Sodium in PDB 5btm: Crystal Structure of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10)

The structure of Crystal Structure of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10), PDB code: 5btm was solved by H.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.12 / 2.78
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	63.120, 63.120, 72.950, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.4

The structure of Crystal Structure of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10) (pdb code 5btm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10), PDB code: 5btm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10)


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 Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:32.1 occ:1.00 O2' A:A21 2.6 26.9 1.0 O6 A:G24 2.6 37.2 1.0 O3' A:A21 3.0 28.1 1.0 N7 A:G23 3.0 45.1 1.0 O6 A:G23 3.1 48.8 1.0 C6 A:G24 3.5 39.1 1.0 OP2 A:A22 3.6 26.4 1.0 C5 A:G23 3.7 48.3 1.0 C6 A:G23 3.7 48.9 1.0 C2' A:A21 3.7 27.3 1.0 P A:A22 3.7 30.7 1.0 C3' A:A21 3.9 27.2 1.0 N7 A:G24 3.9 36.0 1.0 O5' A:A22 3.9 28.0 1.0 C5 A:G24 4.0 39.8 1.0 C8 A:G23 4.2 43.8 1.0 N4 A:C33 4.3 38.8 1.0 C1' A:A21 4.5 29.3 1.0 OP2 A:G23 4.6 31.1 1.0 N1 A:G24 4.7 39.7 1.0 N7 A:A22 4.7 37.1 1.0 C8 A:A22 4.8 36.5 1.0 O4 A:U34 4.8 37.3 1.0 C4 A:G23 5.0 45.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:20.7 occ:1.00 O2' B:A21 2.4 22.5 1.0 O6 B:G24 2.6 17.9 1.0 O3' B:A21 2.9 23.3 1.0 O6 B:G23 3.0 16.3 1.0 N7 B:G23 3.1 19.0 1.0 C6 B:G24 3.5 18.2 1.0 C2' B:A21 3.6 20.4 1.0 C6 B:G23 3.6 17.6 1.0 OP2 B:A22 3.6 25.1 1.0 C5 B:G23 3.7 18.5 1.0 C3' B:A21 3.8 21.1 1.0 P B:A22 3.8 23.3 1.0 N7 B:G24 4.0 18.1 1.0 C5 B:G24 4.1 17.6 1.0 O5' B:A22 4.1 21.6 1.0 N4 B:C33 4.1 14.4 1.0 C8 B:G23 4.2 19.5 1.0 C1' B:A21 4.4 19.9 1.0 O4 B:U34 4.6 18.4 1.0 N1 B:G24 4.7 18.7 1.0 N7 B:A22 4.7 19.1 1.0 C8 B:A22 4.9 18.9 1.0 OP2 B:G23 4.9 17.6 1.0 N3 B:U34 5.0 18.9 1.0 N1 B:G23 5.0 16.8 1.0 C4 B:G23 5.0 17.9 1.0

H.Park, A.L.Gonzalez, I.Yildirim, T.Tran, J.R.Lohman, P.Fang, M.Guo, M.D.Disney. Crystallographic and Computational Analyses of Auucu Repeating Rna That Causes Spinocerebellar Ataxia Type 10 (SCA10). Biochemistry V. 54 3851 2015.
ISSN: ISSN 0006-2960
PubMed: 26039897
DOI: 10.1021/ACS.BIOCHEM.5B00551