Sodium 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:

Barium	(Ba)	15 atoms
Potassium	(K)	8 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine, PDB code: 4aob:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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:Na1113 b:74.7 occ:1.00 OP2 A:A51 3.3 97.0 1.0 OP1 A:A50 3.7 0.9 1.0 P A:A51 4.3 0.8 1.0 OP1 A:A51 4.3 0.8 1.0 P A:A50 4.4 0.7 1.0 OP2 A:A50 4.5 96.3 1.0 O5' A:A50 4.6 96.4 1.0

Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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:Na1114 b:65.3 occ:1.00 OP1 A:A51 3.8 0.8 1.0 O3' A:A50 4.3 0.9 1.0 P A:A51 4.8 0.8 1.0

Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na 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:Na1137 b:58.6 occ:1.00 OP1 A:C60 4.0 62.0 1.0 C4' A:G23 4.5 54.8 1.0 O2' A:G23 4.5 62.6 1.0 O3' A:G23 4.8 59.1 1.0

Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na 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:Na1138 b:63.2 occ:1.00 K A:K1111 3.3 0.2 1.0 OP2 A:U4 4.1 59.5 1.0 OP1 A:U4 4.5 74.0 1.0 OP1 A:A84 4.8 88.2 1.0 P A:U4 4.9 66.3 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