Sodium in PDB 7eaf: Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn

Protein crystallography data

The structure of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn, PDB code: 7eaf 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) 29.22 / 2.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.46, 61.46, 157.91, 90, 90, 90
R / Rfree (%) 26.2 / 29.8

Other elements in 7eaf:

The structure of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn also contains other interesting chemical elements:

Barium (Ba) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn (pdb code 7eaf). 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 Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn, PDB code: 7eaf:

Sodium binding site 1 out of 1 in 7eaf

Go back to Sodium Binding Sites List in 7eaf
Sodium binding site 1 out of 1 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na108

b:61.2
occ:1.00
N7 A:G42 2.9 73.1 1.0
O6 A:G42 3.1 67.7 1.0
OP2 A:C41 3.6 79.8 1.0
C5 A:G42 3.7 70.7 1.0
C6 A:G42 3.7 68.6 1.0
C5 A:C41 3.9 75.1 1.0
C8 A:G42 4.1 73.5 1.0
N4 A:C41 4.4 69.8 1.0
C4 A:C41 4.5 71.9 1.0
C6 A:C41 4.6 76.7 1.0
P A:C41 4.8 85.6 1.0
O5' A:C41 4.9 83.5 1.0
O6 A:G43 5.0 57.3 1.0
C4 A:G42 5.0 71.3 1.0

Reference:

L.Huang, X.Liao, M.Li, J.Wang, X.Peng, T.J.Wilson, D.M.J.Lilley. Structure and Folding of Four Putative Kink Turns Identified in Structured Rna Species in A Test of Structural Prediction Rules. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33978763
DOI: 10.1093/NAR/GKAB333
Page generated: Mon Jul 12 15:56:54 2021

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