Sodium in PDB 2ygh: Sam-I Riboswitch with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine

The structure of Sam-I Riboswitch with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine, PDB code: 2ygh was solved by K.Schroeder, P.Daldrop, D.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.71 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.460, 58.460, 155.260, 90.00, 90.00, 90.00
R / Rfree (%)	19.975 / 25.929

The structure of Sam-I Riboswitch with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the Sam-I Riboswitch with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine (pdb code 2ygh). 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 with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine, PDB code: 2ygh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Sam-I Riboswitch with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine


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 with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1097 b:23.7 occ:1.00 OP2 A:A10 2.3 26.2 1.0 O A:HOH2005 2.4 5.3 1.0 OP2 A:U64 2.4 17.9 1.0 P A:U64 3.6 18.8 1.0 O6 A:G11 3.6 16.0 1.0 P A:A10 3.7 26.1 1.0 N7 A:A10 3.7 19.4 1.0 N7 A:G11 3.7 20.2 1.0 OP1 A:U64 3.9 20.1 1.0 C8 A:A10 4.0 20.3 1.0 O5' A:A10 4.1 25.9 1.0 C6 A:G11 4.4 17.5 1.0 C5 A:G11 4.5 18.3 1.0 OP1 A:A10 4.5 24.1 1.0 O5' A:U64 4.5 18.7 1.0 OP1 A:A62 4.6 18.8 1.0 O3' A:U63 4.7 21.1 1.0 N6 A:A12 4.8 24.1 1.0 O3' A:A9 4.8 29.7 1.0 C5 A:A10 4.8 20.8 1.0 C8 A:G11 4.8 21.5 1.0 O A:HOH2006 4.9 13.8 1.0 OP2 A:G11 5.0 24.9 1.0

Sodium binding site 2 out of 4 in the Sam-I Riboswitch with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine


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 with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1099 b:37.2 occ:1.00 N7 A:G13 2.3 29.7 1.0 C8 A:G13 3.0 29.7 1.0 C5 A:G13 3.6 28.2 1.0 O6 A:G13 4.2 28.9 1.0 OP2 A:G13 4.2 29.3 1.0 C6 A:G13 4.3 28.5 1.0 N9 A:G13 4.3 29.5 1.0 N2 A:G42 4.4 20.2 1.0 O2 A:C60 4.5 18.1 1.0 OP2 A:A61 4.5 19.1 1.0 C2' A:C60 4.5 18.2 1.0 C4 A:G13 4.6 28.9 1.0 C2 A:C60 4.8 17.6 1.0 O5' A:G13 5.0 33.5 1.0

Sodium binding site 3 out of 4 in the Sam-I Riboswitch with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine


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 with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1100 b:7.0 occ:0.50 O A:HOH2014 2.5 28.4 1.0 O A:HOH2013 2.9 29.8 1.0 O6 A:G32 3.6 31.3 1.0 C6 A:G32 3.9 30.3 1.0 N7 A:G32 4.0 28.6 1.0 C5 A:G32 4.0 29.0 1.0 N1 A:G32 4.8 29.6 1.0 C8 A:G32 4.8 27.7 1.0 O A:HOH2011 4.9 19.8 1.0 C4 A:G32 5.0 27.8 1.0

Sodium binding site 4 out of 4 in the Sam-I Riboswitch with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine


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 with A G2NA Mutation in the Kink Turn in Complex with S-Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:38.7 occ:1.00 O A:HOH2015 2.2 21.4 1.0 O A:HOH2016 2.4 13.0 1.0 N1 A:A45 3.8 24.2 1.0 N6 A:A45 4.0 21.1 1.0 C6 A:A45 4.4 23.2 1.0 N1 A:A46 4.6 24.3 1.0 C2 A:A45 4.8 23.5 1.0 N7 A:G55 4.8 26.2 1.0 OP2 A:G55 4.9 32.6 1.0

K.T.Schroeder, P.Daldrop, D.M.J.Lilley. Rna Tertiary Interactions in A Riboswitch Stabilize the Structure of A Kink Turn. Structure V. 19 1233 2011.
ISSN: ISSN 0969-2126
PubMed: 21893284
DOI: 10.1016/J.STR.2011.07.003