Sodium in PDB 6ozs: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+, PDB code: 6ozs was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.25 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.086, 73.257, 155.704, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.6

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+ (pdb code 6ozs). 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 Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+, PDB code: 6ozs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+


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 Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:67.1 occ:1.00 O A:LEU45 2.7 63.1 1.0 O A:HOH424 2.8 62.5 1.0 O A:HOH401 3.1 69.2 1.0 NE2 A:GLN46 3.2 84.5 1.0 O A:TYR72 3.3 68.2 1.0 OE1 A:GLN46 3.3 75.7 1.0 CD A:GLN46 3.5 78.5 1.0 C A:LEU45 3.8 59.0 1.0 C A:TYR72 4.1 58.2 1.0 CD A:PRO73 4.2 58.1 1.0 N A:GLY44 4.3 61.3 1.0 CD2 A:TYR72 4.3 48.1 1.0 N A:LEU45 4.4 50.8 1.0 N A:PRO73 4.5 60.0 1.0 CA A:GLN46 4.6 53.8 1.0 N A:GLN46 4.6 53.0 1.0 O A:PHE42 4.6 62.7 1.0 CA A:LEU45 4.7 53.4 1.0 CG A:GLN46 4.7 72.0 1.0 C A:GLY44 4.8 54.5 1.0 CA A:GLY44 4.9 54.8 1.0 CG A:PRO73 4.9 56.2 1.0 CE2 A:TYR72 5.0 58.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+


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 Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:76.2 occ:1.00 NE2 B:GLN46 2.8 80.2 1.0 O B:TYR72 3.4 68.4 1.0 CD B:GLN46 3.5 76.0 1.0 OE1 B:GLN46 3.6 82.0 1.0 O B:LEU45 3.7 65.7 1.0 CD B:PRO73 3.8 71.5 1.0 C B:TYR72 4.3 66.3 1.0 N B:PRO73 4.5 68.7 1.0 CG B:PRO73 4.6 70.6 1.0 CG B:GLN46 4.7 61.3 1.0 C B:LEU45 4.8 59.5 1.0 CD2 B:TYR72 5.0 54.7 1.0

J.Wu, N.L.Samara, I.Kuraoka, W.Yang. Evolution of Inosine-Specific Endonuclease V From Bacterial Dnase to Eukaryotic Rnase. Mol.Cell V. 76 44 2019.
ISSN: ISSN 1097-2765
PubMed: 31444105
DOI: 10.1016/J.MOLCEL.2019.06.046