Sodium in PDB 6j6o: Crystal Structure of Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050)

The structure of Crystal Structure of Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050), PDB code: 6j6o was solved by T.Xu, L.Lin, Z.Yuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.67 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	55.994, 55.994, 132.598, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 23.4

The structure of Crystal Structure of Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050) (pdb code 6j6o). 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 Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050), PDB code: 6j6o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050)


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 Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3101 b:27.2 occ:1.00 ND2 A:ASN2845 3.0 23.2 1.0 CB A:SER2847 3.2 20.4 1.0 OG A:SER2847 3.4 21.1 1.0 CG A:ASN2845 4.0 22.5 1.0 OD1 A:ASN2845 4.1 19.1 1.0 CA A:SER2847 4.7 17.6 1.0 O A:HOH3313 4.9 26.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050)


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 Diamondback Moth Ryanodine Receptor Phosphorylation Domain(2836-3050) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3102 b:32.8 occ:1.00 OE2 A:GLU2986 2.7 28.4 1.0 NE2 A:GLN3034 2.7 29.3 1.0 O A:GLN2982 2.9 16.3 1.0 CG A:GLU2986 3.5 29.4 1.0 CD A:GLU2986 3.5 27.5 1.0 C A:GLN2982 3.6 19.7 1.0 CD A:GLN3034 3.7 31.4 1.0 CB A:ALA2985 3.7 21.6 1.0 NH1 A:ARG3030 3.7 29.4 1.0 CA A:GLN2982 3.8 15.6 1.0 CG A:GLN3034 3.8 21.1 1.0 O A:HOH3234 3.9 29.4 1.0 N A:GLU2986 3.9 17.4 1.0 CB A:GLN2982 4.0 21.1 1.0 NE A:ARG3030 4.2 27.1 1.0 C A:ALA2985 4.4 16.0 1.0 CZ A:ARG3030 4.4 28.9 1.0 CB A:GLU2986 4.5 21.7 1.0 CA A:GLU2986 4.5 18.4 1.0 CA A:ALA2985 4.6 22.6 1.0 CG A:GLN2982 4.6 17.7 1.0 OE1 A:GLU2986 4.7 25.2 1.0 OE1 A:GLN3034 4.8 33.5 1.0 N A:ASN2983 4.8 16.4 1.0 N A:ALA2985 5.0 18.5 1.0

T.Xu, Z.Yuchi. Crystal Structure of Diamondback Moth Ryanodine Receptor REPEAT34 Domain Reveals Insect-Specific Phosphorylation Sites. Bmc Biol. V. 17 77 2019.
ISSN: ESSN 1741-7007
PubMed: 31597572
DOI: 10.1186/S12915-019-0698-5