86 3.8 53.6 1.0 C6 A:G86 4.1 58.5 1.0 C5 A:A85 4.3 61.8 1.0 C8 A:A85 4.4 68.9 1.0 N6 A:A87 4.5 56.1 1.0 N6 A:A85 4.5 65.2 1.0 OP2 A:A85 4.7 69.8 1.0 C6 A:A85 4.7 60.1 1.0 N7 A:A87 5.0 49.9 1.0 C4 A:G86 5.0 55.0 1.0 N9 A:G86 5.0 52.4 1.0

Barium binding site 2 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1096 b:0.5 occ:1.00 O4 A:U81 2.9 66.3 1.0 O6 A:G82 3.0 87.3 1.0 C4 A:U81 3.8 71.1 1.0 C6 A:G82 4.0 73.3 1.0 N6 A:A83 4.2 87.8 1.0 O A:HOH2008 4.3 44.4 1.0 OP1 A:U67 4.3 62.5 1.0 C5 A:U81 4.3 68.8 1.0 N4 A:C69 4.3 76.5 1.0 N7 A:G82 4.4 74.0 1.0 C5 A:G82 4.6 73.1 1.0 N6 A:A70 4.6 61.4 1.0 O A:HOH2007 4.7 31.2 1.0 N3 A:U81 4.8 71.9 1.0

Barium binding site 3 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1097 b:95.8 occ:1.00 O2 A:U64 2.6 53.0 1.0 O2' A:U64 3.1 53.4 1.0 O4 A:U67 3.2 68.4 1.0 C2 A:U64 3.7 57.5 1.0 C1' A:U64 4.1 53.1 1.0 C4 A:U67 4.1 68.3 1.0 C2' A:U64 4.2 50.5 1.0 N6 A:A24 4.3 69.3 1.0 N1 A:U64 4.4 55.7 1.0 C5 A:U67 4.4 62.6 1.0 OP2 A:C66 4.4 57.4 1.0 N4 A:C25 4.5 68.8 1.0 N3 A:U64 4.7 52.6 1.0 N7 A:A24 4.8 57.4 1.0 O6 A:G68 4.8 67.2 1.0 O3' A:U64 4.8 51.5 1.0

Barium binding site 4 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1098 b:0.3 occ:1.00 N7 A:G27 3.2 94.2 1.0 O6 A:G27 3.3 88.8 1.0 O6 A:G28 3.6 81.5 1.0 O A:HOH2003 3.6 30.4 1.0 C5 A:U26 3.6 73.8 1.0 O4 A:U26 3.9 76.9 1.0 C4 A:U26 3.9 73.8 1.0 C5 A:G27 3.9 81.3 1.0 C6 A:G27 4.0 87.2 1.0 N7 A:G28 4.1 88.0 1.0 C6 A:G28 4.3 76.1 1.0 C8 A:G27 4.3 94.0 1.0 C6 A:U26 4.4 76.2 1.0 C5 A:G28 4.5 76.4 1.0 OP2 A:U26 4.7 68.6 1.0 N3 A:U26 4.9 81.0 1.0 O6 A:G23 4.9 67.5 1.0 N4 A:C66 5.0 71.2 1.0

Barium binding site 5 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1099 b:0.4 occ:1.00 O6 A:G16 3.0 86.8 1.0 N7 A:G16 3.1 88.5 1.0 C6 A:G16 3.7 80.7 1.0 C5 A:G16 3.7 89.0 1.0 O6 A:G15 3.8 92.4 1.0 C6 A:G15 4.0 95.1 1.0 N7 A:G15 4.1 81.7 1.0 C5 A:G15 4.1 93.0 1.0 C8 A:G16 4.2 87.6 1.0 O6 A:G17 4.6 84.3 1.0 N7 A:G17 4.7 83.8 1.0 N1 A:G15 4.8 88.8 1.0 C8 A:G15 4.8 85.6 1.0 C4 A:G15 4.9 95.1 1.0 O A:HOH2002 5.0 26.5 1.0

Barium binding site 6 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1100 b:0.6 occ:1.00 N7 A:G13 3.2 87.0 1.0 O6 A:G13 3.7 0.8 1.0 OP2 A:A61 4.1 68.4 1.0 C5 A:G13 4.1 89.5 1.0 C6 A:G13 4.2 96.2 1.0 C8 A:G13 4.3 97.0 1.0 O2' A:C60 4.3 79.0 1.0 C2' A:C60 4.5 68.2 1.0 O2 A:C60 4.6 73.8 1.0 OP2 A:G13 5.0 87.8 1.0

Barium binding site 7 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1101 b:0.5 occ:1.00 N7 A:G1 2.9 66.1 1.0 O6 A:G1 3.8 75.0 1.0 C8 A:G1 3.9 64.4 1.0 C5 A:G1 3.9 66.6 1.0 C6 A:G1 4.2 69.2 1.0 BA A:BA1121 4.5 0.7 1.0 O A:HOH2010 4.6 33.7 1.0 K A:K1108 5.0 57.4 1.0

Barium binding site 8 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1102 b:0.6 occ:1.00 N1 A:A46 3.0 68.0 1.0 N7 A:G55 3.2 81.7 1.0 C2 A:A46 3.4 74.8 1.0 C8 A:G55 3.9 77.0 1.0 C6 A:A46 4.1 76.6 1.0 OP2 A:G55 4.2 89.9 1.0 C5 A:G55 4.3 78.1 1.0 N6 A:A46 4.4 78.0 1.0 O6 A:G55 4.4 65.9 1.0 N1 A:A45 4.5 72.8 1.0 O4 A:U54 4.5 82.2 1.0 C4 A:U54 4.6 91.3 1.0 C5 A:U54 4.7 91.9 1.0 N6 A:A45 4.7 63.7 1.0 N3 A:A46 4.8 73.5 1.0 C6 A:G55 4.8 73.4 1.0

Barium binding site 9 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1103 b:0.5 occ:1.00 O6 A:G74 2.8 81.5 1.0 C6 A:G74 3.9 70.2 1.0 N1 A:G74 4.4 70.5 1.0 BA A:BA1104 4.6 90.4 1.0

Barium binding site 10 out of 15 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba1104 b:90.4 occ:1.00 N7 A:G74 3.1 68.3 1.0 O6 A:G74 3.6 81.5 1.0 C5 A:G74 3.8 65.3 1.0 C6 A:G74 3.9 70.2 1.0 C8 A:G74 4.0 64.4 1.0 OP2 A:A76 4.5 69.0 1.0 BA A:BA1103 4.6 0.5 1.0 C4 A:G74 4.9 68.4 1.0 N7 A:G73 4.9 58.1 1.0 OP2 A:G73 4.9 70.1 1.0

K.T.Schroeder, P.Daldrop, S.A.Mcphee, D.M.J.Lilley. Structure and Folding of A Rare, Natural Kink Turn in Rna with An A*A Pair at the 2B*2N Position. Rna V. 18 1257 2012.
ISSN: ISSN 1355-8382
PubMed: 22539525
DOI: 10.1261/RNA.032409.112