Sodium in PDB 5fj1: Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group

The structure of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group, PDB code: 5fj1 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)	38.720 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.052, 84.360, 174.499, 90.00, 90.00, 90.00
R / Rfree (%)	16.68 / 18.3

The structure of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group also contains other interesting chemical elements:

Magnesium

(Mg)

21 atoms

The binding sites of Sodium atom in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group (pdb code 5fj1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group, PDB code: 5fj1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1029 b:0.2 occ:1.00 N1 A:A19 3.1 79.0 1.0 C2 A:A19 3.5 72.2 1.0 N7 E:G14 3.5 68.9 1.0 OP2 E:A13 4.2 79.2 1.0 C6 A:A19 4.2 76.6 1.0 C8 E:G14 4.3 67.7 1.0 OP2 E:G14 4.5 87.0 1.0 N6 A:A19 4.5 67.2 1.0 C5 E:G14 4.7 66.5 1.0 OP1 E:A13 4.7 90.1 1.0 N3 A:A19 4.8 62.8 1.0 O6 E:G14 4.9 77.2 1.0 P E:A13 4.9 84.7 1.0

Sodium binding site 2 out of 3 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1030 b:0.3 occ:1.00 N1 E:A19 3.0 87.4 1.0 N7 A:G14 3.2 66.9 1.0 C2 E:A19 3.6 81.4 1.0 C8 A:G14 3.9 71.2 1.0 OP2 A:A13 4.0 91.0 1.0 C6 E:A19 4.1 74.1 1.0 N6 E:A19 4.3 63.4 1.0 OP2 A:G14 4.3 81.2 1.0 C5 A:G14 4.4 69.3 1.0 O6 A:G14 4.6 64.7 1.0 P A:A13 4.8 89.0 1.0 OP1 A:A13 4.8 91.6 1.0 C6 A:G14 4.9 71.2 1.0 N3 E:A19 4.9 72.0 1.0

Sodium binding site 3 out of 3 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ F:Na1028 b:93.0 occ:1.00 N7 F:G14 3.2 67.5 1.0 N1 D:A19 3.2 77.7 1.0 OP2 F:G14 3.5 62.7 1.0 C8 F:G14 3.6 58.7 1.0 C2 D:A19 3.7 79.3 1.0 OP2 F:A13 3.9 66.3 1.0 OP1 F:A13 4.3 62.4 1.0 O F:HOH2003 4.3 69.2 1.0 C6 D:A19 4.4 69.1 1.0 P F:A13 4.4 56.5 1.0 C5 F:G14 4.5 61.7 1.0 N6 D:A19 4.7 73.6 1.0 O5' F:A13 4.7 49.7 1.0 N3 D:A19 5.0 58.9 1.0 P F:G14 5.0 59.5 1.0 N9 F:G14 5.0 52.9 1.0

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