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Sodium in PDB 5fjc: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU

Protein crystallography data

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc 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) 41.134 / 1.71
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 60.398, 60.398, 152.950, 90.00, 90.00, 90.00
R / Rfree (%) 20.09 / 24.05

Other elements in 5fjc:

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 4 atoms
Barium (Ba) 21 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU (pdb code 5fjc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc:

Sodium binding site 1 out of 1 in 5fjc

Go back to Sodium Binding Sites List in 5fjc
Sodium binding site 1 out of 1 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Bearing the H. Marismortui Kt-7 Variant C-2BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na129

b:56.8
occ:1.00
N3 A:A83 2.4 45.0 1.0
O2' A:A83 2.9 42.0 1.0
C2' A:A83 3.1 39.4 1.0
C2 A:A83 3.2 45.7 1.0
O4' A:A84 3.3 41.2 1.0
O2 A:C69 3.4 32.0 1.0
C4 A:A83 3.4 39.0 1.0
C1' A:A83 3.4 42.6 1.0
N2 A:G82 3.8 30.5 1.0
N9 A:A83 3.8 45.3 1.0
C1' A:A84 4.1 46.4 1.0
C4' A:A84 4.3 47.0 1.0
C2 A:C69 4.4 29.5 1.0
O A:HOH2160 4.4 39.8 1.0
N1 A:A83 4.5 41.3 1.0
C3' A:A83 4.6 38.4 1.0
C5' A:A84 4.7 43.3 1.0
C5 A:A83 4.7 42.0 1.0
C2 A:G82 4.7 35.0 1.0
N9 A:A84 4.8 36.6 1.0
O4' A:A83 4.8 43.8 1.0
C1' A:C69 4.8 31.5 1.0

Reference:

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
Page generated: Tue Dec 15 10:59:07 2020

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