Sodium in PDB 6ozl: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+, PDB code: 6ozl 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)	35.82 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.621, 72.519, 155.764, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.7

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+ also contains other interesting chemical elements:

Manganese

(Mn)

4 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 2 Min Soak in MN2+ (pdb code 6ozl). 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 Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+, PDB code: 6ozl:

Sodium binding site 1 out of 1 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+


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 2 Min Soak in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:72.8 occ:1.00 O A:HOH449 2.4 56.6 1.0 OE1 A:GLN46 2.5 81.5 1.0 O A:HOH437 2.5 68.8 1.0 O A:HOH432 2.5 55.1 1.0 O A:LEU45 3.5 35.2 1.0 CD A:GLN46 3.6 70.0 1.0 O A:TYR72 4.1 46.1 1.0 C A:LEU45 4.5 40.4 1.0 CG A:GLN46 4.5 52.3 1.0 NE2 A:GLN46 4.5 74.2 1.0 N A:GLY44 4.6 32.9 1.0 O A:HOH470 4.6 71.0 1.0 CD A:PRO73 4.7 45.0 1.0 N A:LEU45 4.9 31.5 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